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[[Image:DNA-Animation.gif|thumb|220px|Three-dimensional model of the structure of part of a DNA double helix.]]
[[Image:DNA-Animation.gif|thumb|220px|Three-dimensional model of the structure of part of a DNA double helix.]]
'''Deoxyribonucleic acid (DNA)''' is a very large biological [[molecule]] that is vital in providing information for the development and reproduction of living things. Every living organism has its own DNA sequence that is like a unique 'barcode' or 'fingerprint'. This inheritable variation in DNA is the most important factor driving evolutionary change over many generations. But, beyond these general characteristics, what "exactly" is DNA? What are the precise physical attributes of this molecule that make its role so centrally imposing in understanding [[life]]?


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DNA is a long [[polymer]] of simple units called [[nucleotides]], held together by a [[sugar]] [[phosphate]] backbone. Attached to each sugar molecule is a molecule of one of four ''[[Nucleobase|bases]]''; [[adenine]] (A), [[thymine]] (T), [[guanine]] (G) or [[cytosine]] (C), and the order of these bases on the DNA strand encodes information. In most organisms, DNA is a [[double-helix]] (or duplex molecule) consisting of two DNA strands coiled around each other, and held together by [[hydrogen bonds]] between bases. Because of the chemical nature of these bases, adenine always pairs with thymine and guanine always pairs with cytosine. This ''complementarity'' forms the basis of [[semi-conservative DNA replication]] &mdash; it makes it possible for DNA to be copied relatively simply, while accurately preserving its information content.  


Deoxyribonucleic acid, or DNA, is a [[nucleic acid]] [[molecule]] that almost all cellular organisms use to store information for [[development]] and [[reproduction]]. Inheritable variation in DNA facilitates evolutionary change in lineages of organisms. Chemically, DNA is a long [[polymer]] of simple units called [[nucleotides]], held together by a [[sugar]] [[phosphate]] backbone. Attached to each sugar is one of four types of molecules called [[bases]]; these bases are [[adenine]] (A), [[thymine]] (T), [[guanine]] (G)  and [[cytosine]] (C). The order of bases on the DNA strand encodes information. DNA in most organisms comes in a [[double-helix]] form (see right) consisting of two [[complementary]] DNA strands coiled around each other. The two strands are held together by [[hydrogen bonds]] between complementary bases. Because of the chemical nature of these bases, adenine always pairs with thymine and guanine always pairs with cytosine. This complementarity forms the basis of [[semi-conservative DNA replication]].  That is, a double-helix is split in two, and complementary bases added to each separated strand forming the two identical "daughter" double-helices.  
The entire DNA sequence of an organism is called its [[genome]]. In animals and plants, most DNA is stored inside the [[cell nucleus]]. In [[bacteria]], there is no nuclear membrane around the DNA, which is in a region called the ''[[nucleoid]]''. Some organelles in eukaryotic cells ([[mitochondria]] and [[chloroplast]]s) have their own DNA with a similar organisation to bacterial DNA. [[Viruses]] have a single type of [[nucleic acid]], either DNA or RNA, directly encased in a [[protein]] coat.


The full DNA sequence of each organism is called the [[genome]], and it consists of coding regions called [[genes]] and [[non-coding]] regions whose functions are largely unknown. The main distinction between the two regions is that the coding regions (also called [[exons]]) are [[transcribed]] into [[ribonucleic acid]] ([[RNA]]), whereas the non-coding regions (known as [[introns]]) are not. Many of the transcribed RNA sequences are then [[translated]] into the [[amino acid]] sequence of a single [[polypeptide]] chain. Polypeptide chains, either singly or in groups, form [[proteins]], the molecules that perform important regulatory, catalytic and structural roles in [[cell]]s. Other RNA molecules (e.g. [[rRNA]],[[tRNA]], [[RNA interference|RNAi]]) perform important catalytic and regulatory tasks on their own.  
==Overview of biological functions==
DNA contains the genetic information that is the basis for living functions including growth, reproduction and evolution. This information is held in segments of the DNA called ''genes'' that may span in size from scores of DNA base-pairs to many thousands of base-pairs. In [[eukaryotes]] (organisms such as plants, yeasts and animals whose cells have a nucleus) DNA usually occurs as several large, linear [[chromosome]]s, each of which may contain hundreds or thousands of genes. [[Prokaryotes]] (organisms such as common bacteria) generally have a single large circular chromosome, but often possess other miniature chromosomes called [[plasmid]]s. The set of chromosomes in a cell makes up its [[genome]]; the [[human genome]] has about three billion base pairs of DNA arranged into 46 chromosomes <ref name=Venter>{{cite journal | author = Venter J ''et al.'' | title = The sequence of the human genome | journal = Science | volume = 291 | pages = 1304–51 | year = 2001 | id = PMID 11181995}}</ref> and contains 20-25,000 genes.


In [[eukaryote]]s such as [[animals]] and [[plants]], most DNA is stored inside the [[cell nucleus]].  In [[prokaryote]]s such as [[bacteria]], the DNA is found in the cell's [[cytoplasm]]. Viruses have a single type of nucleic acid, either DNA (or RNA) directly encased in a protein coat (although some viruses have, additionally an outer lipid envelope).
There are many interactions that happen between DNA and other molecules to coordinate its functions. When cells divide, the genetic information must be duplicated to produce two daughter copies of DNA in a process called ''[[DNA replication]]''. When a cell uses the information in a gene, the DNA sequence is copied into a complementary single strand of [[RNA]] in a process called ''[[transcription]]''. Of the transcribed sequences, some are used to directly make a matching protein sequence by a process called ''[[translation]]'' (meaning translation from a nucleic acid polymer to an [[amino acid]] polymer). The other transcribed RNA sequences may have regulatory, structural or catalytic roles. This article introduces some of the functions and interactions that characterize the DNA molecules in cells, and touches on some of the more technological uses for this molecule.


==Overview of biological functions==
===Genes===
DNA contains the genetic [[information]] that allows living things to function, grow, reproduce and evolve. This information is held in the [[DNA sequence|sequence]] of pieces of DNA called [[gene]]s. Genetic information in genes is transmitted through complementary base pairing. For example, when a cell uses the information in a gene, the DNA sequence is copied into a complementary RNA sequence in a process called transcription. Usually, this RNA copy is then used to make a matching protein sequence in a process called translation. Alternatively, a cell may simply copy its genetic information in a process called DNA replication. The details of these functions are covered in other articles, here we focus on the interactions that happen in these processes between DNA and other molecules.
Our understanding of the various ways in which genes play a role in cells has been continually revised throughout the history of genetics, starting from abstract concepts of inheritable particles whose composition was unknown. This has led to several modern different definitions of a gene. One of the most straightforward ways to define a gene is simply as a segment of DNA that is transcribed into RNA - that is - ''the gene is a unit of transcription''. This definition encompasses genes for non-translated RNAs, such as [[ribosomal RNA]] ([[rRNA]]) and [[transfer RNA]] ([[tRNA]]), as well as [[messenger RNA]] ([[mRNA]]) which ''is'' used for encoding the sequences of proteins.
 
A second approach is to define a gene as ''a region of DNA that encodes a single polypeptide''. By this definition, any particular mRNA transcription unit can cover more than one gene, and thus a mRNA can carry regions encoding one or more polypeptides. Such a multi-genic transcription unit is called an [[operon]].
 
Other definitions include consideration of genes as ''units of biological function''. This definition can include sites on DNA that are not transcribed, such as DNA sites at which regulatory and catalytically active proteins concerned with gene regulation and expression are located. Examples of such sites (loci, sing. locus) are [[promoter]]s and [[operator]]s. ([[Locus (Genetics)|Locus]] is a genetic term very similar in meaning to gene, and which refers to a site or region on a chromosome concerned with a particular function or trait.)


===Transcription and translation===
All of the cells in our body contain essentially the same DNA, with a few exceptions; red blood cells for example do not have a nucleus and contain no DNA. However although two cells may carry identical DNA, this does not make them identical, because the two cells may have different patterns of ''gene expression''; only some genes will be active in each cell, and the level of activity varies between cells, and this is what makes different cell types different. The "level" of gene expression (for a given gene) is used sometimes to refer to the amount of mRNA made by the cell, and sometimes to refer to the amount of protein produced.
{{further|[[Genetic code]], [[Transcription (genetics)]], [[Protein biosynthesis]]}}
A gene is a sequence of DNA that contains genetic information and can influence the [[phenotype]] of an organism. Within a gene, the sequence of bases along a DNA strand defines a [[messenger RNA]] sequence which then defines a protein sequence. The relationship between the nucleotide sequences of genes and the [[amino acid|amino-acid]] sequences of proteins is determined by the rules of [[Translation (genetics)|translation]], known collectively as the [[genetic code]]. The genetic code consists of three-letter 'words' called ''codons'' formed from a sequence of three nucleotides (e.g. ACT, CAG, TTT). In transcription, the codons of a gene are copied into [[messenger RNA]] by [[RNA polymerase]]. This RNA copy is then decoded by a [[ribosome]] that reads the RNA sequence by base-pairing the messenger RNA to [[transfer RNA]], which carries amino acids. Since there are 4 bases in 3-letter combinations, there are 64 possible codons (<math>4^3</math> combinations). These encode the twenty [[list of standard amino acids|standard amino acids]]. Most amino acids, therefore, have more than one possible codon. There are also three 'stop' or 'nonsense' codons signifying the end of the coding region, these are the TAA, TGA and TAG codons.


==Physical and chemical properties==
Every human has essentially the same genes, but has slightly different DNA; on average the DNA of two individuals differs at about three million bases. These differences are very rarely in the protein-coding sequences of genes, but some affect how particular genes are regulated &mdash; they may affect exactly where in the body a gene is expressed, how intensely it is expressed, or how expression is regulated by other genes or by environmental factors; these slight differences help to make every human being unique. By comparison, the genome of our closest living relative, the [[chimpanzee]], differs from the human genome at about 30 million bases. <ref>Pollard KS ''et al.'' (2006) Forces shaping the fastest evolving regions in the human genome. PLoS Genet 2(10):[http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pgen.0020168 e168] PMID 17040131</ref>
[[Image:DNA_chemical_structure.png|right|thumb|280px|The two strands of DNA are held together by hydrogen bonds between bases. The sugars in the backbone are shown in light blue.]]


DNA is a long [[polymer]] made from repeating units called [[nucleotide]]s.<ref name=Alberts>{{cite book | last = Alberts| first = Bruce| coauthors = Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walters | title = Molecular Biology of the Cell; Fourth Edition | publisher = Garland Science| date = 2002 | location = New York and London | url = http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=mboc4.TOC&depth=2 | id = ISBN 0-8153-3218-1}}</ref><ref name=Butler>Butler, John M. (2001) ''Forensic DNA Typing'' "Elsevier". pp. 14-15. ISBN 978-0-12-147951-0.</ref> The DNA chain is 22 to 26 [[Ångström|angstroms]] wide (2.2 to 2.6 nanometers) and one nucleotide unit is 3.3&nbsp;angstroms long (0.33nm).<ref>{{cite journal | author = Mandelkern M, Elias J, Eden D, Crothers D | title = The dimensions of DNA in solution | journal = J Mol Biol | volume = 152 | issue = 1 | pages = 153-61 | year = 1981 | id = PMID 7338906}}</ref> Although these repeating units are very small, DNA polymers can be enormous molecules containing millions of nucleotides. For instance, the DNA strand contained in the largest human chromosome (Chromosome 1) is 220 million base pairs long.<ref>{{cite journal | author = Gregory S, ''et al.'' | title = The DNA sequence and biological annotation of human chromosome 1 | journal = Nature | volume = 441 | issue = 7091 | pages = 315-21 | year = 2006 | id = PMID 16710414}}</ref>
===Genomes===
In eukaryotes, DNA is located mainly in the cell nucleus (there are also small amounts in mitochondria and chloroplasts). In prokaryotes, the DNA is in an irregularly shaped body in the cytoplasm called the [[nucleoid]].<ref>{{cite journal | author = Thanbichler M ''et al.''| title = The bacterial nucleoid: a highly organized and dynamic structure | journal = J Cell Biochem | volume = 96 | pages = 506–21 | year = 2005 | id = PMID 15988757}}</ref> The DNA is usually in linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. The [[human genome]] has about three billion base pairs of DNA arranged into 46 chromosomes<ref name=Venter/>, and contains 20-25,000 genes <ref>Human Genome Project Information [http://www.ornl.gov/sci/techresources/Human_Genome/home.shtml]</ref>, the simple [[nematode]] ''[[C elegans]]'' has almost as many genes (more than 19,000)<ref>The C. elegans Sequencing Consortium (1998)Genome Sequence of the Nematode C. elegans: A Platform for Investigating Biology. Science
282: 2012-8
[http://www.sciencemag.org/cgi/content/abstract/282/5396/2012?maxtoshow=&HITS=10&hits=10&RESULTFORMAT=&searchid=1&FIRSTINDEX=0&volume=282&firstpage=2012&resourcetype=HWCIT]</ref>.


In living organisms, DNA does not usually exist as a single molecule, but instead as a tightly-associated pair of molecules running in opposite directions.<ref name=Watson>{{cite journal | author = Watson J, Crick F | title = Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid | url=http://profiles.nlm.nih.gov/SC/B/B/Y/W/_/scbbyw.pdf | journal = Nature | volume = 171 | issue = 4356 | pages = 737-8 | year = 1953 | id = PMID 13054692}}</ref><ref name=berg>Berg J., Tymoczko J. and Stryer L. (2002) ''Biochemistry.'' W. H. Freeman and Company ISBN 0-7167-4955-6</ref> These two long strands entwine like vines, in the shape of a [[helix|double helix]]. DNA can thus be thought of as an anti-parallel double helix. The nucleotide repeats contain both the backbone of the molecule, which holds the chain together, and a base, which interacts with the other DNA strand in the helix. In general, a base linked to a sugar is called a [[nucleoside]] and a base linked to a sugar and one or more phosphate groups is called a [[nucleotide]]. If multiple nucleotides are linked together, as in DNA, this polymer is referred to as a [[polynucleotide]].<ref name=IUPAC>[http://www.chem.qmul.ac.uk/iupac/misc/naabb.html Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents] IUPAC-IUB Commission on Biochemical Nomenclature (CBN) Accessed 03 Jan 2006</ref>
In many species, only a small fraction of the genome encodes protein: only about 1.5% of the human genome consists of protein-coding exons, while over 50% consists of non-coding [[repeated sequence (DNA)|repetitive sequences]].<ref>{{cite journal | author = Wolfsberg T ''et al.''| title = Guide to the draft human genome | journal = Nature | volume = 409 | pages = 824-6 | year = 2001 | id = PMID 11236998}}</ref> Some have concluded that much of human DNA is "junk DNA" because most of the non-coding elements appear to have no function, Some other vertebrates, including the puffer fish ''[[Fugu]]'' have very much more compact genomes, and (for multicellular organisms) there seems to be no consistent relationship between the size of the genome and the complexity of the organism <ref> See Sydney Brenner's Nobel lecture (2002) [http://nobelprize.org/nobel_prizes/medicine/laureates/2002/brenner-lecture.pdf]</ref>. Some non-coding DNA sequences are now known to have a structural role in chromosomes. In particular, [[telomere]]s and [[centromere]]s contain few genes, but are important for the function and stability of chromosomes.<ref name=wright>{{cite journal | author = Wright W ''et al.''| title = Normal human chromosomes have long, G-rich telomeric overhangs at one end | url=http://www.genesdev.org/cgi/content/full/11/21/2801#B34 | journal = Genes Dev | volume = 11 | pages = 2801-9 | year = 1997 | id = PMID 9353250}}</ref><ref>{{cite journal | author = Pidoux A, Allshire R | title = The role of heterochromatin in centromere function | url=http://www.journals.royalsoc.ac.uk/media/804t6y8vmh5utlb6ua5y/contributions/p/x/7/a/px7ahm740dq5ueuk.pdf | journal = Philos Trans R Soc Lond B | volume = 360 | pages = 569-79 | year = 2005 | id = PMID 15905142}}</ref> An abundant form of non-coding DNA in humans are [[pseudogene]]s, which are copies of genes that have been disabled by mutation;<ref>{{cite journal | author = Harrison P ''et al.'' | title = Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22 | url=http://www.genome.org/cgi/content/full/12/2/272 | journal = Genome Res | volume = 12 | pages = 272-80 | year = 2002 | id = PMID 11827946}}</ref> these are usually just molecular 'fossils', but they can provide the raw genetic material for new genes.<ref>{{cite journal | author = Harrison P, Gerstein M | title = Studying genomes through the aeons: protein families, pseudogenes and proteome evolution | journal = J Mol Biol | volume = 318 |pages = 1155-74 | year = 2002 | id = PMID 12083509}}</ref>


The backbone of the DNA strand is made from alternating [[phosphate]] and [[sugar]] residues.<ref name=Ghosh>{{cite journal | author = Ghosh A, Bansal M | title = A glossary of DNA structures from A to Z | journal = Acta Crystallogr D Biol Crystallogr | volume = 59 | issue = Pt 4 | pages = 620-6 | year = 2003 | id = PMID 12657780}}</ref> The sugar in DNA is the [[pentose]] (five carbon) sugar 2-deoxyribose. The sugars are joined together by phosphate groups that form [[phosphodiester bond]]s between the third and fifth carbon atoms in the sugar rings. These asymmetric bonds mean a strand of DNA has a direction. In a double helix the direction of the nucleotides in one strand is opposite to their direction in the other strand. This arrangement of DNA strands is called antiparallel. The asymmetric ends of a strand of DNA bases are referred to as the [[5' end|5']] (''five prime'') and [[3' end|3']] (''three prime'') ends. One of the major differences between DNA and RNA is the sugar, with 2-deoxyribose being replaced by the alternative pentose sugar [[ribose]] in RNA.<ref name=berg/>
A recent challenge to the long-standing view that the human genome consists of relatively few genes along with a vast amount of "[[junk DNA]]" comes from the ENCyclopedia Of DNA Elements ([[ENCODE]]) consortium.<ref>{{cite journal | author = Weinstock GM | title = ENCODE: More genomic empowerment | journal = Genome Research| volume = 17 | pages = 667-668 | year = 2007 | id = PMID 17567987}}</ref><ref name=ENCODE>{{cite journal | author = ENCODE Project Consortium | title = Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project| journal = Nature| volume = 447 | pages = 799-816 | year = 2007 | id = PMID 17571346}}</ref> Their survey of the human genome shows that most of the DNA is transcribed into molecules of [[RNA]]. This broad pattern of transcription was unexpected, but whether these transcribed (but not translated) elements have any biological function is not yet clear.<ref name=ENCODE/>


The DNA double helix is held together by [[hydrogen bond]]s between the bases attached to the two strands. The four bases found in DNA are [[adenine]] (abbreviated A), [[cytosine]] (C), [[guanine]] (G) and [[thymine]] (T). These four bases are shown below and are attached to the sugar/phosphate to form the complete nucleotide, as shown for adenosine monophosphate.
===Replication===
{{further|[[Replication of a circular bacterial chromosome]]}}
[[Image:DNAreplicationFORK.jpg|thumb|400px| '''DNA-replication''' illustrated by the bacterial [[replication fork]]. The helix unwinds and both strands replicate simultaneously as they unwind. The ''[[leading strand]]'' replicates continuously from the 3' end, with the newest end of the forming strand facing into the replication fork. The ''[[lagging strand]]'' replicates by a series of fragments ([[Okazaki fragments]] placed end-to-end, with the newest ends  facing away from the fork; the Okazaki fragments are later joined together by DNA ligase. During replication, DNA polymerase III proofreads for mismatched bases]]


These bases are classified into two types, adenine and guanine are fused five- and six-membered [[heterocyclic compound]]s called [[purine]]s, while cytosine and thymine are six-membered rings called [[pyrimidine]]s.<ref name=IUPAC/> A fifth pyrimidine base, called [[uracil]] (U), replaces thymine in [[RNA]] and differs from thymine by lacking a [[methyl group]] on its ring. Uracil is normally only found in DNA as a breakdown product of cytosine, but an exception to this rule are [[phage|bacterial viruses]] such as phage  PBS1 that contains uracil in its DNA.<ref name="nature1963-takahashi">{{cite journal | author=Takahashi I, Marmur J. | title=Replacement of thymidylic acid by deoxyuridylic acid in the deoxyribonucleic acid of a transducing phage for Bacillus subtilis | journal=Nature | year=1963 | pages=794-5 | volume=197 | id=PMID 13980287}}</ref>
For an organism to grow, its cells must multiply, and this occurs by [[cell division]]: one cell splits to create two new 'daughter' cells. When a cell divides it must replicate its DNA so that the two daughter cells have the same genetic information as the parent cell. The double-stranded structure of DNA provides a simple mechanism for this replication. The two strands of DNA separate, and then each strand's complementary DNA sequence is recreated by an enzyme called [[DNA polymerase]]. This makes the complementary strand by finding the correct base (through complementary base pairing), and bonding it to the original strand. DNA polymerases can only extend a DNA strand in a 5' to 3' direction, so other mechanisms are needed to copy the antiparallel strands of the double helix.<ref>{{cite journal | author = Albà M | title = Replicative DNA polymerases | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11178285 | journal = Genome Biol | volume = 2 | pages = REVIEWS3002 | year = 2001 | id = PMID 11178285}}</ref> In this way, the base on the old strand dictates which base appears on the new strand, and the cell (usually) ends up with a perfect copy of its DNA. However, occasionally mistakes (called [[mutation]]s) occur, contributing to the [[genetic variation]] that is the raw material for evolutionary change.


The double helix is a right-handed spiral. As the DNA strands wind around each other, they leave gaps between each set of phosphate backbones, revealing the sides of the bases inside (see animation). There are two of these grooves twisting around the surface of the double helix: one groove is 22&nbsp;angstroms wide and the other 12&nbsp;angstroms wide.<ref>{{cite journal | author = Wing R, Drew H, Takano T, Broka C, Tanaka S, Itakura K, Dickerson R | title = Crystal structure analysis of a complete turn of B-DNA | journal = Nature | volume = 287 | issue = 5784 | pages = 755-8 | year = 1980 | id = PMID 7432492}}</ref> The larger groove is called the major groove, while the smaller, narrower groove is called the minor groove. The narrowness of the minor groove means that the edges of the bases are more accessible in the major groove. As a result, proteins like [[transcription factor]]s that can bind to specific sequences in double-stranded DNA usually read the sequence by making contacts to the sides of the bases exposed in the major groove.<ref>{{cite journal | author = Pabo C, Sauer R | title = Protein-DNA recognition | journal = Annu Rev Biochem | volume = 53 | issue = | pages = 293-321 | year = | id = PMID 6236744}}</ref>
DNA replication requires a complex set of proteins, each dedicated to one of several different tasks needed to replicate this large molecule in an orderly and precise fashion. Further capacity for DNA replication with substantial rearrangement (which has major implications for understanding mechanisms of [[molecular evolution]], is provided by mechanisms for DNA movement, inversion, and duplication, illustrated by various [[Mobile DNA|mobile DNA]]s such as [[transposons]] and [[proviruses]].


===Base pairing===
===Transcription and translation===
{{further|[[Base pair]]}}
Each type of base on one strand forms a bond with just one type of base on the other strand. This is called complementary [[base pair]]ing. Here, purines form [[hydrogen bond]]s to pyrimidines, with A bonding only to T, and C bonding only to G. This arrangement of two nucleotides joined together across the double helix is called a base pair. In a double helix, the two strands are also held together by [[force]]s generated by the [[hydrophobic effect]] and [[pi stacking]], but these forces are not affected by the sequence of the DNA.<ref>{{cite journal | author = Ponnuswamy P, Gromiha M | title = On the conformational stability of oligonucleotide duplexes and tRNA molecules | journal = J Theor Biol | volume = 169 | issue = 4 | pages = 419-32 | year = 1994 | id = PMID 7526075}}</ref> As hydrogen bonds are not [[covalent bond|covalent]], they can be broken and rejoined relatively easily. The two strands of DNA in a double helix can therefore be pulled apart like a zipper, either by a mechanical force or high temperature.<ref>{{cite journal | author = Clausen-Schaumann H, Rief M, Tolksdorf C, Gaub H | title = Mechanical stability of single DNA molecules | url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1300792&blobtype=pdf | journal = Biophys J | volume = 78 | issue = 4 | pages = 1997-2007 | year = 2000 | id = PMID 10733978}}</ref> As a result of this complementarity, all the information in the double-stranded sequence of a DNA helix is duplicated on each strand, which is vital in DNA replication. Indeed, this reversible and specific interaction between complementary base pairs is critical for all the functions of DNA in living organisms.<ref name=Alberts/> Kornberg considers the introduction of the concept of complementarity as the most important feature of the duplex model for DNA structure.


The two types of base pairs form different numbers of [[hydrogen bond]]s, AT forming two hydrogen bonds, and GC forming three hydrogen bonds (see figures, left). The GC base-pair is therefore stronger than the AT base pair. As a result, it is both the percentage of GC base pairs and the overall length of a DNA double helix that determine the strength of the association between the two strands of DNA. Long DNA helices with a high GC content have strongly interacting strands, while short helices with high AT content have weakly interacting strands.<ref>{{cite journal | author = Chalikian T, Völker J, Plum G, Breslauer K | title = A more unified picture for the thermodynamics of nucleic acid duplex melting: a characterization by calorimetric and volumetric techniques | url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=22151&blobtype=pdf | journal = Proc Natl Acad Sci U S A | volume = 96 | issue = 14 | pages = 7853-8 | year = 1999 | id = PMID 10393911}}</ref> Parts of the DNA double helix that need to separate easily, such as the TATAAT [[Pribnow box]] in bacterial [[promoter]]s, tend to have sequences with a high AT content, making the strands easier to pull apart.<ref>{{cite journal | author = deHaseth P, Helmann J | title = Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase-induced strand separation of double helical DNA | journal = Mol Microbiol | volume = 16 | issue = 5 | pages = 817-24 | year = 1995 | id = PMID 7476180}}</ref> In the laboratory, the strength of this interaction can be measured by finding the temperature required to break the hydrogen bonds, their [[melting temperature]] (also called ''T<sub>m</sub>'' value). When all the base pairs in a DNA double helix melt, the strands separate and exist in solution as two entirely independent molecules. These single-stranded DNA molecules have no single shape, but some conformations are more stable than others.<ref>{{cite journal | author = Isaksson J, Acharya S, Barman J, Cheruku P, Chattopadhyaya J | title = Single-stranded adenine-rich DNA and RNA retain structural characteristics of their respective double-stranded conformations and show directional differences in stacking pattern | journal = Biochemistry | volume = 43 | issue = 51 | pages = 15996-6010 | year = 2004 | id = PMID 15609994}}</ref> The base pairing, or lack of it, can create various topologies at the [[DNA end]]. These can be exploited in [[biotechnology]].
Within most (but not all) genes, the nucleotides define a [[messenger RNA]] (mRNA) which in turn defines one or more protein sequences. This is possible because of the [[genetic code]] which [[Translation (genetics)|translate]]s the nucleic acid sequence to an [[amino acid|amino-acid]] sequence. The genetic code consists of three-letter 'words' called ''[[codon]]s'' formed from a sequence of three nucleotides. For example, the sequences ACU, CAG and UUU in mRNA are translated to threonine, glutamine and phenylalanine respectively.  


===Sense and antisense===
In transcription, the codons are copied into mRNA by [[RNA polymerase]]. This copy is then decoded by a [[ribosome]] that reads the RNA sequence by base-pairing the mRNA to a specific [[aminoacyl-tRNA]]; an amino acid carried by a [[transfer RNA]] (tRNA). As there are four bases in three-letter combinations, there are 64 possible codons, and these encode the twenty [[list of standard amino acids|standard amino acids]]. Most amino acids, therefore, have more than one possible codon (for example, ACU and ACA both code for threonine). There is one start codon (AUG) that also encodes for [[methionine]]) and three 'stop' or 'nonsense' codons (UAA, UGA and UAG) that signify the end of the coding region.
{{further|[[Sense (molecular biology)]]}}


DNA is copied into RNA by [[RNA polymerase]] enzymes that only work in the 5' to 3' direction.<ref name=Joyce>{{cite journal | author = Joyce C, Steitz T | title = Polymerase structures and function: variations on a theme? | url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=177480&blobtype=pdf | journal = J Bacteriol | volume = 177 | issue = 22 | pages = 6321-9 | year = 1995 | id = PMID 7592405}}</ref> A DNA sequence is called "sense" if its sequence is copied by these enzymes and then translated into protein. The sequence on the opposite strand is complementary to the sense sequence and is therefore called the "antisense" sequence. Both sense and antisense sequences can exist on different parts of the same strand of DNA. In both prokaryotes and eukaryotes, antisense sequences are transcribed, and elucidation of the often important functions of these anti-sense RNAs is an exciting topic in modern biological research.<!--NEED A RELEVANT REF HERE ON MICRORNA--><ref>{{cite journal | author = Hüttenhofer A, Schattner P, Polacek N | title = Non-coding RNAs: hope or hype? | journal = Trends Genet | volume = 21 | issue = 5 | pages = 289-97 | year = 2005 | id = PMID 15851066}}</ref> One proposal is that antisense RNAs are involved in regulating gene expression through RNA-RNA base pairing.<ref>{{cite journal | author = Munroe S | title = Diversity of antisense regulation in eukaryotes: multiple mechanisms, emerging patterns | journal = J Cell Biochem | volume = 93 | issue = 4 | pages = 664-71 | year = 2004 | id = PMID 15389973}}</ref>. (''See [[Micro RNA]], [[RNA interference]], [[sRNA]]''.)
===Regulation of gene expression===
How genes are regulated &mdash; how they are turned on or off &mdash; is an important topic in modern biology, and research continually yields surprising insights into how [[phenotypic]] traits and biological [[adaptations]] are determined.


A few DNA sequences in [[prokaryotes]] and [[eukaryotes]], and more in [[plasmids]] and [[viruses]], blur the distinction made above between sense and antisense strands by having overlapping genes.<ref>{{cite journal | author = Makalowska I, Lin C, Makalowski W | title = Overlapping genes in vertebrate genomes | journal = Comput Biol Chem | volume = 29 | issue = 1 | pages = 1-12 | year = 2005 | id = PMID 15680581}}</ref> In these cases, some DNA sequences do double duty, encoding one protein when read 5' to 3' along one strand, and a second protein when read in the opposite direction (still 5' to 3') along the other strand. In bacteria, this overlap may be involved in the regulation of gene transcription.<ref>{{cite journal | author = Johnson Z, Chisholm S | title = Properties of overlapping genes are conserved across microbial genomes | journal = Genome Res | volume = 14 | issue = 11 | pages = 2268-72 | year = 2004 | id = PMID 15520290}}</ref> While in viruses, overlapping genes increase the amount of information that can be encoded within the small viral genome.<ref>{{cite journal | author = Lamb R, Horvath C | title = Diversity of coding strategies in influenza viruses | journal = Trends Genet | volume = 7 | issue = 8 | pages = 261-6 | year = 1991 | id = PMID 1771674}}</ref> Another way of reducing genome size is seen in some viruses that contain linear or circular single-stranded DNA as their genetic material.<ref>{{cite journal | author = Davies J, Stanley J | title = Geminivirus genes and vectors | journal = Trends Genet | volume = 5 | issue = 3 | pages = 77-81 | year = 1989 | id = PMID 2660364}}</ref><ref>{{cite journal | author = Berns K | title = Parvovirus replication | journal = Microbiol Rev | volume = 54 | issue = 3 | pages = 316-29 | year = 1990 | id = PMID 2215424}}</ref>
In the 1950's, investigations of the bacterium ''[[Escherichia coli]]'' led to the recognition that the region upstream of a transcribed region provides a place for the enzyme [[RNA polymerase]] to attach to DNA and start transcribing RNA in the 5' to 3' direction of the nucleic acid chain. The site at which this occurs came to be called the ''[[promoter (genetics)|promoter]]''. Other regulatory proteins (such as ''repressors)'' influence transcription by binding to a region near to or overlapping the promoter, called the ''[[operator]]''. In the early years of modern genetics, emphasis was given to transcriptional regulation as an important and common means of modulating gene expression, but today we realize that there are a wide range of mechanisms by which the expression of mRNA and proteins can be modulated by both external and internal signals in cells.


===Supercoiling===
==Physical and chemical properties==
{{Further|[[DNA supercoil]]}}
[[Image:DNA_chemical_structure.png|right|thumb|280px|The two strands of DNA are held together by hydrogen bonds between bases. The sugars in the backbone are shown in light blue.]]
DNA can be twisted like a rope in a process called [[DNA supercoil|DNA supercoiling]]. Normally, with DNA in its "relaxed" state a strand circles the axis of the double helix once every 10.4 base pairs, but if the DNA is twisted the strands become more tightly or more loosely wound.<ref>{{cite journal | author = Benham C, Mielke S | title = DNA mechanics | journal = Annu Rev Biomed Eng | volume = 7 | issue = | pages = 21-53 | year = | id = PMID 16004565}}</ref> If the DNA is twisted in the direction of the helix this is positive supercoiling and the bases are held more tightly together. If they are twisted in the opposite direction this is negative supercoiling and the bases come apart more easily. In nature, most DNA has slight negative supercoiling that is introduced by enzymes called [[topoisomerase]]s.<ref name=Champoux>{{cite journal | author = Champoux J | title = DNA topoisomerases: structure, function, and mechanism | journal = Annu Rev Biochem | volume = 70 | issue = | pages = 369-413 | year = | id = PMID 11395412}}</ref> These enzymes are also needed to relieve the twisting stresses introduced into DNA strands during processes such as [[transcription]] and [[DNA replication]].<ref name=Wang>{{cite journal | author = Wang J | title = Cellular roles of DNA topoisomerases: a molecular perspective | journal = Nat Rev Mol Cell Biol | volume = 3 | issue = 6 | pages = 430-40 | year = 2002 | id = PMID 12042765}}</ref>


===Alternative double-helical structures===
DNA is a long chain of repeating units called ''nucleotides'' (a nucleotide is a base linked to a sugar and one or more phosphate groups)<ref name=Alberts>{{cite book | last = Alberts| first = Bruce| coauthors = Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walters | title = Molecular Biology of the Cell; Fourth Edition | publisher = Garland Science| date = 2002 | location = New York and London | url = http://www.ncbi.nlm.nih.gov/books/bv.fcgi?call=bv.View..ShowTOC&rid=mboc4.TOC&depth=2 | id = ISBN 0-8153-3218-1}}</ref> The DNA chain is 22-26 Å wide (2.2-2.6nm)<ref>{{cite journal | author = Mandelkern M ''et al.'' | title = The dimensions of DNA in solution | journal = J Mol Biol | volume = 152 | pages = 153-61 | year = 1981 | id = PMID 7338906}}</ref> The nucleotides are very small (just 3.3Å long), but DNA can contain millions of them: the DNA in the largest human chromosome (Chromosome 1) has 220 million base pairs.<ref>{{cite journal | author = Gregory S ''et al.'' | title = The DNA sequence and biological annotation of human chromosome 1 | journal = Nature | volume = 441 | pages = 315-21 | year = 2006 | id = PMID 16710414}}</ref>
{{Further|[[Mechanical properties of DNA]]}}


DNA exists in several possible conformations. The conformations so far identified are: A-DNA, B-DNA, C-DNA, D-DNA,<ref name=Hayashi2005>{{cite journal | author = Hayashi G, Hagihara M, Nakatani K | title = Application of L-DNA as a molecular tag | journal = Nucleic Acids Symp Ser (Oxf) | volume = 49 | pages = 261-262 | year = 2005 | id = PMID 17150733}}</ref> E-DNA,<ref name=Vargason2000>{{cite journal | author = Vargason JM, Eichman BF, Ho PS | title = The extended and eccentric E-DNA structure induced by cytosine methylation or bromination | journal = Nature Structural Biology | volume = 7 | pages = 758-761 | year = 2000 | id = PMID 10966645}}</ref> H-DNA,<ref name=Wang2006>{{cite journal | author = Wang G, Vasquez KM | title = Non-B DNA structure-induced genetic instability | journal = Mutat Res | volume = 598 | issue = 1-2 | pages = 103-119 | year = 2006 | id = PMID 16516932}}</ref> L-DNA,<ref name=Hayashi2005>{{cite journal | author = Hayashi G, Hagihara M, Nakatani K | title = Application of L-DNA as a molecular tag | journal = Nucleic Acids Symp Ser (Oxf) | volume = 49 | pages = 261-262 | year = 2005 | id = PMID 17150733}}</ref> and [[Z-DNA]].<ref name=Ghosh/><ref>{{cite journal | author = Palecek E | title = Local supercoil-stabilized DNA structures | journal = Crit Rev Biochem Mol Biol | volume = 26 | issue = 2 | pages = 151-226 | year = 1991 | id = PMID 1914495}}</ref> However, only A-DNA, B-DNA, and Z-DNA are believed to be found in nature. Which conformation DNA adopts depends on the sequence of the DNA, the amount and direction of supercoiling, chemical modifications of the bases and also solution conditions, such as the concentration of metal ions and [[polyamine]]s.<ref>{{cite journal | author = Basu H, Feuerstein B, Zarling D, Shafer R, Marton L | title = Recognition of Z-RNA and Z-DNA determinants by polyamines in solution: experimental and theoretical studies | journal = J Biomol Struct Dyn | volume = 6 | issue = 2 | pages = 299-309 | year = 1988 | id = PMID 2482766}}</ref> Of these three conformations, the "B" form described above is most common under the conditions found in cells. The two alternative double-helical forms of DNA differ in their geometry and dimensions.
In living organisms, DNA does not usually exist as a single molecule, but as a tightly-associated pair of molecules.<ref name=Watson>{{cite journal | author = Watson J, Crick F | title = Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid | url=http://profiles.nlm.nih.gov/SC/B/B/Y/W/_/scbbyw.pdf | journal = Nature | volume = 171 | pages = 737-8 | year = 1953 | id = PMID 13054692}}</ref><ref name=berg>Berg J ''et al.'' (2002) ''Biochemistry.'' WH Freeman and Co. ISBN 0-7167-4955-6</ref> These two long strands are entwined in the shape of a [[helix|double helix]]. DNA can thus be thought of as an anti-parallel double helix. The nucleotide repeats contain both the backbone of the molecule, which holds the chain together, and a base, which interacts with the other DNA strand. The double helix is held together by [[hydrogen bond]]s between the bases attached to the two strands. If many nucleotides are linked together, as in DNA, the [[polymer]] is referred to as a [[polynucleotide]].<ref name=IUPAC>[http://www.chem.qmul.ac.uk/iupac/misc/naabb.html Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents] IUPAC-IUB Commission on Biochemical Nomenclature (CBN) Accessed 03 Jan 2006</ref>


The A form is a wider right-handed spiral, with a shallow and wide minor groove and a narrower and deeper major groove. The A form occurs under non-physiological conditions in dehydrated samples of DNA, while in the cell it may be produced in hybrid pairings of DNA and RNA strands.<ref>{{cite journal | author = Wahl M, Sundaralingam M | title = Crystal structures of A-DNA duplexes | journal = Biopolymers | volume = 44 | issue = 1 | pages = 45-63 | year = 1997 | id = PMID 9097733}}</ref> Segments of DNA where the bases have been [[methylation|methylated]] may undergo a larger change in conformation and adopt the [[Z-DNA|Z form]]. Here, the strands turn about the helical axis in a left-handed spiral, a mirror image of the more common B form.<ref>{{cite journal | author = Rothenburg S, Koch-Nolte F, Haag F | title = DNA methylation and Z-DNA formation as mediators of quantitative differences in the expression of alleles | journal = Immunol Rev | volume = 184 | issue = | pages = 286-98 | year = | id = PMID 12086319}}</ref>
The backbone of the DNA strand has alternating phosphate and sugar residues<ref name=Ghosh>{{cite journal | author = Ghosh A, Bansal M | title = A glossary of DNA structures from A to Z | journal = Acta Crystallogr D Biol Crystallogr | volume = 59 | pages = 620-6 | year = 2003 | id = PMID 12657780}}</ref>: the sugar is the [[pentose]] (five carbon) sugar 2-deoxyribose. The sugar molecules are joined together by phosphate groups that form [[phosphodiester bond]]s between the third and fifth carbon atoms in the sugar rings. Because these bonds are asymmetric, a strand of DNA has a 'direction'. In a double helix, the direction of the nucleotides in one strand is opposite to that in the other strand. This arrangement of DNA strands is called ''antiparallel''. The asymmetric ends of a strand of DNA bases are referred to as the [[5' end|5']] (''five prime'') and [[3' end|3']] (''three prime'') ends. One of the major differences between DNA and RNA is the sugar: 2-deoxyribose is replaced by [[ribose]] in RNA.<ref name=berg/>


===Quadruplex structures===
The four bases in DNA are adenine (A), cytosine (C), guanine (G) and thymine (T), and these bases are attached to the sugar/phosphate to form the complete nucleotide. Adenine and guanine are fused five- and six-membered [[heterocyclic compound]]s called [[purine]]s, while cytosine and thymine are six-membered rings called [[pyrimidine]]s.<ref name=IUPAC/> A fifth pyrimidine base, [[uracil]] (U), replaces thymine in RNA. Uracil is normally only found in DNA as a breakdown product of cytosine, but [[phage|bacterial viruses]] contain uracil in their DNA.<ref name="nature1963-takahashi">{{cite journal | author=Takahashi I, Marmur J | title=Replacement of thymidylic acid by deoxyuridylic acid in the deoxyribonucleic acid of a transducing phage for Bacillus subtilis | journal=Nature | year=1963 | pages=794-5 | volume=197 | id=PMID 13980287}}</ref> In contrast, following synthesis of certain RNA molecules, many uracils are converted to thymines. This occurs mostly on structural and enzymatic RNAs like tRNAs and [[ribosomal RNA]].<ref>{{cite journal |author=Agris P |title=Decoding the genome: a modified view |
At the ends of the linear [[chromosome]]s are specialized regions of DNA called [[telomere]]s. The main function of these regions is to allow the cell to replicate chromosome ends using the enzyme [[telomerase]], as normal [[DNA polymerase]]s working on the [[lagging strand]] cannot copy the extreme 3' ends of their DNA templates.<ref name=Greider>{{cite journal | author = Greider C, Blackburn E | title = Identification of a specific telomere terminal transferase activity in Tetrahymena extracts | journal = Cell | volume = 43 | issue = 2 Pt 1 | pages = 405-13 | year = 1985 | id = PMID 3907856}}</ref> If a chromosome lacked telomeres it would become shorter each time it was replicated. These specialized chromosome caps also help protect the DNA ends from [[exonuclease]]s and stop the [[DNA repair]] systems in the cell from treating them as damage to be corrected.<ref name=Nugent>{{cite journal | author = Nugent C, Lundblad V | title = The telomerase reverse transcriptase: components and regulation | url=http://www.genesdev.org/cgi/content/full/12/8/1073 | journal = Genes Dev | volume = 12 | issue = 8 | pages = 1073-85 | year = 1998 | id = PMID 9553037}}</ref> In human cells, telomeres are usually lengths of single-stranded DNA containing several thousand repeats of a simple TTAGGG sequence.<ref>{{cite journal | author = Wright W, Tesmer V, Huffman K, Levene S, Shay J | title = Normal human chromosomes have long G-rich telomeric overhangs at one end | url=http://www.genesdev.org/cgi/content/full/11/21/2801#B34 | journal = Genes Dev | volume = 11 | issue = 21 | pages = 2801-9 | year = 1997 | id = PMID 9353250}}</ref>
url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=14715921 |journal=Nucleic Acids Res |volume=32 |pages=223 – 38 |year=2004 |pmid=14715921}}</ref>


These guanine-rich sequences may stabilise chromosome ends by forming very unusual quadruplex structures. Here, four guanine bases form a flat plate, through hydrogen bonding, and these flat four-base units then stack on top of each other, to form a stable quadruplex.<ref name=Burge>{{cite journal | author = Burge S, Parkinson G, Hazel P, Todd A, Neidle S | title = Quadruplex DNA: sequence, topology and structure | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17012276 | journal = Nucleic Acids Res | volume = 34 | issue = 19 | pages = 5402-15 | year = 2006 | id = PMID 17012276}}</ref> These structures are often stabilized by [[chelation]] of a metal ion in the centre of each four-base unit. The structure shown to the left is of a quadruplex formed by a DNA sequence containing four consecutive human telomere repeats. The single DNA strand forms a loop, with the sets of four bases stacking in a central quadruplex three plates deep. In the space at the centre of the stacked bases are three chelated potassium ions.<ref>{{cite journal | author = Parkinson G, Lee M, Neidle S | title = Crystal structure of parallel quadruplexes from human telomeric DNA | journal = Nature | volume = 417 | issue = 6891 | pages = 876-80 | year = 2002 | id = PMID 12050675}}</ref> Other structures can also be formed and the central set of four bases can come from either one folded strand, or several different parallel strands.
The double helix is a right-handed spiral. As the DNA strands wind around each other, gaps between the two phosphate backbones reveal the sides of the bases inside (see animation). Two of these grooves twist around the surface of the double helix: the major groove is 22&nbsp;Å wide and the minor groove is 12&nbsp;Å wide.<ref>{{cite journal | author = Wing R ''et al.''| title = Crystal structure analysis of a complete turn of B-DNA | journal = Nature | volume = 287 | pages = 755 – 8 | year = 1980 | id = PMID 7432492}}</ref> The edges of the bases are more accessible in the major groove, so proteins like [[transcription factor]]s that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove.<ref name=Pabo>{{cite journal | author = Pabo C, Sauer R | title = Protein-DNA recognition | journal = Ann Rev Biochem | volume = 53 |pages = 293-321 | year = | id = PMID 6236744}}</ref>


In addition to these stacked structures, telomeres also form large loop structures called telomere loops, or T-loops. Here, the single-stranded DNA curls around in a circle stabilized by telomere-binding proteins.<ref>{{cite journal | author = Griffith J, Comeau L, Rosenfield S, Stansel R, Bianchi A, Moss H, de Lange T | title = Mammalian telomeres end in a large duplex loop | journal = Cell | volume = 97 | issue = 4 | pages = 503-14 | year = 1999 | id = PMID 10338214}}</ref> The very end of the T-loop, the single-stranded telomere DNA is held onto a region of double-stranded DNA by the telomere strand disrupting the double-helical DNA and base pairing to one of the two strands. This triple-stranded structure is called a displacement loop or D-loop.<ref name=Burge/>
===Base pairing===
Each type of base on one strand of DNA forms a bond with just one type of base on the other strand, called 'complementary [[base pair]]ing'. Purines form hydrogen bonds to pyrimidines; for example, A bonds only to T, and C bonds only to G. This arrangement of two nucleotides joined together across the double helix is called a ''base pair''. In a double helix, the two strands are also held together by [[hydrophobic effect]]s and by a variation of [[pi stacking]].<ref>{{cite journal | author = Ponnuswamy P, Gromiha M | title = On the conformational stability of oligonucleotide duplexes and tRNA molecules | journal = J Theor Biol | volume = 169 |  pages = 419-32 | year = 1994 | id = PMID 7526075}}</ref> Hydrogen bonds can be broken and rejoined quite easily, so the two strands of DNA in a double helix can be pulled apart like a zipper, either by  mechanical force or by high temperatures.<ref>{{cite journal | author = Clausen-Schaumann H ''et al.'' | title = Mechanical stability of single DNA molecules | url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1300792&blobtype=pdf | journal = Biophys J | volume = 78 | pages = 1997-2007 | year = 2000 | id = PMID 10733978}}</ref> Becauseof this complementarity, the information in the double-stranded sequence of a DNA helix is duplicated on each strand, and this is vital in DNA replication. The reversible and specific interaction between complementary base pairs is critical for all the functions of DNA in living organisms.<ref name=Alberts/>  


==Chemical modifications==
The two types of base pairs form different numbers of hydrogen bonds; AT forms two hydrogen bonds, and GC forms three, so the GC base-pair is stronger than the AT pair. Thus, long DNA helices with a high GC content have strongly interacting strands, while short helices with high AT content have weakly interacting strands.<ref>{{cite journal | author = Chalikian T ''et al.''| title = A more unified picture for the thermodynamics of nucleic acid duplex melting: a characterization by calorimetric and volumetric techniques | url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=22151&blobtype=pdf | journal = Proc Natl Acad Sci USA | volume = 96 | pages = 7853-8 | year = 1999 | id = PMID 10393911}}</ref> Parts of the DNA double helix that need to separate easily tend to have a high AT content, making the strands easier to pull apart.<ref>{{cite journal | author = deHaseth P, Helmann J | title = Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase-induced strand separation of double helical DNA | journal = Mol Microbiol | volume = 16 | pages = 817-24 | year = 1995 | id = PMID 7476180}}</ref> The strength of this interaction can be measured by finding the temperature required to break the hydrogen bonds (their '[[melting temperature]]'). When all the base pairs in a DNA double helix melt, the strands separate, leaving two single-stranded molecules in solution. These molecules have no single shape, but some conformations are more stable than others.
===Regulatory base modifications===
{{further|[[DNA methylation]]}}
The expression of genes is influenced by modifications of the bases in DNA. In humans, the most common base modification is [[cytosine]] [[methylation]] to produce [[5-Methylcytosine|5-methylcytosine]]. This modification reduces gene expression and is important in [[X-inactivation|X-chromosome inactivation]].<ref>{{cite journal | author = Klose R, Bird A | title = Genomic DNA methylation: the mark and its mediators | journal = Trends Biochem Sci | volume = 31 | issue = 2 | pages = 89-97 | year = 2006 | id = PMID 16403636}}</ref> The level of methylation varies between organisms, with ''[[Caenorhabditis elegans]]'' lacking cytosine methylation, while vertebrates show high levels, with up to 1% of their DNA being 5-methylcytosine.<ref>{{cite journal | author = Bird A | title = DNA methylation patterns and epigenetic memory | journal = Genes Dev | volume = 16 | issue = 1 | pages = 6-21 | year = 2002 | id = PMID 11782440}}</ref> Unfortunately, the spontaneous [[deamination]] of 5-methylcytosine produces thymine and methylated cytosines are therefore mutation hotspots.<ref>{{cite journal | author = Walsh C, Xu G | title = Cytosine methylation and DNA repair | journal = Curr Top Microbiol Immunol | volume = 301 | issue = | pages = 283-315 | year = | id = PMID 16570853}}</ref> Other base modifications include adenine methylation in bacteria and the [[glycosylation]] of uracil to produce the "J-base" in [[kinetoplastid]]s.<ref>{{cite journal | author = Ratel D, Ravanat J, Berger F, Wion D | title = N6-methyladenine: the other methylated base of DNA | journal = Bioessays | volume = 28 | issue = 3 | pages = 309-15 | year = 2006 | id = PMID 16479578}}</ref><ref>{{cite journal | author = Gommers-Ampt J, Van Leeuwen F, de Beer A, Vliegenthart J, Dizdaroglu M, Kowalak J, Crain P, Borst P | title = beta-D-glucosyl-hydroxymethyluracil: a novel modified base present in the DNA of the parasitic protozoan T. brucei | journal = Cell | volume = 75 | issue = 6 | pages = 1129-36 | year = 1993 | id = PMID 8261512}}</ref>


===DNA damage===
===Sense and antisense===
{{further|[[Mutation]]}}
DNA is copied into RNA by [[RNA polymerase]]s.<ref name=Joyce>{{cite journal | author = Joyce C, Steitz T | title = Polymerase structures and function: variations on a theme? | url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=177480&blobtype=pdf | journal = J Bacteriol | volume = 177 | pages = 6321-9 | year = 1995 | id = PMID 7592405}}</ref> A DNA sequence is called a "sense" sequence if it is copied by these enzymes (which only work in the 5' to 3' direction) and then translated into protein. The sequence on the opposite strand is complementary to the sense sequence and is called the "antisense" sequence. Sense and antisense sequences can co-exist on the same strand of DNA; in both prokaryotes and eukaryotes, antisense sequences are transcribed<ref>{{cite journal | author = Hüttenhofer A ''et al.''| title = Non-coding RNAs: hope or hype? | journal = Trends Genet | volume = 21 |pages = 289-97 | year = 2005 | id = PMID 15851066}}</ref>, and antisense RNAs might be involved in regulating gene expression.<ref>{{cite journal | author = Munroe S | title = Diversity of antisense regulation in eukaryotes: multiple mechanisms, emerging patterns | journal = J Cell Biochem | volume = 93 | pages = 664-71 | year = 2004 | id = PMID 15389973}}</ref>. (''See [[Micro RNA]], [[RNA interference]], [[sRNA]]''.)


DNA can be damaged by many different sorts of [[mutagen]]s. These include [[oxidizing agent]]s, [[alkylating agent]]s and also high-energy [[electromagnetic radiation]] such as [[ultraviolet light]] and [[x-rays]]. The type of DNA damage produced depends on the type of mutagen. For example, UV light mostly damages DNA by producing [[thymine dimer]]s, which are cross-links between adjacent pyrimidine bases in a DNA strand.<ref>{{cite journal | author = Douki T, Reynaud-Angelin A, Cadet J, Sage E | title = Bipyrimidine photoproducts rather than oxidative lesions are the main type of DNA damage involved in the genotoxic effect of solar UVA radiation | journal = Biochemistry | volume = 42 | issue = 30 | pages = 9221-6 | year = 2003 | id = PMID 12885257}},</ref> On the other hand, oxidants such as [[free radical]]s or [[hydrogen peroxide]] produce multiple forms of damage, including base modifications, particularly of guanosine, as well as double-strand breaks.<ref>{{cite journal | author = Cadet J, Delatour T, Douki T, Gasparutto D, Pouget J, Ravanat J, Sauvaigo S | title = Hydroxyl radicals and DNA base damage | journal = Mutat Res | volume = 424 | issue = 1-2 | pages = 9-21 | year = 1999 | id = PMID 10064846}}</ref> It has been estimated that in each human cell, about 500 bases suffer oxidative damage per day.<ref>{{cite journal | author = Shigenaga M, Gimeno C, Ames B | title = Urinary 8-hydroxy-2'-deoxyguanosine as a biological marker of ''in vivo'' oxidative DNA damage | url=http://www.pnas.org/cgi/reprint/86/24/9697 | journal = Proc Natl Acad Sci U S A | volume = 86 | issue = 24 | pages = 9697-701 | year = 1989 | id = PMID 2602371}}</ref><ref>{{cite journal | author = Cathcart R, Schwiers E, Saul R, Ames B | title = Thymine glycol and thymidine glycol in human and rat urine: a possible assay for oxidative DNA damage | url=http://www.pnas.org/cgi/reprint/81/18/5633.pdf | journal = Proc Natl Acad Sci U S A | volume = 81 | issue = 18 | pages = 5633-7 | year = 1984 | id = PMID 6592579}}</ref> Of these oxidative lesions, the most damaging are double-strand breaks, as they can produce [[point mutation]]s, insertions and deletions from the DNA sequence, as well as [[chromosomal translocation]]s.<ref>{{cite journal | author = Valerie K, Povirk L | title = Regulation and mechanisms of mammalian double-strand break repair | journal = Oncogene | volume = 22 | issue = 37 | pages = 5792-812 | year = 2003 | id = PMID 12947387}}</ref>
Many DNA sequences in prokaryotes and eukaryotes (and more in plasmids and viruses) have overlapping genes which may both occur in the same direction, on the same strand (parallel) or in opposite directions, on opposite strands (antiparallel), blurring the distinction between sense and antisense strands.<ref>{{cite journal | author = Makalowska I ''et al.''| title = Overlapping genes in vertebrate genomes | journal = Comput Biol Chem | volume = 29 | pages = 1–12 | year = 2005 | url=http://warta.bio.psu.edu/PDF/cbac_2005_29_1.pdf | id = PMID 15680581}}</ref><ref name="johnson">{{cite journal | author = Johnson Z, Chisholm S | title = Properties of overlapping genes are conserved across microbial genomes | journal = Genome Res | volume = 14 | pages = 2268–72 | year = 2004 | url=http://www.genome.org/cgi/content/full/14/11/2268 | id = PMID 15520290}}</ref> In these cases, some DNA sequences encode one protein when read from 5′ to 3′ along one strand, and a different protein when read in the opposite direction (but still from 5′ to 3′) along the other strand. In bacteria, this overlap may be involved in regulating gene transcription,<ref name="johnson" /> while in [[viruses]], overlapping genes increase the information that can be encoded within the small viral genome.<ref>{{cite journal | author = Lamb R, Horvath C | title = Diversity of coding strategies in [[influenza]] viruses | journal = Trends Genet | volume = 7 | pages = 261–6 | year = 1991 | id = PMID 1771674}}</ref> Another way of reducing genome size is seen in some viruses that contain linear or circular ''single-stranded'' DNA.<ref>{{cite journal | author = Davies J, Stanley J | title = Geminivirus genes and vectors | journal = Trends Genet | volume = 5 | pages = 77–81 | year = 1989 | id = PMID 2660364}}</ref>


Many mutagens [[intercalation (chemistry)|intercalate]] into the space between two adjacent [[base pair]]s. These molecules are mostly polycyclic, [[aromatic]], and planar molecules and include [[ethidium]], [[proflavin]], [[daunomycin]], [[doxorubicin]] and [[thalidomide]]. DNA intercalators are used in [[chemotherapy]] to inhibit DNA replication in rapidly-growing cancer cells.<ref>{{cite journal | author = Braña M, Cacho M, Gradillas A, de Pascual-Teresa B, Ramos A | title = Intercalators as anticancer drugs | journal = Curr Pharm Des | volume = 7 | issue = 17 | pages = 1745-80 | year = 2001 | id = PMID 11562309}}</ref> In order for an intercalator to fit between base pairs, the bases must separate, distorting the DNA strand by unwinding of the double helix. These structural modifications inhibit [[transcription (genetics)|transcription]] and [[DNA replication|replication]] processes, causing both toxicity and mutations. As a result, DNA intercalators are often [[carcinogen]]s, with [[benzopyrene|benzopyrene diol epoxide]], [[acridine]]s, [[aflatoxin]] and [[ethidium bromide]] being well-known examples.<ref>{{cite journal | author = Ferguson L, Denny W | title = The genetic toxicology of acridines | journal = Mutat Res | volume = 258 | issue = 2 | pages = 123-60 | year = 1991 | id = PMID 1881402}}</ref><ref>{{cite journal | author = Jeffrey A | title = DNA modification by chemical carcinogens | journal = Pharmacol Ther | volume = 28 | issue = 2 | pages = 237-72 | year = 1985 | id = PMID 3936066}}</ref>
===Supercoiling===
DNA can be 'twisted' in a process called [[DNA supercoil]]ing. In its "relaxed" state, a DNA strand usually circles the axis of the double helix once every 10.4 base pairs, but if the DNA is twisted, the strands become more tightly or more loosely wound.<ref>{{cite journal | author = Benham C, Mielke S | title = DNA mechanics | journal = Ann Rev Biomed Eng | volume = 7 | pages = 21–53 | year = | id = PMID 16004565}}</ref> If the DNA is twisted in the direction of the helix (positive supercoiling), and the bases are held more tightly together. If they are twisted in the opposite direction (negative supercoiling) the bases come apart more easily. Most DNA has slight negative supercoiling that is introduced by [[topoisomerase]]s. These enzymes are also needed to relieve the twisting stresses introduced into DNA strands during processes such as [[transcription (genetics)|transcription]] and [[DNA replication]].<ref name=Wang>{{cite journal | author = Wang J | title = Cellular roles of DNA topoisomerases: a molecular perspective | journal = Nat Rev Mol Cell Biol | volume = 3 |pages = 430–40 | year = 2002 | id = PMID 12042765}}</ref>


===Replication===
===Alternative conformations===
{{further|[[DNA replication]], [[Replication of a circular bacterial chromosome]]}}
The conformation of a DNA molecule depends on its sequence, the amount and direction of supercoiling, chemical modifications of the bases, and also solution conditions, such as the concentration of metal ions.<ref>{{cite journal | author = Basu H ''et al.'' | title = Recognition of Z-RNA and Z-DNA determinants by polyamines in solution: experimental and theoretical studies | journal = J Biomol Struct Dyn | volume = 6 |  pages = 299-309 | year = 1988 | id = PMID 2482766}}</ref> Accordingly, DNA can exist in several possible conformations, but only a few of these ("A-DNA", "B-DNA", and "Z-DNA") are thought to occur naturally. Of these, the "B" form is most common. The A form is a wider right-handed spiral, with a shallow and wide minor groove and a narrower and deeper major groove; this form occurs in dehydrated samples of DNA, while in the cell it may be produced in hybrid pairings of DNA and [[RNA]] strands, as well as in enzyme-DNA complexes.<ref>{{cite journal |author=Lu XJ ''et al.'' |title=A-form conformational motifs in ligand-bound DNA structures |journal=J Mol Biol |volume=300|pages=819-40 |year=2000 |pmid=10891271}}</ref> Segments of DNA where the bases have been modified by [[methylation]] may undergo a larger change in conformation and adopt the Z form. Here, the strands turn about the helical axis in a left-handed spiral, the opposite of the more common B form.<ref>{{cite journal | author = Rothenburg S ''et al.'' | title = DNA methylation and Z-DNA formation as mediators of quantitative differences in the expression of alleles | journal = Immunol Rev | volume = 184 |  pages = 286–98 | year = | id = PMID 12086319}}</ref> These unusual structures can be recognized by specific Z-DNA binding proteins and may be involved in regulating transcription.<ref>{{cite journal |author=Oh D ''et al.'' |title=Z-DNA-binding proteins can act as potent effectors of gene expression ''in vivo'' |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12486233 |journal=Proc Natl Acad Sci USA |volume=99 |pages=16666-71 |year=2002 |pmid=12486233}}</ref>


[[Image:DNAreplicationFORK.jpg|thumb|400px| '''DNA-replication''' illustrated by the bacterial replication fork. The helix unwinds and both strands replicate simultaneously, during the unwinding process. The ''leading'' strand replicates continuously from 3' end of existing strand, with newest end of forming strand facing into replication fork. The ''lagging'' strand replicates by a series of fragments (Okazaki-fragments placed end-to-end, with newest ends of fragments facing away from fork; the Okazaki-fragments later ligated together. During replication, DNA polymerase III proofreads for mismatched bases]]
===Quadruplex structures===
At the ends of the linear chromosomes, specialized regions called [[telomere]]s allow the cell to replicate chromosome ends using the enzyme [[telomerase]].<ref name=Greider>{{cite journal | author = Greider C, Blackburn E | title = Identification of a specific telomere terminal transferase activity in Tetrahymena extracts | journal = Cell | volume = 43 | pages = 405-13 | year = 1985 | id = PMID 3907856}}</ref> Without telomeres, a chromosome would become shorter each time it was replicated. These specialized 'caps' also help to protect the DNA ends from [[exonuclease]]s and stop the [[DNA repair]] systems in the cell from treating them as damage to be corrected. In human cells, telomeres are usually lengths of single-stranded DNA that contain several thousand repeats of a TTAGGG sequence.<ref name=wright/> These sequences may stabilize chromosome ends by forming unusual quadruplex structures. Here, four guanine bases form a flat plate, through[[ hydrogen bonding]], and these plates then stack on top of each other to form a stable quadruplex.<ref name=Burge>{{cite journal | author = Burge S ''et al.'' | title = Quadruplex DNA: sequence, topology and structure | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17012276 | journal = Nucleic Acids Res | volume = 34 | pages = 5402-15 | year = 2006 | id = PMID 17012276}}</ref> Other structures can also be formed, and the central set of four bases can come from either one folded strand, or several different parallel strands, each contributing one base to the central structure.


Telomeres also form large loops called '[[telomere loops]]', or '[[T-loops]]'. Here, the single-stranded DNA curls around in a circle stabilized by telomere-binding proteins.<ref>{{cite journal | author = Griffith J ''et al.'' | title = Mammalian telomeres end in a large duplex loop | journal = Cell | volume = 97 |  pages = 503-14 | year = 1999 | id = PMID 10338214}}</ref>


[[Cell division]] is essential for an organism to grow, but when a cell divides it must replicate the DNA in its genome so that the two daughter cells have the same genetic information as their parent. The double-stranded structure of DNA provides a simple mechanism for [[DNA replication]]. Here, the two strands are separated and then each strand's complementary DNA sequence is recreated by an enzyme called [[DNA polymerase]]. This enzyme makes the complementary strand by finding the correct base through complementary base pairing, and bonding it onto the original strand. As DNA polymerases can only extend a DNA strand in a 5' to 3' direction, different mechanisms are used to copy the antiparallel strands of the double helix.<ref>{{cite journal | author = Albà M | title = Replicative DNA polymerases | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11178285 | journal = Genome Biol | volume = 2 | issue = 1 | pages = REVIEWS3002 | year = 2001 | id = PMID 11178285}}</ref> In this way, the base on the old strand dictates which base appears on the new strand, and the cell ends up with a perfect copy of its DNA.
==Chemical modifications==
===DNA methylation===
The expression of genes is influenced by the [[chromatin]] structure of a chromosome, and regions of [[heterochromatin]] (with little or no gene expression) correlate with the [[methylation]] of [[cytosine]].<ref> For example, cytosine methylation, to produce [[5-Methylcytosine|5-methylcytosine]], is important for [[X-inactivation|X-chromosome inactivation]]. {{cite journal | author = Klose R, Bird A | title = Genomic DNA methylation: the mark and its mediators | journal = Trends Biochem Sci | volume = 31 |  pages = 89–97 | year = 2006 | id = PMID 16403636}}</ref> These structural changes to the DNA are one type of [[epigenetic]] change that can alter chromatin structure, and they are inheritable. ''Epigenetics'' refers to features of organisms that are stable over successive rounds of cell division but which do not involve changes in the underlying DNA sequence<ref>{{cite journal| title=Perceptions of epigenetics| author=Adrian Bird| journal=Nature| volume=447| pages=396-398| year=2007}} PMID 17522671</ref>. Epigenetic changes are important in [[morphogenesis|cellular differentiation]], allowing cells to maintain different characteristics despite containing the same genomic material. Some epigenetic features can be inherited from one generation to the next.<ref>{{cite journal| title=Paramutation: From Maize to Mice| author=V.L. Chandler| journal=Cell| volume=128| pages=641-645| year=2007}}</ref>


Despite the apparent simplicity of DNA replication, the duplication of DNA prior to cell division is carried out by a complex and efficient set of catalytically active proteins, each dedicated to the different tasks needed to replicate this large molecule in an orderly and extremely precise fashion. Further capacity for DNA replication with substantial rearrangement (which has major implications for understanding mechanisms of  [[molecular evolution]], is provided by mechanisms for DNA movement, inversion, and duplication, illustrated by various [[Mobile DNA|mobile DNA]]s such as transposons and proviruses.
The level of methylation varies between organisms; the nematode ''C. elegans'' lacks any cytosine methylation, while up to 1% of the DNA of vertebrates contains 5-methylcytosine.<ref>{{cite journal | author = Bird A | title = DNA methylation patterns and epigenetic memory | journal = Genes Dev | volume = 16 | pages = 6–21 | year = 2002 | id = PMID 11782440}}</ref> Despite the biological importance of 5-methylcytosine, it is susceptible to spontaneous [[deamination]], and methylated cytosines are therefore [[mutation]] 'hotspots'.<ref>{{cite journal | author = Walsh C, Xu G | title = Cytosine methylation and DNA repair | journal = Curr Top Microbiol Immunol | volume = 301 | pages = 283–315 | year = | id = PMID 16570853}}</ref> Other base modifications include adenine methylation in bacteria and the [[glycosylation]] of uracil to produce the "J-base" in [[kinetoplastid]]s.<ref>{{cite journal | author = Ratel D ''et al.''| title = N6-methyladenine: the other methylated base of DNA | journal = Bioessays | volume = 28 | pages = 309–15 | year = 2006 | id = PMID 16479578}}</ref><ref>{{cite journal | author = Gommers-Ampt J ''et al.''| title = beta-D-glucosyl-hydroxymethyluracil: a novel modified base present in the DNA of the parasitic protozoan T. brucei | journal = Cell | volume = 75 | pages = 1129–36 | year = 1993 | id = PMID 8261512}}</ref>


==Genes and genomes==
===Mutations===
{{further|[[Cell nucleus]], [[Gene]], [[Non-coding DNA]]}}
DNA can be damaged by many different agents. [[Mutagen]]s are agents which can produce genetic [[mutation]]s - these are alterations of one DNA base to another base. Examples of mutagens include [[oxidizing agent]]s, [[alkylating agent]]s and high-energy [[electromagnetic radiation]] such as [[ultraviolet light]] and [[x-rays]]. ''Lesions'' of DNA, in which residues are changed to a structure that is not a normal feature of DNA, are different from mutations. However, damaged DNA can give rise to mutations, and indeed, some DNA repair processes are ''error prone'' and thus themselves generate mutations.
DNA is located in the [[cell nucleus]] of eukaryotes, as well as small amounts in [[mitochondrion|mitochondria]] and [[chloroplast]]s. In prokaryotes, the DNA is held within an irregularly shaped body in the cytoplasm called the [[nucleoid]].<ref>{{cite journal | author = Thanbichler M, Wang S, Shapiro L | title = The bacterial nucleoid: a highly organized and dynamic structure | journal = J Cell Biochem | volume = 96 | issue = 3 | pages = 506–21 | year = 2005 | id = PMID 15988757}}</ref> The DNA is usually in linear [[chromosome]]s in eukaryotes, and circular chromosomes in prokaryotes. In the [[human genome]], there is approximately 3 billion base pairs of DNA arranged into 46 chromosomes.<ref>{{cite journal | author = Venter J, ''et al.'' | title = The sequence of the human genome | journal = Science | volume = 291 | issue = 5507 | pages = 1304-51 | year = 2001 | id = PMID 11181995}}</ref> The genetic information in a genome is held within [[gene]]s. A gene is a unit of heredity and is a region of DNA that influences a particular characteristic in an organism. Genes contain an [[open reading frame]] that can be transcribed, as well as [[regulatory sequence]]s such as [[promoter]]s and [[enhancer (genetics)|enhancers]], which control the expression of the open reading frame.


In many [[species]], only a small fraction of the total sequence of the [[genome]] encodes protein. For example, only about 1.5% of the [[human genome]] consists of protein-coding [[exons]], with over 50% of human DNA consisting of non-coding [[repeated sequence (DNA)|repetitive sequences]].<ref>{{cite journal | author = Wolfsberg T, McEntyre J, Schuler G | title = Guide to the draft human genome | journal = Nature | volume = 409 | issue = 6822 | pages = 824-6 | year = 2001 | id = PMID 11236998}}</ref> The reasons for the presence of so much [[non-coding DNA]] in [[eukaryotic]] genomes and the extraordinary differences in [[genome size]], or ''[[C-value]]'', among species represent a long-standing puzzle known as the "[[C-value enigma]]".<ref>{{cite journal | author = Gregory T | title = The C-value enigma in plants and animals: a review of parallels and an appeal for partnership | url=http://aob.oxfordjournals.org/cgi/content/full/95/1/133 | journal = Ann Bot (Lond) | volume = 95 | issue = 1 | pages = 133-46 | year = 2005 | id = PMID 15596463}}</ref>
Ultraviolet radiation damages DNA mostly by producing [[thymine dimer]]s.<ref>{{cite journal | author = Douki T ''et al.'' | title = Bipyrimidine photoproducts rather than oxidative lesions are the main type of DNA damage involved in the genotoxic effect of solar ultraviolet radiation | journal = Biochemistry | volume = 42 |  pages = 9221-6 | year = 2003 | id = PMID 12885257}}</ref> Oxidants such as [[free radical]]s or [[hydrogen peroxide]] can cause several forms of damage, including base modifications (particularly of guanosine) as well as double-strand breaks.<ref>{{cite journal | author = Cadet J ''et al.'' | title = Hydroxyl radicals and DNA base damage | journal = Mutat Res | volume = 424 | issue = 1-2 | pages = 9-21 | year = 1999 | id = PMID 10064846}}</ref> It has been estimated that, in each human cell, about 500 bases suffer oxidative damage every day.<ref>{{cite journal | author = Shigenaga M ''et al.'' | title = Urinary 8-hydroxy-2'-deoxyguanosine as a biological marker of ''in vivo'' oxidative DNA damage | url=http://www.pnas.org/cgi/reprint/86/24/9697 | journal = Proc Natl Acad Sci USA | volume = 86 | pages = 9697-701 | year = 1989 | id = PMID 2602371}}</ref><ref>{{cite journal | author = Cathcart R ''et al.'' | title = Thymine glycol and thymidine glycol in human and rat urine: a possible assay for oxidative DNA damage | url=http://www.pnas.org/cgi/reprint/81/18/5633.pdf | journal = Proc Natl Acad Sci USA | volume = 81 |  pages = 5633-7 | year = 1984 | id = PMID 6592579}}</ref> Of these lesions, the most damaging are double-strand breaks, as they can produce [[point mutation]]s, insertions and deletions from the DNA sequence, as well as [[chromosomal translocation]]s.<ref>{{cite journal | author = Valerie K, Povirk L | title = Regulation and mechanisms of mammalian double-strand break repair | journal = Oncogene | volume = 22 | pages = 5792-812 | year = 2003 | id = PMID 12947387}}</ref>


Some non-coding DNA sequences play structural roles in chromosomes. [[Telomere]]s and [[centromere]]s typically contain few genes, but are important for the function and stability of chromosomes.<ref name=Nugent/><ref>{{cite journal | author = Pidoux A, Allshire R | title = The role of heterochromatin in centromere function | url=http://www.journals.royalsoc.ac.uk/media/804t6y8vmh5utlb6ua5y/contributions/p/x/7/a/px7ahm740dq5ueuk.pdf | journal = Philos Trans R Soc Lond B Biol Sci | volume = 360 | issue = 1455 | pages = 569-79 | year = 2005 | id = PMID 15905142}}</ref> An abundant form of non-coding DNA in humans are [[pseudogene]]s, which are copies of genes that have been disabled by mutation.<ref>{{cite journal | author = Harrison P, Hegyi H, Balasubramanian S, Luscombe N, Bertone P, Echols N, Johnson T, Gerstein M | title = Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22 | url=http://www.genome.org/cgi/content/full/12/2/272 | journal = Genome Res | volume = 12 | issue = 2 | pages = 272-80 | year = 2002 | id = PMID 11827946}}</ref> These sequences are usually just molecular fossils, although they can occasionally serve as raw genetic material for the creation of new genes through the process of [[gene duplication]] and [[divergent evolution|divergence]].<ref>{{cite journal | author = Harrison P, Gerstein M | title = Studying genomes through the aeons: protein families, pseudogenes and proteome evolution | journal = J Mol Biol | volume = 318 | issue = 5 | pages = 1155-74 | year = 2002 | id = PMID 12083509}}</ref>
Many mutagens [[intercalation (chemistry)|intercalate]] into the space between two adjacent base pairs. These are mostly polycyclic, [[aromatic]], and planar molecules, and include [[ethidium]], [[proflavin]], [[daunomycin]], [[doxorubicin]] and [[thalidomide]]. DNA intercalators are used in [[chemotherapy]] to inhibit DNA replication in rapidly-growing cancer cells.<ref name=brana>{{cite journal | author = Braña M ''et al.'' | title = Intercalators as anticancer drugs | journal = Curr Pharm Des | volume = 7 | pages = 1745-80 | year = 2001 | id = PMID 11562309}}</ref> For an intercalator to fit between base pairs, the bases must separate, distorting the DNA strand by unwinding of the double helix. These structural modifications inhibit transcription and replication processes, causing both toxicity and mutations. As a result, DNA intercalators are often [[carcinogen]]s. Nevertheless, because they can inhibit DNA transcription and replication, they are also used in [[chemotherapy]] to suppress rapidly-growing [[cancer]] cells.<ref name=brana/>


==Interactions with proteins==
==Interactions with proteins==
All the functions of DNA depend on interactions with proteins. These protein interactions can either be non-specific, or the protein can only bind to a particular DNA sequence. Enzymes can also bind to DNA and of these, the polymerases that copy the DNA base sequence in transcription and DNA replication are particularly important.
All of the functions of DNA depend on its interactions with proteins. some of these interactions are non-specific, others are specific in that the protein can only bind to a particular DNA sequence. Some enzymes can also bind to DNA and of these, the polymerases that copy the DNA base sequence in transcription and DNA replication are particularly important.


===DNA-binding proteins===
===DNA-binding proteins===
Line 104: Line 113:
<div style="border: none; width:260px;"><div class="thumbcaption">Interaction of DNA with [[histone]]s (shown in white, top). These proteins' basic amino acids (below left, blue) bind to the acidic phosphate groups on DNA (below right, red).</div></div></div>
<div style="border: none; width:260px;"><div class="thumbcaption">Interaction of DNA with [[histone]]s (shown in white, top). These proteins' basic amino acids (below left, blue) bind to the acidic phosphate groups on DNA (below right, red).</div></div></div>


Structural proteins that bind DNA are well-understood examples of non-specific DNA-protein interactions. Within chromosomes, DNA is held in complexes between DNA and structural proteins. These proteins organize the DNA into a compact structure called [[chromatin]]. In eukaryotes this structure involves DNA binding to a complex of small basic proteins called [[histone]]s, while in prokaryotes multiple types of proteins are involved.<ref>{{cite journal | author = Sandman K, Pereira S, Reeve J | title = Diversity of prokaryotic chromosomal proteins and the origin of the nucleosome | journal = Cell Mol Life Sci | volume = 54 | issue = 12 | pages = 1350-64 | year = 1998 | id = PMID 9893710}}</ref> The histones form a disk-shaped complex called a [[nucleosome]], which contains two complete turns of double-stranded DNA wrapped around its surface. These non-specific interactions are formed through basic residues in the histones making [[ionic bond]]s to the acidic sugar-phosphate backbone of the DNA, and are therefore largely independent of the base sequence.<ref>{{cite journal | author = Luger K, Mäder A, Richmond R, Sargent D, Richmond T | title = Crystal structure of the nucleosome core particle at 2.8 A resolution | journal = Nature | volume = 389 | issue = 6648 | pages = 251-60 | year = 1997 | id = PMID 9305837}}</ref> Chemical modifications of these basic amino acid residues include [[methylation]], [[phosphorylation]] and [[acetylation]].<ref>{{cite journal | author = Jenuwein T, Allis C | title = Translating the histone code | journal = Science | volume = 293 | issue = 5532 | pages = 1074-80 | year = 2001 | id = PMID 11498575}}</ref> These chemical changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to [[transcription factor]]s and changing the rate of [[transcription]].<ref>{{cite journal | author = Ito T | title = Nucleosome assembly and remodelling | journal = Curr Top Microbiol Immunol | volume = 274 | issue = | pages = 1-22 | year = | id = PMID 12596902}}</ref> Other non-specific DNA-binding proteins found in chromatin include the high-mobility group proteins, which bind preferentially to bent or distorted DNA.<ref>{{cite journal | author = Thomas J | title = HMG1 and 2: architectural DNA-binding proteins | journal = Biochem Soc Trans | volume = 29 | issue = Pt 4 | pages = 395-401 | year = 2001 | id = PMID 11497996}}</ref> These proteins are important in bending arrays of nucleosomes and arranging them into more complex chromatin structures.<ref>{{cite journal | author = Grosschedl R, Giese K, Pagel J | title = HMG domain proteins: architectural elements in the assembly of nucleoprotein structures | journal = Trends Genet | volume = 10 | issue = 3 | pages = 94-100 | year = 1994 | id = PMID 8178371}}</ref>
Within chromosomes, DNA is held in complexes between DNA and structural proteins. These proteins organize the DNA into a compact structure called [[chromatin]]. In eukaryotes, this structure involves DNA binding to small basic proteins called [[histone]]s, while in prokaryotes many types of proteins are involved.<ref>{{cite journal | author = Sandman K ''et al.'' | title = Diversity of prokaryotic chromosomal proteins and the origin of the nucleosome | journal = Cell Mol Life Sci | volume = 54 |pages = 1350-64 | year = 1998 | id = PMID 9893710}}</ref> The histones form a disk-shaped complex called a [[nucleosome]] which has two complete turns of double-stranded DNA wrapped around it. These interactions are formed through basic residues in the histones making [[ionic bond]]s to the acidic sugar-phosphate backbone of the DNA, and are largely independent of the base sequence.<ref>{{cite journal | author = Luger K ''et al.'' | title = Crystal structure of the nucleosome core particle at 2.8 A resolution | journal = Nature | volume = 389 | pages = 251-60 | year = 1997 | id = PMID 9305837}}</ref> Chemical modifications of these basic amino acid residues include [[methylation]], [[phosphorylation]] and [[acetylation]].<ref>{{cite journal | author = Jenuwein T, Allis C | title = Translating the histone code | journal = Science | volume = 293 | pages = 1074-80 | year = 2001 | id = PMID 11498575}}</ref> These changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to transcription factors and changing the rate of transcription.<ref>{{cite journal | author = Ito T | title = Nucleosome assembly and remodelling | journal = Curr Top Microbiol Immunol | volume = 274 | pages = 1-22 | year = | id = PMID 12596902}}</ref> Other non-specific DNA-binding proteins found in chromatin include the high-mobility group proteins, which bind preferentially to bent or distorted DNA.<ref>{{cite journal | author = Thomas J | title = HMG1 and 2: architectural DNA-binding proteins | journal = Biochem Soc Trans | volume = 29 | pages = 395-401 | year = 2001 | id = PMID 11497996}}</ref> These proteins are important in bending arrays of nucleosomes and arranging them into more complex chromatin structures.<ref>{{cite journal | author = Grosschedl R ''et al.''| title = HMG domain proteins: architectural elements in the assembly of nucleoprotein structures | journal = Trends Genet | volume = 10 | pages = 94-100 | year = 1994 | id = PMID 8178371}}</ref>


A distinct group of DNA-binding proteins are the single-stranded DNA-binding proteins. that specifically bind single-stranded DNA. In humans, replication protein A is the best-characterised member of this family and is essential for most processes where the double helix is separated, including DNA replication, recombination and DNA repair.<ref>{{cite journal | author = Iftode C, Daniely Y, Borowiec J | title = Replication protein A (RPA): the eukaryotic SSB | journal = Crit Rev Biochem Mol Biol | volume = 34 | issue = 3 | pages = 141-80 | year = 1999 | id = PMID 10473346}}</ref> These binding proteins seem to stabilize single-stranded DNA and protect it from forming [[stem loop]]s or being degraded by [[nuclease]]s.
Another group of DNA-binding proteins bind single-stranded DNA. In humans, replication protein A is the best-characterised member of this family, and is essential for most processes where the double helix is separated (including DNA replication, recombination and DNA repair).<ref>{{cite journal | author = Iftode C ''et al.''| title = Replication protein A (RPA): the eukaryotic SSB | journal = Crit Rev Biochem Mol Biol | volume = 34 | pages = 141-80 | year = 1999 | id = PMID 10473346}}</ref> These proteins seem to stabilize single-stranded DNA and protect it from forming [[stem loop]]s or being degraded by [[nuclease]]s.


In contrast, other proteins have evolved to specifically bind particular DNA sequences. The most intensively studied of these are the various classes of [[transcription factor]]s. These proteins control gene transcription. Each one of these proteins bind to one particular set of DNA sequences and thereby activates or inhibits the transcription of genes with these sequences close to their [[promoter]]s. The transcription factors do this in two ways. Firstly, they can bind the RNA polymerase responsible for transcription, either directly or through other mediator proteins, this locates the polymerase at the promoter and allows it to begin transcription.<ref>{{cite journal | author = Myers L, Kornberg R | title = Mediator of transcriptional regulation | journal = Annu Rev Biochem | volume = 69 | issue = | pages = 729-49 | year = | id = PMID 10966474}}</ref> Alternatively, transcription factors can bind enzymes that modify the histones at the promoter, this will change the accessibility of the DNA template to the polymerase.<ref>{{cite journal | author = Spiegelman B, Heinrich R | title = Biological control through regulated transcriptional coactivators | journal = Cell | volume = 119 | issue = 2 | pages = 157-67 | year = 2004 | id = PMID 15479634}}</ref>
Other proteins bind to particular DNA sequences. The most intensively studied of these are the [[transcription factors]]. Each of these proteins binds to a particular set of DNA sequences and thereby activates or inhibits the transcription of genes with these sequences close to their [[promoter]]s. Transcription factors do this in two ways. Some can bind the RNA polymerase responsible for transcription, either directly or through other mediator proteins; this locates the polymerase at the promoter and allows it to begin transcription.<ref>{{cite journal | author = Myers L, Kornberg R | title = Mediator of transcriptional regulation | journal = Ann Rev Biochem | volume = 69 | issue = | pages = 729-49 | year = | id = PMID 10966474}}</ref> Other transcription factors can bind enzymes that modify the histones at the promoter, this will change the accessibility of the DNA template to the polymerase.<ref>{{cite journal | author = Spiegelman B, Heinrich R | title = Biological control through regulated transcriptional coactivators | journal = Cell | volume = 119 | pages = 157-67 | year = 2004 | id = PMID 15479634}}</ref>


As these DNA targets can occur throughout an organism's genome, changes in the activity of one type of transcription factor can affect thousands of genes.<ref>{{cite journal | author = Li Z, Van Calcar S, Qu C, Cavenee W, Zhang M, Ren B | title = A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12808131 | journal = Proc Natl Acad Sci U S A | volume = 100 | issue = 14 | pages = 8164-9 | year = 2003 | id = PMID 12808131}}</ref> Consequently, these proteins are often the targets of the [[signal transduction]] processes that mediate responses to environmental changes or cellular differentiation and development. The specificity of these transcription factors' interactions with DNA come from the proteins making multiple contacts to the edges of the DNA bases, allowing them to "read" the DNA sequence. Most of these base interactions are made in the major groove, where the bases are most accessible.<ref>{{cite journal | author = Pabo C, Sauer R | title = Protein-DNA recognition | journal = Annu Rev Biochem | volume = 53 | issue = | pages = 293-321 | year = | id = PMID 6236744}}</ref>
These DNA targets can occur throughout an organism's genome, so changes in the activity of one type of transcription factor in a given cell can affect the expression of many genes in that cell.<ref>{{cite journal | author = Li Z ''et al.'' | title = A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12808131 | journal = Proc Natl Acad Sci USA | volume = 100 | pages = 8164-9 | year = 2003 | id = PMID 12808131}}</ref> Consequently, these proteins are often the targets of the [[signal transduction]] processes that mediate responses to environmental changes or cellular differentiation and development. The specificity of transcription factor interactions with DNA arises because the proteins make multiple contacts to the edges of the DNA bases, allowing them to "read" the DNA sequence. Most of these interactions occur in the major groove, where the bases are most accessible.<ref name=Pabo/>


===DNA-modifying enzymes===
===DNA-modifying enzymes===
====Nucleases and ligases====
====Nucleases and ligases====
Nucleases are [[enzyme]]s that cut DNA strands by catalyzing the [[hydrolysis]] of the [[phosphodiester bond]]s. Nucleases that hydrolyse nucleotides from the ends of DNA strands are called [[exonuclease]]s, while [[endonuclease]]s cut within strands. The most frequently-used nucleases in [[molecular biology]] are the [[restriction enzyme|restriction endonucleases]], which cut DNA at specific sequences. For instance, the EcoRV enzyme shown to the left recognizes the 6-base sequence 5'-GAT|ATC-3' and makes a cut at the vertical line. In nature, these enzymes protect [[bacteria]] against [[phage]] infection by digesting the phage DNA when it enters the bacterial cell, acting as part of the [[restriction modification system]].<ref>{{cite journal | author = Bickle T, Krüger D | title = Biology of DNA restriction | url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=372918&blobtype=pdf | journal = Microbiol Rev | volume = 57 | issue = 2 | pages = 434-50 | year = 1993 | id = PMID 8336674}}</ref> In technology, these sequence-specific nucleases are used in [[clone (genetics)|molecular cloning]] and [[DNA fingerprinting]].
Nucleases cut DNA strands by catalyzing the [[hydrolysis]] of the [[phosphodiester bond]]s (nucleases that hydrolyse nucleotides from the ends of DNA strands are called [[exonuclease]]s, while [[endonuclease]]s cut within strands). The most frequently-used nucleases in [[molecular biology]] are the [[restriction enzyme|restriction endonucleases]], which cut DNA at specific sequences. For instance, the EcoRV enzyme recognizes the 6-base sequence 5′-GAT|ATC-3′ and makes a cut at the vertical line. In nature, these enzymes protect [[bacteria]] against [[phage]] infection by digesting the phage DNA when it enters the bacterial cell, acting as part of the [[restriction modification system]].<ref>{{cite journal | author = Bickle T, Krüger D | title = Biology of DNA restriction | url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=372918&blobtype=pdf | journal = Microbiol Rev | volume = 57 | pages = 434–50 | year = 1993 | id = PMID 8336674}}</ref> In technology, these sequence-specific nucleases are used in [[clone (genetics)|molecular cloning]] and [[DNA fingerprinting]].


Enzymes called [[DNA ligase]]s can rejoin cut or broken DNA strands, using the energy from either [[adenosine triphosphate]] or [[nicotinamide adenine dinucleotide]].<ref name=Doherty>{{cite journal | author = Doherty A, Suh S | title = Structural and mechanistic conservation in DNA ligases. | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11058099 | journal = Nucleic Acids Res | volume = 28 | issue = 21 | pages = 4051-8 | year = 2000 | id = PMID 11058099}}</ref> Ligases are particularly important in [[lagging strand]] DNA replication, as they join together the short segments of DNA produced at the [[replication fork]] into a complete copy of the DNA template. They are also used in [[DNA repair]] and [[genetic recombination]].<ref name=Doherty/>
[[DNA ligase]]s can rejoin cut or broken DNA strands, using the energy from either [[adenosine triphosphate]] or [[nicotinamide adenine dinucleotide]]. Ligases are particularly important in [[lagging strand]] DNA replication, as they join together the short segments of DNA produced at the [[replication fork]] into a complete copy of the DNA template. They are also used in [[DNA repair]] and [[genetic recombination]].<ref name=Doherty>{{cite journal | author = Doherty A, Suh S | title = Structural and mechanistic conservation in DNA ligases. | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11058099 | journal = Nucleic Acids Res | volume = 28 | pages = 4051–8 | year = 2000 | id = PMID 11058099}}</ref>


====Topoisomerases and helicases====
====Topoisomerases and helicases====
[[Image:Topisomerasesv2.jpg|thumb|250px|Topoisomerase activities illustrated with  on covalently closed circular DNA. Topisomerase enzymes are able to form supercoils in DNA, and interconvert covalentely closed circular DNA and their catenated forms.]]
[[Image:Topisomerasesv2.jpg|thumb|250px|Topoisomerase activities illustrated with  on covalently closed circular DNA. Topisomerases can form supercoils in DNA, and can interconvert covalently closed circular DNA and their catenated forms.]]
[[Topoisomerase]]s have both nuclease and ligase activity, and they can change the amount of [[DNA supercoil|supercoiling]] in DNA. Some work by cutting the DNA helix and allowing one section to rotate; the enzyme then seals the DNA break.<ref>{{cite journal | author = Champoux J | title = DNA topoisomerases: structure, function, and mechanism | journal = Ann Rev Biochem | volume = 70 | issue = | pages = 369–413 | year = | url=http://www.fhcrc.org/science/labs/stoddard/MCB_542/champoux_review_2001.pdf | id = PMID 11395412}}</ref> Others can cut one DNA helix and then pass a second strand of DNA through this break, before rejoining the helix.<ref>{{cite journal | author = Schoeffler A, Berger J | title = Recent advances in understanding structure-function relationships in the type II topoisomerase mechanism | journal = Biochem Soc Trans | volume = 33 | pages = 1465–70 | year = 2005 | id = PMID 16246147}}</ref> Topoisomerases are required for many processes involving DNA, such as DNA replication and transcription.<ref name=Wang/>


[[Topoisomerase]]s are enzymes with both nuclease and ligase activity. These proteins change the amount of [[DNA supercoil|supercoiling]] in DNA. Some of these enzyme work by cutting the DNA helix and allowing one section to rotate, thereby reducing its level of supercoiling, the enzyme then seals the DNA break.<ref name=Champoux/> Other types of these enzymes are capable of cutting one DNA helix and then passing a second strand of DNA through this break, before rejoining the helix.<ref>{{cite journal | author = Schoeffler A, Berger J | title = Recent advances in understanding structure-function relationships in the type II topoisomerase mechanism | journal = Biochem Soc Trans | volume = 33 | issue = Pt 6 | pages = 1465-70 | year = 2005 | id = PMID 16246147}}</ref> Topoisomerases are required for many processes involving DNA, such as DNA replication and transcription.<ref name=Wang/>
[[Helicase]]s are a type of '[[molecular motor]]'; they use the chemical energy in [[nucleoside triphosphate]]s (predominantly [[Adenosine triphosphate|ATP]]) to break hydrogen bonds between bases and unwind the DNA double helix into single strands.<ref>{{cite journal | author = Tuteja N, Tuteja R | title = Unraveling DNA helicases. Motif, structure, mechanism and function | url=http://www.blackwell-synergy.com/links/doi/10.1111%2Fj.1432-1033.2004.04094.x | journal = Eur J Biochem | volume = 271 | pages = 1849–63 | year = 2004 | id = PMID 15128295}}</ref> These enzymes are essential for most processes where enzymes need to access the DNA bases.
 
Helicases are proteins that are a type of [[molecular motor]]. They use the chemical energy in [[adenosine triphosphate]] to break the hydrogen bonds between bases and unwind a DNA double helix into single strands.<ref>{{cite journal | author = Tuteja N, Tuteja R | title = Unraveling DNA helicases. Motif, structure, mechanism and function | url=http://www.blackwell-synergy.com/links/doi/10.1111%2Fj.1432-1033.2004.04094.x | journal = Eur J Biochem | volume = 271 | issue = 10 | pages = 1849-63 | year = 2004 | id = PMID 15128295}}</ref> These enzymes are essential for most processes where enzymes need to access the DNA bases.


====Polymerases====
====Polymerases====
Polymerases are enzymes that synthesise polynucleotide chains from [[nucleoside triphosphate]]s. They function by adding nucleotides onto the [[hydroxyl|hydroxyl group]] of the previous nucleotide in the DNA strand. As a consequence, all polymerases work in a 5' to 3' direction.<ref name=Joyce/> In the [[active site]] of these enzymes, the nucleoside triphosphate substrate base-pairs to a single-stranded polynucleotide template: this allows polymerases to accurately synthesise the complementary strand of this template. Polymerases are classified depending of the type of template they use.
Polymerases synthesise polynucleotides from [[nucleoside triphosphate]]s. They add nucleotides onto the 3′ [[hydroxyl|hydroxyl group]] of the previous nucleotide in the DNA strand, so all polymerases work in a 5′ to 3′ direction.<ref name=Joyce /> In the [[active site]] of these enzymes, the nucleoside triphosphate substrate base-pairs to a single-stranded polynucleotide template: this allows polymerases to synthesise the complementary strand of this template accurately.  


In [[DNA replication]] a DNA-dependent [[DNA polymerase]] make a DNA copy of a DNA sequence. Accuracy is vital in this process, so many of these polymerases have a [[proofreading]] activity. Here, the polymerase recognizes the occasional mistakes in the synthesis reaction by the lack of base pairing between the mismatched nucleotides. If a mismatch is detected, a 3' to 5' [[exonuclease]] activity is activated and the incorrect base removed.<ref>{{cite journal | author = Hubscher U, Maga G, Spadari S | title = Eukaryotic DNA polymerases | journal = Annu Rev Biochem | volume = 71 | issue = | pages = 133-63 | year = | id = PMID 12045093}}</ref> In most organisms DNA polymerases function in a large complex called the [[replisome]] that contains multiple accessory subunits, such as the [[DNA clamp]] or [[helicase]]s.<ref>{{cite journal | author = Johnson A, O'Donnell M | title = Cellular DNA replicases: components and dynamics at the replication fork | journal = Annu Rev Biochem | volume = 74 | issue = | pages = 283-315 | year = | id = PMID 15952889}}</ref>
[[DNA polymerase]]s copy DNA sequences. Accuracy is very important for this, so many polymerases have a [[Proofreading#Proofreading in biology|proofreading]] activity: they can recognizes the occasional mistakes that can occur during synthesis. These enzymes detect the lack of base pairing between mismatched nucleotides, and if a mismatch is detected, a 3′ to 5′ [[exonuclease]] activity is activated and the incorrect base is removed.<ref>{{cite journal | author = Hubscher U ''et al.'' | title = Eukaryotic DNA polymerases | journal = Annu Rev Biochem | volume = 71 |pages = 133–63 | year = | id = PMID 12045093}}</ref> In most organisms, DNA polymerases function in a large complex called the [[replisome]].


RNA-dependent DNA polymerases are a specialised class of polymerases that copy the sequence of a RNA strand into DNA. They include [[reverse transcriptase]], which is a [[virus|viral]] enzyme involved in the infection of cells by [[retrovirus]]es, and [[telomerase]], which is required for the replication of [[telomere]]s.<ref>{{cite journal | author = Tarrago-Litvak L, Andréola M, Nevinsky G, Sarih-Cottin L, Litvak S | title = The reverse transcriptase of HIV-1: from enzymology to therapeutic intervention | url=http://www.fasebj.org/cgi/reprint/8/8/497 | journal = FASEB J | volume = 8 | issue = 8 | pages = 497-503 | year = 1994 | id = PMID 7514143}}</ref><ref name=Greider/> Telomerase is an unusual polymerase because it contains its own RNA template as part of its structure.<ref name=Nugent/>
RNA-dependent DNA polymerases copy the sequence of an RNA strand into DNA. One example is [[reverse transcriptase]], which is a viral enzyme involved in the infection of cells by [[retrovirus]]es; another example is [[telomerase]], which is required for the replication of [[telomere]]s.<ref>{{cite journal | author = Tarrago-Litvak L ''et al.'' | title = The reverse transcriptase of HIV-1: from enzymology to therapeutic intervention | url=http://www.fasebj.org/cgi/reprint/8/8/497 | journal = FASEB J | volume = 8 | pages = 497–503 | year = 1994 | id = PMID 7514143}}</ref><ref name=Greider/> Telomerase is an unusual polymerase because it contains its own RNA template as part of its structure.<ref>{{cite journal |author=Nugent C, Lundblad V |title=The telomerase reverse transcriptase: components and regulation | url=http://www.genesdev.org/cgi/content/full/12/8/1073 | journal=Genes Dev |volume=12 |issue=8 | pages=1073&ndash;85 |year=1998 |pmid=9553037}}</ref>


Transcription is carried out by a DNA-dependent [[RNA polymerase]] that copies the sequence of a DNA strand into RNA. To begin transcribing a gene, the RNA polymerase binds to a sequence of DNA called a [[promoter]] and separates the DNA strands. It then copies the gene sequence into a [[messenger RNA]] transcript until it reaches a region of DNA called the [[terminator (genetics)|terminator]], where it halts and detaches from the DNA. As with human DNA-dependent DNA polymerases, RNA polymerase II, the enzyme that transcribes most of the genes in the [[human genome]], operates as part of a large protein complex with multiple regulatory and accessory subunits.<ref>{{cite journal | author = Martinez E | title = Multi-protein complexes in eukaryotic gene transcription | journal = Plant Mol Biol | volume = 50 | issue = 6 | pages = 925-47 | year = 2002 | id = PMID 12516863}}</ref>
Transcription is carried out by a [[RNA polymerase]] that copies a DNA sequence into RNA. The enzyme binds to a promoter and separates the DNA strands. It then copies the gene sequence into a mRNA transcript until it reaches a region of DNA called the ''[[terminator (genetics)|terminator]]'', where it halts and detaches from the DNA. RNA polymerase II, which transcribes most of the genes in the human genome, operates as part of a large protein complex with multiple regulatory and accessory subunits.<ref>{{cite journal | author = Martinez E | title = Multi-protein complexes in eukaryotic gene transcription | journal = Plant Mol Biol | volume = 50 | pages = 925–47 | year = 2002 | id = PMID 12516863}}</ref>


==Genetic recombination==
==Genetic recombination==
A DNA helix does not usually interact with other segments of DNA, and in human cells the different chromosomes even occupy different regions of the nucleus (called "chromosome territories").<ref>{{cite journal | author = Cremer T, Cremer C | title = Chromosome territories, nuclear architecture and gene regulation in mammalian cells | journal = Nat Rev Genet | volume = 2 |  pages = 292-301 | year = 2001 | id = PMID 11283701}}</ref> This physical separation of chromosomes is important for the ability of DNA to function as a stable repository for information, as one of the few times chromosomes interact is when they [[genetic recombination|recombine]]. Recombination is when two DNA helices break, swap a section and then rejoin. In eukaryotes, this usually occurs during [[meiosis]], when two [[chromatid]]s are paired together in the center of the cell. This allows chromosomes to exchange genetic information and produces new combinations of genes.<ref>{{cite journal | author = Pál C ''et al.'' | title = An integrated view of protein evolution | journal = Nat Rev Genet | volume = 7 |  pages = 337-48 | year = 2006 | id = PMID 16619049}}</ref> Genetic recombination can also be involved in DNA repair.<ref>{{cite journal | author = O'Driscoll M, Jeggo P | title = The role of double-strand break repair - insights from human genetics | journal = Nat Rev Genet | volume = 7 | pages = 45-54 | year = 2006 | id = PMID 16369571}}</ref> The most common form of recombination is [[chromosomal crossover|homologous recombination]], where the two chromosomes involved share very similar sequences. However, recombination can also damage cells, by producing [[chromosomal translocation]]s and genetic abnormalities. Recombination reactions are catalyzed by ''recombinases'',<ref>{{cite journal | author = Sung P ''et al.'' | title = Rad51 recombinase and recombination mediators | journal = J Biol Chem | volume = 278 | pages = 42729-32 | year = 2003 | url = http://www.jbc.org/cgi/content/full/278/44/42729 | id = PMID 12912992}}</ref> which have a DNA-dependent ATPase activity. The recombinase makes a 'nick' in one strand of a DNA double helix, allowing the nicked strand to separate from its complementary strand and [[Annealing (biology)|anneal]] to one strand of the double helix on the opposite chromatid. A second nick allows the strand in the second chromatid to separate and anneal to the strand in the first helix, forming a ''cross-strand exchange'' (also called a [[Holliday junction]]). The Holliday junction is a tetrahedral junction structure which can be moved along the pair of chromosomes, swapping one strand for another. The recombination is then halted by cleavage of the junction and re-ligation of the released DNA.<ref>{{cite journal | author = Dickman M ''et al.'' | title = The RuvABC resolvasome | journal = Eur J Biochem | volume = 269 | pages = 5492-501 | year = 2002 | id = PMID 12423347}}</ref>


{{further|[[Genetic recombination, Phylogenetics]]}}
==DNA and molecular evolution==
 
As well as being susceptible to largely random mutations (that usually affect just a single base), some regions of DNA are specialised to undergo dramatic, rapid, non-random rearrangements, or to undergo more subtle changes at a high frequency so that the expression of a gene is dramatically altered. Such rearrangements include various versions of [[site-specific recombination]]. This depends on enzymes that recognise particular sites on DNA and create novel structures such as insertions, deletions and inversions. For instance, DNA regions in the small genome of the bacterial virus P1 can invert, enabling different versions of tail fibers to be expressed in different viruses. Similarly, site-specific recombinase enzymes are responsible for mating type variation in yeast, and for flagellum type (phase) changes in the bacterium ''Salmonella enterica'' Typhimurium.
A DNA helix does not usually interact with other segments of DNA and in human cells the different chromosomes even occupy separate areas in the nucleus called "chromosome territories".<ref>{{cite journal | author = Cremer T, Cremer C | title = Chromosome territories, nuclear architecture and gene regulation in mammalian cells | journal = Nat Rev Genet | volume = 2 | issue = 4 | pages = 292-301 | year = 2001 | id = PMID 11283701}}</ref> This physical separation of different chromosomes is important for the ability of DNA to function as a stable repository for information, as one of the few times chromosomes interact is when they [[genetic recombination|recombine]]. Recombination is when two DNA helices break, swap a section and then rejoin. In eukaryotes this process usually occurs during [[meiosis]], when the two sister [[chromatid]]s are paired together in the center of the cell. Recombination allows chromosomes to exchange genetic information and produces new combinations of genes, which increases the efficiency of [[selection]] and can be important in the rapid evolution of new proteins.<ref>{{cite journal | author = Pál C, Papp B, Lercher M | title = An integrated view of protein evolution | journal = Nat Rev Genet | volume = 7 | issue = 5 | pages = 337-48 | year = 2006 | id = PMID 16619049}}</ref> Genetic recombination can also be involved in DNA repair, particularly in the cell's response to double-strand breaks.<ref>{{cite journal | author = O'Driscoll M, Jeggo P | title = The role of double-strand break repair - insights from human genetics | journal = Nat Rev Genet | volume = 7 | issue = 1 | pages = 45-54 | year = 2006 | id = PMID 16369571}}</ref>


The most common form of recombination is [[chromosomal crossover|homologous recombination]], where the two chromosomes involved share very similar sequences. Non-homologous recombination can be damaging to cells, as it can produce [[chromosomal translocation]]s and genetic abnormalities. The recombination reaction is catalyzed by enzymes known as ''recombinases'', such as [[Cre recombinase]].<ref>{{cite journal | author = Ghosh K, Van Duyne G | title = Cre-loxP biochemistry | journal = Methods | volume = 28 | issue = 3 | pages = 374-83 | year = 2002 | id = PMID 12431441}}</ref> In the first step, the recombinase creates a nick in one strand of a DNA double helix, allowing the nicked strand to pull apart from its [[complementarity (molecular biology)|complementary]] strand and [[Annealing (biology)|anneal]] to one strand of the double helix on the opposite chromatid. A second nick allows the strand in the second chromatid to pull apart and anneal to the remaining strand in the first helix, forming a structure known as a ''cross-strand exchange'' or a [[Holliday junction]]. The Holliday junction is a tetrahedral junction structure which can be moved along the pair of chromosomes, swapping one strand for another. The recombination reaction is then halted by cleavage of the junction and re-ligation of the released DNA.<ref>{{cite journal | author = Dickman M, Ingleston S, Sedelnikova S, Rafferty J, Lloyd R, Grasby J, Hornby D | title = The RuvABC resolvasome | journal = Eur J Biochem | volume = 269 | issue = 22 | pages = 5492-501 | year = 2002 | id = PMID 12423347}}</ref>
More subtle mutations can occur in [[micro-satellite]] repeats (also called homopolymeric tracts of DNA). An example of such a structure are short DNA intervals where the same base is tandemly repeated, as in 5'-gcAAAAAAAAAAAttg-3', or a dinucleotide or even a triplet as in 5'- ATGATGATGATGATGATGATG-3'. [[DNA polymerase III]] is prone to make 'stuttering errors' at such repeats. As a consequence, changes in repeat number occur quite often during cell replication, and when they appear at a position where the spacing of nucleotide residues is critical for gene function, they can cause changes to the phenotype.  


==DNA and molecular evolution==
The stomach ulcer bacterium ''Helicobacter pylori'' is a good example of how homopolymeric tracts can enable quasi-directed evolution of particular genes. ''H. pylori'' has 46 genes that contain homopolymeric runs of nucleotides or dinucleotide repeats that are prone to frequent length changes as a consequence of stuttering errors during replication. These changes can lead to frequent reversible inactivation of these genes, or to changed gene transcription if the repeat is located in a regulatory sequence. This generates highly diverse populations of ''H. pylori'' in an individual human host, and this diversity helps the bacterium evade the immune system.<ref>Suerbaum S, Josenhans C (2007) ''Helicobacter pylori'' evolution and phenotypic diversification in a changing host. Nat Rev Microbiol 5:441-52 PMID 17505524</ref>


{{further|[[Molecular evolution, Phylogenetics]]}}
Triplet repeats behave similarly, but are particularly suited to evolution of proteins with differing characteristics. In the clock-like ''period'' gene of the fruit fly, triplet repeats 'fine tune' an insect's biological clock in response to changes in environmental temperatures. Triplet repeats are widely distributed in genomes, and their high frequency of mutation is responsible for several genetically determined disorders in humans.<ref>Christopher Wills discusses the evolutionary significance of these concepts in ''The Runaway Brain: The Evolution of Human Uniqueness'' ISBN 0-00-654672-2 (1995)</ref>


==Uses in technology==
==Uses in technology==
===Forensics ===
===Forensics ===
{{further|[[Genetic fingerprinting]]}}
[[Forensic science|Forensic scientists]] can use DNA in blood, semen, skin, saliva or hair to match samples collected at a crime scene to samples taken from possible suspects. This process is called [[genetic fingerprinting]] or more formally, DNA profiling. In DNA profiling, the lengths of variable sections of repetitive DNA (such as [[short tandem repeats]] and [[minisatellite]]s) are compared between people. This is usually very reliable for identifying the source of a sample,<ref>{{cite journal | author = Collins A, Morton N | title = Likelihood ratios for DNA identification | url=http://www.pnas.org/cgi/reprint/91/13/6007.pdf | journal = Proc Natl Acad Sci USA | volume = 91 | pages = 6007-11 | year = 1994 | id = PMID 8016106}}</ref> but identification can be complicated if the samples that are collected include DNA from several people.<ref>{{cite journal | author = Weir B ''et al.'' | title = Interpreting DNA mixtures | journal = J Forensic Sci | volume = 42 | pages = 213-22 | year = 1997 | id = PMID 9068179}}</ref> DNA profiling was developed in 1984 by British geneticist Sir [[Alec Jeffreys]],<ref>{{cite journal | author = Jeffreys A ''et al.'' | title = Individual-specific 'fingerprints' of human DNA. | journal = Nature | volume = 316 | pages = 76-9 | year = 1985| id = PMID 2989708}}</ref> and first used in forensic science to convict Colin Pitchfork (and to clear the prime suspect) in the 1988 [[Enderby murders]] case.<ref>[http://www.forensic.gov.uk/forensic_t/inside/news/list_casefiles.php?case=1 Colin Pitchfork - first murder conviction on DNA evidence also clears the prime suspect] Forensic Science Service Accessed 23 Dec 2006</ref> People convicted of certain types of crimes may be required to provide a sample of DNA for a database. This has helped investigators solve old cases where only a DNA sample was obtained from the scene. DNA profiling can also be used to identify victims of mass casualty incidents.<ref>{{cite web |url=http://massfatality.dna.gov/Introduction/ |title=DNA Identification in Mass Fatality Incidents |date=September 2006 |publisher=National Institute of Justice}}</ref>
 
[[Forensic science|Forensic scientists]] can use DNA in [[blood]], [[semen]], [[skin]], [[saliva]] or [[hair]] at a crime scene to identify a perpetrator. This process is called [[genetic fingerprinting]] or more accurately, DNA profiling. In DNA profiling, the lengths of variable sections of repetitive DNA, such as [[short tandem repeats]] and [[minisatellite]]s, are compared between people. This method is usually an extremely reliable technique for identifying a criminal.<ref>{{cite journal | author = Collins A, Morton N | title = Likelihood ratios for DNA identification | url=http://www.pnas.org/cgi/reprint/91/13/6007.pdf | journal = Proc Natl Acad Sci U S A | volume = 91 | issue = 13 | pages = 6007-11 | year = 1994 | id = PMID 8016106}}</ref> However, identification can be complicated if the scene is contaminated with DNA from several people.<ref>{{cite journal | author = Weir B, Triggs C, Starling L, Stowell L, Walsh K, Buckleton J | title = Interpreting DNA mixtures | journal = J Forensic Sci | volume = 42 | issue = 2 | pages = 213-22 | year = 1997 | id = PMID 9068179}}</ref> DNA profiling was developed in 1984 by British geneticist Sir [[Alec Jeffreys]],<ref>{{cite journal | author = Jeffreys A, Wilson V, Thein S | title = Individual-specific 'fingerprints' of human DNA. | journal = Nature | volume = 316 | issue = 6023 | pages = 76-9 | year = | id = PMID 2989708}}</ref> and first used in forensic science to convict Colin Pitchfork in the 1988 [[Enderby murders]] case.<ref>[http://www.forensic.gov.uk/forensic_t/inside/news/list_casefiles.php?case=1 Colin Pitchfork - first murder conviction on DNA evidence also clears the prime suspect] Forensic Science Service Accessed 23 Dec 2006</ref> People convicted of certain types of crimes may be required to provide a sample of DNA for a database. This has helped investigators solve old cases where only a DNA sample was obtained from the scene. DNA profiling can also be used to identify victims of mass casualty incidents.<ref>{{cite web |url=http://massfatality.dna.gov/Introduction/ |title=DNA Identification in Mass Fatality Incidents |date=September 2006 |publisher=National Institute of Justice}}</ref>


===Bioinformatics===
===Bioinformatics===
{{further|[[Bioinformatics]]}}
[[Bioinformatics]] involves the analysis of DNA sequence data; DNA from hundreds of different organisms has now been partially sequenced, and this information is stored in massive databases. The development of techniques to store and search DNA sequences has led to many applications in [[computer science]].<ref>Baldi, Pierre. Brunak, Soren. ''Bioinformatics: The Machine Learning Approach'' MIT Press (2001) ISBN 978-0-262-02506-5</ref> String-searching or 'matching' algorithms, which identify a given sequence of letters inside a larger sequence of letters, are used to search for specific sequences of nucleotides. The related problem of [[sequence alignment]] aims to identify [[homology (biology)|homologous]] sequences; these are sequences that are very similar but not identical. When two different genes in an organism have very similar sequences, this is evidence that, at some stage in evolution, a single gene was duplicated, and the sequences subsequently diverged (under different selection pressures) by incorporating different mutations. Identifying such holologies can give valuable clues about the likely function of novel genes. Similarly, identifying homologies between genes in different organisms can be used to reconstruct the [[phylogenetics|evolutionary]] relationships between organisms.<ref>{{cite journal | author = Sjölander K | title = Phylogenomic inference of protein molecular function: advances and challenges | url=http://bioinformatics.oxfordjournals.org/cgi/reprint/20/2/170 | journal = Bioinformatics | volume = 20 | pages = 170-9 | year = 2004 | id = PMID 14734307}}</ref> Data sets representing entire genomes' worth of DNA sequences, such as those produced by the [[Human Genome Project]], are difficult to use without [[annotations]], which label the locations of genes and regulatory elements on each chromosome. Regions of DNA sequence that have patterns that are characteristic of protein- or RNA-coding genes can be identified by [[gene finding]] algorithms, allowing researchers to predict the presence of particular [[gene product]]s in an organism.<ref name="Mount">{{cite book|author = Mount DM | title = Bioinformatics: Sequence and Genome Analysis | edition = 2 | publisher = Cold Spring Harbor Laboratory Press | location | Cold Spring Harbor, NY | date = 2004 | isbn = 0879697121}}</ref>
[[Bioinformatics]] involves the manipulation, searching, and [[data mining]] DNA sequence data. The development of techniques to store and search DNA sequences have led to widely-applied advances in [[computer science]], especially [[string searching algorithm]]s, [[machine learning]] and [[database theory]].<ref>Baldi, Pierre. Brunak, Soren. ''Bioinformatics: The Machine Learning Approach'' MIT Press (2001) ISBN 978-0-262-02506-5</ref> String searching or matching algorithms, which find an occurrence of a sequence of letters inside a larger sequence of letters, was developed to search for specific sequences of nucleotides.<ref>Gusfield, Dan. ''Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology''. Cambridge University Press, 15 January [[1997]]. ISBN 978-0-521-58519-4.</ref> In other applications such as [[text editor]]s, even simple algorithms for this problem usually suffice, but DNA sequences cause these algorithms to exhibit near-worst-case behaviour due to their small number of distinct characters. The related problem of [[sequence alignment]] aims to identify [[homology (biology)|homologous]] sequences and locate the specific [[mutation]]s that make them distinct. These techniques, especially [[multiple sequence alignment]], are used in studying [[phylogenetics|phylogenetic]] relationships and [[protein]] function.<ref>{{cite journal | author = Sjölander K | title = Phylogenomic inference of protein molecular function: advances and challenges | url=http://bioinformatics.oxfordjournals.org/cgi/reprint/20/2/170 | journal = Bioinformatics | volume = 20 | issue = 2 | pages = 170-9 | year = 2004 | id = PMID 14734307}}</ref> Data sets representing entire genomes' worth of DNA sequences, such as those produced by the [[Human Genome Project]], are difficult to use without annotations, which label the locations of genes and regulatory elements on each chromosome. Regions of DNA sequence that have the characteristic patterns associated with protein- or RNA-coding genes can be identified by [[gene finding]] algorithms, which allow researchers to predict the presence of particular [[gene product]]s in an organism even before they have been isolated experimentally.<ref name="Mount">{{cite book|author = Mount DM | title = Bioinformatics: Sequence and Genome Analysis | edition = 2 | publisher = Cold Spring Harbor Laboratory Press | location | Cold Spring Harbor, NY | date = 2004 | isbn = 0879697121}}</ref>
 
===DNA and computation ===
{{further|[[DNA computing]]}}
DNA was first used in computing to solve a small version of the directed [[Hamiltonian path problem]], an [[NP-complete]] problem.<ref>{{cite journal | author = Adleman L | title = Molecular computation of solutions to combinatorial problems | journal = Science | volume = 266 | issue = 5187 | pages = 1021-4 | year = 1994 | id = PMID 7973651}}</ref> [[DNA computing]] is advantageous over electronic computers in power use, space use, and efficiency, due to its ability to compute in a highly parallel fashion (see [[parallel computing]]). A number of other problems, including simulation of various [[abstract machine]]s, the [[boolean satisfiability problem]], and the bounded version of the [[travelling salesman problem]], have since been analysed using DNA computing.<ref>{{cite journal | author = Parker J | title = Computing with DNA. | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12524509 | journal = EMBO Rep | volume = 4 | issue = 1 | pages = 7-10 | year = 2003 | id = PMID 12524509}}</ref> Due to its compactness, DNA also has a theoretical role in [[cryptography]], where in particular it allows unbreakable [[one-time pad]]s to be efficiently constructed and used.<ref>Ashish Gehani, Thomas LaBean and John Reif. [http://citeseer.ist.psu.edu/gehani99dnabased.html DNA-Based Cryptography].
Proceedings of the 5th DIMACS Workshop on DNA Based Computers, Cambridge, MA, USA, 14 – 15 June 1999.</ref>


===History and anthropology===
===Molecular cloning===
{{further|[[Phylogenetics]]}}
Because DNA collects mutations over time, which are then inherited, it contains historical information and by comparing DNA sequences, geneticists can infer the evolutionary history of organisms, their [[phylogeny]].<ref>{{cite journal | author = Wray G | title = Dating branches on the tree of life using DNA | url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11806830 | journal = Genome Biol | volume = 3 | issue = 1 | pages = REVIEWS0001 | year = 2002 | id = PMID 11806830}}</ref> This field of [[phylogenetics]] is a powerful tool in [[evolutionary biology]]. If DNA sequences within a species are compared, [[population genetics|population geneticists]] can learn the history of particular populations. This can be used in studies ranging from [[ecological genetics]] to [[anthropology]], for example, DNA evidence is being used to try to identify the [[Ten Lost Tribes of Israel]].<ref>''Lost Tribes of Israel'', [[NOVA (TV series)|NOVA]], PBS airdate: 22 February 2000. Transcript available from [http://www.pbs.org/wgbh/nova/transcripts/2706israel.html PBS.org,] (last accessed on 4 March 2006)</ref><ref>Kleiman, Yaakov. [http://www.aish.com/societywork/sciencenature/the_cohanim_-_dna_connection.asp "The Cohanim/DNA Connection: The fascinating story of how DNA studies confirm an ancient biblical tradition".] ''aish.com'' (January 13, 2000). Accessed 4 March 2006.</ref>


DNA has also been used to look at modern family relationships, such as establishing family relationships between the descendants of [[Sally Hemings]] and [[Thomas Jefferson]]. This usage is closely related to the use of DNA in criminal investigations detailed above. Indeed, some criminal investigations have been solved when DNA from crime scenes has matched relatives of the guilty individual.<ref>Bhattacharya, Shaoni. [http://www.newscientist.com/article.ns?id=dn4908 "Killer convicted thanks to relative's DNA".] ''newscientist.com'' (20 April 2004). Accessed 22 Dec 06</ref>
The small chromosomes of bacteria have proved extraordinarily useful for analysing genetic mechanisms and genome structure in many organisms, including humans. This utility arose because of several important discoveries made by microbiologists in the 1950-70's that provided new laboratory tools for directly manipulating genes. The principal laboratory tools and techniques discovered in this period were:


==History==
* Compact circular plasmid molecules such as [[ColE1]] that were relatively easy to extract and purify from bacterial cells, and when inserted back inside living bacterial cells could serve as genetically stable carriers (''vectors'') of novel DNA fragments. These vectors were propagated in bacterial cell lines termed "clones". Since each plasmid vector in these clones carried a single DNA molecular fragment, these could be considered to be 'molecular clones'.
[[Image:Francis Crick.png|thumb|right|[[Francis Crick]]]]
* Convenient methods for extracting plasmid DNA from cells, physical analysis of this DNA, and reinsertion of circular plasmid DNA back inside living cells. The main method for DNA re-insertion is termed [[DNA transformation]] - that is, direct uptake of naked DNA molecules by cells. One technique that assisted DNA transformation was the use of selectable genetic markers, and plasmid-borne bacterial [[antibiotic resistance]] provided such markers in the form of traits like [[ampicillin resistance]] and [[tetracycline resistance]].
[[Image:JamesWatson.jpg|thumb|[[James D. Watson|James Watson]] in the [[Cavendish Laboratory]] at the [[University of Cambridge]].]]
* [[Restriction endonuclease]]s such as the enzymes [[EcoRI]] or [[HindIII]], were found to be useful for specifically digesting DNA at particular sites and creating novel combinations of DNA fragments in the laboratory.
{{further|[[History of molecular biology]]}}
* Restriction enzymes enabled re-annealing different DNA fragments, such as circular plasmid DNA which had been linearised at a single EcoRI restriction endonuclease target site together with another fragment, say an EcoRI generated fragment of a human chromosome. By sealing together two such fragments with the enzyme DNA ligase, novel hybrid-plasmid molecules could be created in which "foreign" DNA inserts were carried in a ''chimeric'' or hybrid plasmid, often called a recombinant DNA molecule.
DNA was first isolated by [[Friedrich Miescher]] who discovered a substance he called "nuclein" in 1869.<ref>{{cite journal | author = Dahm R | title = Friedrich Miescher and the discovery of DNA | journal = Dev Biol | volume = 278 | issue = 2 | pages = 274-88 | year = 2005 | id = PMID 15680349}}</ref> In 1929 this discovery was followed by [[Phoebus Levene]]'s identification of the base, sugar and phosphate nucleotide unit.<ref>{{cite journal | author = Levene P, | title = The structure of yeast nucleic acid | url=http://www.jbc.org/cgi/reprint/40/2/415 | journal = J Biol Chem | volume = 40 | issue = 2 | pages = 415-24 | year = 1919}}</ref> Levene suggested that DNA consisted of a string of nucleotide units linked together through the phosphate groups. However Levene thought the chain was short and the bases repeated in a fixed order. In 1937 [[William Astbury]] produced the first [[X-ray diffraction]] patterns that showed that DNA had a regular structure.<ref>{{cite journal | author =Astbury W, | title = Nucleic acid | journal = Symp. SOC. Exp. Bbl | volume = 1 | issue = 66 | year = 1947}}</ref>


In 1943, [[Oswald Theodore Avery]] discovered that traits of the "smooth" form of the ''Pneumococcus'' could be transferred to the "rough" form of the same bacteria by mixing killed "smooth" bacteria with the live "rough" form. Avery identified DNA as this [[transforming principle]].<ref>{{cite journal | author = Avery O, MacLeod C, McCarty M | title = Studies on the chemical nature of the substance inducing transformation of pneumococcal types. Inductions of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III | url=http://www.jem.org/cgi/reprint/149/2/297 | journal = J Exp Med | volume = 149 | issue = 2 | pages = 297-326 | year = 1979 | id = PMID 33226}}</ref> DNA's role in heredity was confirmed in 1953, when [[Alfred Hershey]] and [[Martha Chase]] in the [[Hershey-Chase experiment]], showed that DNA is is the [[genetic material]] of the [[T2 phage]].<ref>{{cite journal | author = Hershey A, Chase M | title = Independent functions of viral protein and nucleic acid in growth of bacteriophage | url=http://www.jgp.org/cgi/reprint/36/1/39.pdf | journal = J Gen Physiol | volume = 36 | issue = 1 | pages = 39-56 | year = 1952 | id = PMID 12981234}}</ref>
After the mid-1970's, re-insertion of recombinant DNA plasmids into living bacterial cells, such as those of ''Escherichia coli'' opened up many new approaches in [[biotechnology]]. These made it possible to manufacture, for example, human hormones such as [[insulin]] in microbial cell-based protein factories. When combined with other genetic techniques, the field of "recombinant DNA technology" opened up the possibility of decoding the gene sequence of whole genomes. This latter area is now usually referred to as [[genomics]], and includes the [[Human Genome Project]].
 
Using [[X-ray diffraction]] data from [[Rosalind Franklin]] and the information that the bases were paired, [[James D. Watson]] and [[Francis Crick]] produced the first accurate model of DNA structure in 1953 in their article [[Molecular structure of Nucleic Acids]].<ref name=Watson/> Watson and Crick proposed the [[The central dogma]] of molecular biology in 1957, describing how proteins are produced from [[cell nucleus|nucleic]] DNA. In 1962 Watson, Crick, and [[Maurice Wilkins]] jointly received the [[Nobel Prize]].<ref>[http://nobelprize.org/nobel_prizes/medicine/laureates/1962/ The Nobel Prize in Physiology or Medicine 1962] Nobelprize.org Accessed 22 Dec 06</ref>
 
In an influential presentation in 1957, Crick laid out [[The Central Dogma]], which foretold the relationship between DNA, RNA, and proteins, and articulated the "adaptor hypothesis".<ref>Crick, F.H.C. [http://genome.wellcome.ac.uk/assets/wtx030893.pdf On degenerate templates and the adaptor hypothesis (PDF).] genome.wellcome.ac.uk (Lecture, 1955). Accessed 22 Dec 2006</ref> Final confirmation of the replication mechanism that was implied by the double-helical structure followed in 1958 through the [[Meselson-Stahl experiment]].<ref>{{cite journal | author = Meselson M, Stahl F | title = The replication of DNA in Escherichia coli | journal = Proc Natl Acad Sci U S A | volume = 44 | issue = 7 | pages = 671-82 | year = 1958 | id = PMID 16590258}}</ref> Further work by Crick and coworkers showed that the genetic code was based on non-overlapping triplets of bases, called codons, allowing [[Har Gobind Khorana]], [[Robert W. Holley]] and [[Marshall Warren Nirenberg]] to decipher the [[genetic code]].<ref>[http://nobelprize.org/nobel_prizes/medicine/laureates/1968/ The Nobel Prize in Physiology or Medicine 1968] Nobelprize.org Accessed 22 Dec 06</ref> These findings represent the birth of [[molecular biology]].


==References==
==References==
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<references/>
</div>
</div>
==Further reading==
* Clayton, Julie. (Ed.). ''50 Years of DNA'', Palgrave MacMillan Press, 2003. ISBN 978-1-40-391479-8
* Judson, Horace Freeland. ''The Eighth Day of Creation: Makers of the Revolution in Biology'', Cold Spring Harbor Laboratory Press, 1996. ISBN 978-0-87-969478-4
* [[Robert Olby|Olby, Robert]]. ''The Path to The Double Helix: Discovery of DNA'', first published in October 1974 by MacMillan, with foreword by Francis Crick; ISBN 978-0-48-668117-7; the definitive DNA textbook, revised in 1994, with a 9 page postscript.
* [[Matt Ridley|Ridley, Matt]]. ''Francis Crick: Discoverer of the Genetic Code (Eminent Lives)'' first published in June 2006 in the USA and then to be in the UK September 2006, by HarperCollins Publishers; 192 pp, ISBN 978-0-06-082333-7
* Rose, Steven. ''The Chemistry of Life'', Penguin, ISBN 978-0-14-027273-4.
* Watson, James D. and Francis H.C. Crick. [http://www.nature.com/nature/dna50/watsoncrick.pdf A structure for Deoxyribose Nucleic Acid] (PDF). ''[[Nature (journal)|Nature]]'' 171, 737 – 738, [[25 April]] [[1953]].
* Watson, James D. ''DNA: The Secret of Life'' ISBN 978-0-375-41546-3.
* Watson, James D. ''[[The Double Helix|The Double Helix: A Personal Account of the Discovery of the Structure of DNA (Norton Critical Editions)]]''. ISBN 978-0-393-95075-5
==External links==
* [http://www.dnaftb.org/dnaftb/ DNA from the beginning]
* [http://www.nature.com/nature/dna50/archive.html Double helix: 50 years of DNA], [[Nature (journal)|Nature]].
* [http://mason.gmu.edu/~emoody/rfranklin.html Rosalind Franklin's contributions to the study of DNA].
* [http://www.genome.gov/10506367 U.S. National DNA Day] Watch videos and participate in real-time chat with top scientists
* [http://www.genome.gov/10506718 Genetic Education Modules for Teachers] ''DNA from the Beginning'' Study Guide
* [http://www.bbc.co.uk/bbcfour/audiointerviews/profilepages/crickwatson1.shtml Listen to Francis Crick and James Watson talking on the BBC in 1962, 1972, and 1974]
* [http://www.dnakin.com Using DNA in Genealogical Research]
* [http://www.dnai.org DNA Interactive] (requires [[Adobe Flash]])
* [http://www.rcsb.org/pdb/static.do?p=education_discussion/molecule_of_the_month/pdb23_1.html DNA: RCSB PDB Molecule of the Month]
* [http://www.fidelitysystems.com/Unlinked_DNA.html DNA under electron microscope]
* [http://dnawiz.com/ DNA Articles] DNA Articles and Information collected from various sources.
* [http://biostudio.com/c_%20education%20mac.htm DNA coiling to form chromosomes]
[[Category:Biology Workgroup]]
[[Category:Chemistry Workgroup]]
[[Category:CZ Live]]

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Three-dimensional model of the structure of part of a DNA double helix.

Deoxyribonucleic acid (DNA) is a very large biological molecule that is vital in providing information for the development and reproduction of living things. Every living organism has its own DNA sequence that is like a unique 'barcode' or 'fingerprint'. This inheritable variation in DNA is the most important factor driving evolutionary change over many generations. But, beyond these general characteristics, what "exactly" is DNA? What are the precise physical attributes of this molecule that make its role so centrally imposing in understanding life?

DNA is a long polymer of simple units called nucleotides, held together by a sugar phosphate backbone. Attached to each sugar molecule is a molecule of one of four bases; adenine (A), thymine (T), guanine (G) or cytosine (C), and the order of these bases on the DNA strand encodes information. In most organisms, DNA is a double-helix (or duplex molecule) consisting of two DNA strands coiled around each other, and held together by hydrogen bonds between bases. Because of the chemical nature of these bases, adenine always pairs with thymine and guanine always pairs with cytosine. This complementarity forms the basis of semi-conservative DNA replication — it makes it possible for DNA to be copied relatively simply, while accurately preserving its information content.

The entire DNA sequence of an organism is called its genome. In animals and plants, most DNA is stored inside the cell nucleus. In bacteria, there is no nuclear membrane around the DNA, which is in a region called the nucleoid. Some organelles in eukaryotic cells (mitochondria and chloroplasts) have their own DNA with a similar organisation to bacterial DNA. Viruses have a single type of nucleic acid, either DNA or RNA, directly encased in a protein coat.

Overview of biological functions

DNA contains the genetic information that is the basis for living functions including growth, reproduction and evolution. This information is held in segments of the DNA called genes that may span in size from scores of DNA base-pairs to many thousands of base-pairs. In eukaryotes (organisms such as plants, yeasts and animals whose cells have a nucleus) DNA usually occurs as several large, linear chromosomes, each of which may contain hundreds or thousands of genes. Prokaryotes (organisms such as common bacteria) generally have a single large circular chromosome, but often possess other miniature chromosomes called plasmids. The set of chromosomes in a cell makes up its genome; the human genome has about three billion base pairs of DNA arranged into 46 chromosomes [1] and contains 20-25,000 genes.

There are many interactions that happen between DNA and other molecules to coordinate its functions. When cells divide, the genetic information must be duplicated to produce two daughter copies of DNA in a process called DNA replication. When a cell uses the information in a gene, the DNA sequence is copied into a complementary single strand of RNA in a process called transcription. Of the transcribed sequences, some are used to directly make a matching protein sequence by a process called translation (meaning translation from a nucleic acid polymer to an amino acid polymer). The other transcribed RNA sequences may have regulatory, structural or catalytic roles. This article introduces some of the functions and interactions that characterize the DNA molecules in cells, and touches on some of the more technological uses for this molecule.

Genes

Our understanding of the various ways in which genes play a role in cells has been continually revised throughout the history of genetics, starting from abstract concepts of inheritable particles whose composition was unknown. This has led to several modern different definitions of a gene. One of the most straightforward ways to define a gene is simply as a segment of DNA that is transcribed into RNA - that is - the gene is a unit of transcription. This definition encompasses genes for non-translated RNAs, such as ribosomal RNA (rRNA) and transfer RNA (tRNA), as well as messenger RNA (mRNA) which is used for encoding the sequences of proteins.

A second approach is to define a gene as a region of DNA that encodes a single polypeptide. By this definition, any particular mRNA transcription unit can cover more than one gene, and thus a mRNA can carry regions encoding one or more polypeptides. Such a multi-genic transcription unit is called an operon.

Other definitions include consideration of genes as units of biological function. This definition can include sites on DNA that are not transcribed, such as DNA sites at which regulatory and catalytically active proteins concerned with gene regulation and expression are located. Examples of such sites (loci, sing. locus) are promoters and operators. (Locus is a genetic term very similar in meaning to gene, and which refers to a site or region on a chromosome concerned with a particular function or trait.)

All of the cells in our body contain essentially the same DNA, with a few exceptions; red blood cells for example do not have a nucleus and contain no DNA. However although two cells may carry identical DNA, this does not make them identical, because the two cells may have different patterns of gene expression; only some genes will be active in each cell, and the level of activity varies between cells, and this is what makes different cell types different. The "level" of gene expression (for a given gene) is used sometimes to refer to the amount of mRNA made by the cell, and sometimes to refer to the amount of protein produced.

Every human has essentially the same genes, but has slightly different DNA; on average the DNA of two individuals differs at about three million bases. These differences are very rarely in the protein-coding sequences of genes, but some affect how particular genes are regulated — they may affect exactly where in the body a gene is expressed, how intensely it is expressed, or how expression is regulated by other genes or by environmental factors; these slight differences help to make every human being unique. By comparison, the genome of our closest living relative, the chimpanzee, differs from the human genome at about 30 million bases. [2]

Genomes

In eukaryotes, DNA is located mainly in the cell nucleus (there are also small amounts in mitochondria and chloroplasts). In prokaryotes, the DNA is in an irregularly shaped body in the cytoplasm called the nucleoid.[3] The DNA is usually in linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. The human genome has about three billion base pairs of DNA arranged into 46 chromosomes[1], and contains 20-25,000 genes [4], the simple nematode C elegans has almost as many genes (more than 19,000)[5].

In many species, only a small fraction of the genome encodes protein: only about 1.5% of the human genome consists of protein-coding exons, while over 50% consists of non-coding repetitive sequences.[6] Some have concluded that much of human DNA is "junk DNA" because most of the non-coding elements appear to have no function, Some other vertebrates, including the puffer fish Fugu have very much more compact genomes, and (for multicellular organisms) there seems to be no consistent relationship between the size of the genome and the complexity of the organism [7]. Some non-coding DNA sequences are now known to have a structural role in chromosomes. In particular, telomeres and centromeres contain few genes, but are important for the function and stability of chromosomes.[8][9] An abundant form of non-coding DNA in humans are pseudogenes, which are copies of genes that have been disabled by mutation;[10] these are usually just molecular 'fossils', but they can provide the raw genetic material for new genes.[11]

A recent challenge to the long-standing view that the human genome consists of relatively few genes along with a vast amount of "junk DNA" comes from the ENCyclopedia Of DNA Elements (ENCODE) consortium.[12][13] Their survey of the human genome shows that most of the DNA is transcribed into molecules of RNA. This broad pattern of transcription was unexpected, but whether these transcribed (but not translated) elements have any biological function is not yet clear.[13]

Replication

Further information: Replication of a circular bacterial chromosome
DNA-replication illustrated by the bacterial replication fork. The helix unwinds and both strands replicate simultaneously as they unwind. The leading strand replicates continuously from the 3' end, with the newest end of the forming strand facing into the replication fork. The lagging strand replicates by a series of fragments (Okazaki fragments placed end-to-end, with the newest ends facing away from the fork; the Okazaki fragments are later joined together by DNA ligase. During replication, DNA polymerase III proofreads for mismatched bases

For an organism to grow, its cells must multiply, and this occurs by cell division: one cell splits to create two new 'daughter' cells. When a cell divides it must replicate its DNA so that the two daughter cells have the same genetic information as the parent cell. The double-stranded structure of DNA provides a simple mechanism for this replication. The two strands of DNA separate, and then each strand's complementary DNA sequence is recreated by an enzyme called DNA polymerase. This makes the complementary strand by finding the correct base (through complementary base pairing), and bonding it to the original strand. DNA polymerases can only extend a DNA strand in a 5' to 3' direction, so other mechanisms are needed to copy the antiparallel strands of the double helix.[14] In this way, the base on the old strand dictates which base appears on the new strand, and the cell (usually) ends up with a perfect copy of its DNA. However, occasionally mistakes (called mutations) occur, contributing to the genetic variation that is the raw material for evolutionary change.

DNA replication requires a complex set of proteins, each dedicated to one of several different tasks needed to replicate this large molecule in an orderly and precise fashion. Further capacity for DNA replication with substantial rearrangement (which has major implications for understanding mechanisms of molecular evolution, is provided by mechanisms for DNA movement, inversion, and duplication, illustrated by various mobile DNAs such as transposons and proviruses.

Transcription and translation

Within most (but not all) genes, the nucleotides define a messenger RNA (mRNA) which in turn defines one or more protein sequences. This is possible because of the genetic code which translates the nucleic acid sequence to an amino-acid sequence. The genetic code consists of three-letter 'words' called codons formed from a sequence of three nucleotides. For example, the sequences ACU, CAG and UUU in mRNA are translated to threonine, glutamine and phenylalanine respectively.

In transcription, the codons are copied into mRNA by RNA polymerase. This copy is then decoded by a ribosome that reads the RNA sequence by base-pairing the mRNA to a specific aminoacyl-tRNA; an amino acid carried by a transfer RNA (tRNA). As there are four bases in three-letter combinations, there are 64 possible codons, and these encode the twenty standard amino acids. Most amino acids, therefore, have more than one possible codon (for example, ACU and ACA both code for threonine). There is one start codon (AUG) that also encodes for methionine) and three 'stop' or 'nonsense' codons (UAA, UGA and UAG) that signify the end of the coding region.

Regulation of gene expression

How genes are regulated — how they are turned on or off — is an important topic in modern biology, and research continually yields surprising insights into how phenotypic traits and biological adaptations are determined.

In the 1950's, investigations of the bacterium Escherichia coli led to the recognition that the region upstream of a transcribed region provides a place for the enzyme RNA polymerase to attach to DNA and start transcribing RNA in the 5' to 3' direction of the nucleic acid chain. The site at which this occurs came to be called the promoter. Other regulatory proteins (such as repressors) influence transcription by binding to a region near to or overlapping the promoter, called the operator. In the early years of modern genetics, emphasis was given to transcriptional regulation as an important and common means of modulating gene expression, but today we realize that there are a wide range of mechanisms by which the expression of mRNA and proteins can be modulated by both external and internal signals in cells.

Physical and chemical properties

The two strands of DNA are held together by hydrogen bonds between bases. The sugars in the backbone are shown in light blue.

DNA is a long chain of repeating units called nucleotides (a nucleotide is a base linked to a sugar and one or more phosphate groups)[15] The DNA chain is 22-26 Å wide (2.2-2.6nm)[16] The nucleotides are very small (just 3.3Å long), but DNA can contain millions of them: the DNA in the largest human chromosome (Chromosome 1) has 220 million base pairs.[17]

In living organisms, DNA does not usually exist as a single molecule, but as a tightly-associated pair of molecules.[18][19] These two long strands are entwined in the shape of a double helix. DNA can thus be thought of as an anti-parallel double helix. The nucleotide repeats contain both the backbone of the molecule, which holds the chain together, and a base, which interacts with the other DNA strand. The double helix is held together by hydrogen bonds between the bases attached to the two strands. If many nucleotides are linked together, as in DNA, the polymer is referred to as a polynucleotide.[20]

The backbone of the DNA strand has alternating phosphate and sugar residues[21]: the sugar is the pentose (five carbon) sugar 2-deoxyribose. The sugar molecules are joined together by phosphate groups that form phosphodiester bonds between the third and fifth carbon atoms in the sugar rings. Because these bonds are asymmetric, a strand of DNA has a 'direction'. In a double helix, the direction of the nucleotides in one strand is opposite to that in the other strand. This arrangement of DNA strands is called antiparallel. The asymmetric ends of a strand of DNA bases are referred to as the 5' (five prime) and 3' (three prime) ends. One of the major differences between DNA and RNA is the sugar: 2-deoxyribose is replaced by ribose in RNA.[19]

The four bases in DNA are adenine (A), cytosine (C), guanine (G) and thymine (T), and these bases are attached to the sugar/phosphate to form the complete nucleotide. Adenine and guanine are fused five- and six-membered heterocyclic compounds called purines, while cytosine and thymine are six-membered rings called pyrimidines.[20] A fifth pyrimidine base, uracil (U), replaces thymine in RNA. Uracil is normally only found in DNA as a breakdown product of cytosine, but bacterial viruses contain uracil in their DNA.[22] In contrast, following synthesis of certain RNA molecules, many uracils are converted to thymines. This occurs mostly on structural and enzymatic RNAs like tRNAs and ribosomal RNA.[23]

The double helix is a right-handed spiral. As the DNA strands wind around each other, gaps between the two phosphate backbones reveal the sides of the bases inside (see animation). Two of these grooves twist around the surface of the double helix: the major groove is 22 Å wide and the minor groove is 12 Å wide.[24] The edges of the bases are more accessible in the major groove, so proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove.[25]

Base pairing

Each type of base on one strand of DNA forms a bond with just one type of base on the other strand, called 'complementary base pairing'. Purines form hydrogen bonds to pyrimidines; for example, A bonds only to T, and C bonds only to G. This arrangement of two nucleotides joined together across the double helix is called a base pair. In a double helix, the two strands are also held together by hydrophobic effects and by a variation of pi stacking.[26] Hydrogen bonds can be broken and rejoined quite easily, so the two strands of DNA in a double helix can be pulled apart like a zipper, either by mechanical force or by high temperatures.[27] Becauseof this complementarity, the information in the double-stranded sequence of a DNA helix is duplicated on each strand, and this is vital in DNA replication. The reversible and specific interaction between complementary base pairs is critical for all the functions of DNA in living organisms.[15]

The two types of base pairs form different numbers of hydrogen bonds; AT forms two hydrogen bonds, and GC forms three, so the GC base-pair is stronger than the AT pair. Thus, long DNA helices with a high GC content have strongly interacting strands, while short helices with high AT content have weakly interacting strands.[28] Parts of the DNA double helix that need to separate easily tend to have a high AT content, making the strands easier to pull apart.[29] The strength of this interaction can be measured by finding the temperature required to break the hydrogen bonds (their 'melting temperature'). When all the base pairs in a DNA double helix melt, the strands separate, leaving two single-stranded molecules in solution. These molecules have no single shape, but some conformations are more stable than others.

Sense and antisense

DNA is copied into RNA by RNA polymerases.[30] A DNA sequence is called a "sense" sequence if it is copied by these enzymes (which only work in the 5' to 3' direction) and then translated into protein. The sequence on the opposite strand is complementary to the sense sequence and is called the "antisense" sequence. Sense and antisense sequences can co-exist on the same strand of DNA; in both prokaryotes and eukaryotes, antisense sequences are transcribed[31], and antisense RNAs might be involved in regulating gene expression.[32]. (See Micro RNA, RNA interference, sRNA.)

Many DNA sequences in prokaryotes and eukaryotes (and more in plasmids and viruses) have overlapping genes which may both occur in the same direction, on the same strand (parallel) or in opposite directions, on opposite strands (antiparallel), blurring the distinction between sense and antisense strands.[33][34] In these cases, some DNA sequences encode one protein when read from 5′ to 3′ along one strand, and a different protein when read in the opposite direction (but still from 5′ to 3′) along the other strand. In bacteria, this overlap may be involved in regulating gene transcription,[34] while in viruses, overlapping genes increase the information that can be encoded within the small viral genome.[35] Another way of reducing genome size is seen in some viruses that contain linear or circular single-stranded DNA.[36]

Supercoiling

DNA can be 'twisted' in a process called DNA supercoiling. In its "relaxed" state, a DNA strand usually circles the axis of the double helix once every 10.4 base pairs, but if the DNA is twisted, the strands become more tightly or more loosely wound.[37] If the DNA is twisted in the direction of the helix (positive supercoiling), and the bases are held more tightly together. If they are twisted in the opposite direction (negative supercoiling) the bases come apart more easily. Most DNA has slight negative supercoiling that is introduced by topoisomerases. These enzymes are also needed to relieve the twisting stresses introduced into DNA strands during processes such as transcription and DNA replication.[38]

Alternative conformations

The conformation of a DNA molecule depends on its sequence, the amount and direction of supercoiling, chemical modifications of the bases, and also solution conditions, such as the concentration of metal ions.[39] Accordingly, DNA can exist in several possible conformations, but only a few of these ("A-DNA", "B-DNA", and "Z-DNA") are thought to occur naturally. Of these, the "B" form is most common. The A form is a wider right-handed spiral, with a shallow and wide minor groove and a narrower and deeper major groove; this form occurs in dehydrated samples of DNA, while in the cell it may be produced in hybrid pairings of DNA and RNA strands, as well as in enzyme-DNA complexes.[40] Segments of DNA where the bases have been modified by methylation may undergo a larger change in conformation and adopt the Z form. Here, the strands turn about the helical axis in a left-handed spiral, the opposite of the more common B form.[41] These unusual structures can be recognized by specific Z-DNA binding proteins and may be involved in regulating transcription.[42]

Quadruplex structures

At the ends of the linear chromosomes, specialized regions called telomeres allow the cell to replicate chromosome ends using the enzyme telomerase.[43] Without telomeres, a chromosome would become shorter each time it was replicated. These specialized 'caps' also help to protect the DNA ends from exonucleases and stop the DNA repair systems in the cell from treating them as damage to be corrected. In human cells, telomeres are usually lengths of single-stranded DNA that contain several thousand repeats of a TTAGGG sequence.[8] These sequences may stabilize chromosome ends by forming unusual quadruplex structures. Here, four guanine bases form a flat plate, throughhydrogen bonding, and these plates then stack on top of each other to form a stable quadruplex.[44] Other structures can also be formed, and the central set of four bases can come from either one folded strand, or several different parallel strands, each contributing one base to the central structure.

Telomeres also form large loops called 'telomere loops', or 'T-loops'. Here, the single-stranded DNA curls around in a circle stabilized by telomere-binding proteins.[45]

Chemical modifications

DNA methylation

The expression of genes is influenced by the chromatin structure of a chromosome, and regions of heterochromatin (with little or no gene expression) correlate with the methylation of cytosine.[46] These structural changes to the DNA are one type of epigenetic change that can alter chromatin structure, and they are inheritable. Epigenetics refers to features of organisms that are stable over successive rounds of cell division but which do not involve changes in the underlying DNA sequence[47]. Epigenetic changes are important in cellular differentiation, allowing cells to maintain different characteristics despite containing the same genomic material. Some epigenetic features can be inherited from one generation to the next.[48]

The level of methylation varies between organisms; the nematode C. elegans lacks any cytosine methylation, while up to 1% of the DNA of vertebrates contains 5-methylcytosine.[49] Despite the biological importance of 5-methylcytosine, it is susceptible to spontaneous deamination, and methylated cytosines are therefore mutation 'hotspots'.[50] Other base modifications include adenine methylation in bacteria and the glycosylation of uracil to produce the "J-base" in kinetoplastids.[51][52]

Mutations

DNA can be damaged by many different agents. Mutagens are agents which can produce genetic mutations - these are alterations of one DNA base to another base. Examples of mutagens include oxidizing agents, alkylating agents and high-energy electromagnetic radiation such as ultraviolet light and x-rays. Lesions of DNA, in which residues are changed to a structure that is not a normal feature of DNA, are different from mutations. However, damaged DNA can give rise to mutations, and indeed, some DNA repair processes are error prone and thus themselves generate mutations.

Ultraviolet radiation damages DNA mostly by producing thymine dimers.[53] Oxidants such as free radicals or hydrogen peroxide can cause several forms of damage, including base modifications (particularly of guanosine) as well as double-strand breaks.[54] It has been estimated that, in each human cell, about 500 bases suffer oxidative damage every day.[55][56] Of these lesions, the most damaging are double-strand breaks, as they can produce point mutations, insertions and deletions from the DNA sequence, as well as chromosomal translocations.[57]

Many mutagens intercalate into the space between two adjacent base pairs. These are mostly polycyclic, aromatic, and planar molecules, and include ethidium, proflavin, daunomycin, doxorubicin and thalidomide. DNA intercalators are used in chemotherapy to inhibit DNA replication in rapidly-growing cancer cells.[58] For an intercalator to fit between base pairs, the bases must separate, distorting the DNA strand by unwinding of the double helix. These structural modifications inhibit transcription and replication processes, causing both toxicity and mutations. As a result, DNA intercalators are often carcinogens. Nevertheless, because they can inhibit DNA transcription and replication, they are also used in chemotherapy to suppress rapidly-growing cancer cells.[58]

Interactions with proteins

All of the functions of DNA depend on its interactions with proteins. some of these interactions are non-specific, others are specific in that the protein can only bind to a particular DNA sequence. Some enzymes can also bind to DNA and of these, the polymerases that copy the DNA base sequence in transcription and DNA replication are particularly important.

DNA-binding proteins

Nucleosome 2.jpg
Nucleosome (opposites attracts).JPG
Interaction of DNA with histones (shown in white, top). These proteins' basic amino acids (below left, blue) bind to the acidic phosphate groups on DNA (below right, red).

Within chromosomes, DNA is held in complexes between DNA and structural proteins. These proteins organize the DNA into a compact structure called chromatin. In eukaryotes, this structure involves DNA binding to small basic proteins called histones, while in prokaryotes many types of proteins are involved.[59] The histones form a disk-shaped complex called a nucleosome which has two complete turns of double-stranded DNA wrapped around it. These interactions are formed through basic residues in the histones making ionic bonds to the acidic sugar-phosphate backbone of the DNA, and are largely independent of the base sequence.[60] Chemical modifications of these basic amino acid residues include methylation, phosphorylation and acetylation.[61] These changes alter the strength of the interaction between the DNA and the histones, making the DNA more or less accessible to transcription factors and changing the rate of transcription.[62] Other non-specific DNA-binding proteins found in chromatin include the high-mobility group proteins, which bind preferentially to bent or distorted DNA.[63] These proteins are important in bending arrays of nucleosomes and arranging them into more complex chromatin structures.[64]

Another group of DNA-binding proteins bind single-stranded DNA. In humans, replication protein A is the best-characterised member of this family, and is essential for most processes where the double helix is separated (including DNA replication, recombination and DNA repair).[65] These proteins seem to stabilize single-stranded DNA and protect it from forming stem loops or being degraded by nucleases.

Other proteins bind to particular DNA sequences. The most intensively studied of these are the transcription factors. Each of these proteins binds to a particular set of DNA sequences and thereby activates or inhibits the transcription of genes with these sequences close to their promoters. Transcription factors do this in two ways. Some can bind the RNA polymerase responsible for transcription, either directly or through other mediator proteins; this locates the polymerase at the promoter and allows it to begin transcription.[66] Other transcription factors can bind enzymes that modify the histones at the promoter, this will change the accessibility of the DNA template to the polymerase.[67]

These DNA targets can occur throughout an organism's genome, so changes in the activity of one type of transcription factor in a given cell can affect the expression of many genes in that cell.[68] Consequently, these proteins are often the targets of the signal transduction processes that mediate responses to environmental changes or cellular differentiation and development. The specificity of transcription factor interactions with DNA arises because the proteins make multiple contacts to the edges of the DNA bases, allowing them to "read" the DNA sequence. Most of these interactions occur in the major groove, where the bases are most accessible.[25]

DNA-modifying enzymes

Nucleases and ligases

Nucleases cut DNA strands by catalyzing the hydrolysis of the phosphodiester bonds (nucleases that hydrolyse nucleotides from the ends of DNA strands are called exonucleases, while endonucleases cut within strands). The most frequently-used nucleases in molecular biology are the restriction endonucleases, which cut DNA at specific sequences. For instance, the EcoRV enzyme recognizes the 6-base sequence 5′-GAT|ATC-3′ and makes a cut at the vertical line. In nature, these enzymes protect bacteria against phage infection by digesting the phage DNA when it enters the bacterial cell, acting as part of the restriction modification system.[69] In technology, these sequence-specific nucleases are used in molecular cloning and DNA fingerprinting.

DNA ligases can rejoin cut or broken DNA strands, using the energy from either adenosine triphosphate or nicotinamide adenine dinucleotide. Ligases are particularly important in lagging strand DNA replication, as they join together the short segments of DNA produced at the replication fork into a complete copy of the DNA template. They are also used in DNA repair and genetic recombination.[70]

Topoisomerases and helicases

Topoisomerase activities illustrated with on covalently closed circular DNA. Topisomerases can form supercoils in DNA, and can interconvert covalently closed circular DNA and their catenated forms.

Topoisomerases have both nuclease and ligase activity, and they can change the amount of supercoiling in DNA. Some work by cutting the DNA helix and allowing one section to rotate; the enzyme then seals the DNA break.[71] Others can cut one DNA helix and then pass a second strand of DNA through this break, before rejoining the helix.[72] Topoisomerases are required for many processes involving DNA, such as DNA replication and transcription.[38]

Helicases are a type of 'molecular motor'; they use the chemical energy in nucleoside triphosphates (predominantly ATP) to break hydrogen bonds between bases and unwind the DNA double helix into single strands.[73] These enzymes are essential for most processes where enzymes need to access the DNA bases.

Polymerases

Polymerases synthesise polynucleotides from nucleoside triphosphates. They add nucleotides onto the 3′ hydroxyl group of the previous nucleotide in the DNA strand, so all polymerases work in a 5′ to 3′ direction.[30] In the active site of these enzymes, the nucleoside triphosphate substrate base-pairs to a single-stranded polynucleotide template: this allows polymerases to synthesise the complementary strand of this template accurately.

DNA polymerases copy DNA sequences. Accuracy is very important for this, so many polymerases have a proofreading activity: they can recognizes the occasional mistakes that can occur during synthesis. These enzymes detect the lack of base pairing between mismatched nucleotides, and if a mismatch is detected, a 3′ to 5′ exonuclease activity is activated and the incorrect base is removed.[74] In most organisms, DNA polymerases function in a large complex called the replisome.

RNA-dependent DNA polymerases copy the sequence of an RNA strand into DNA. One example is reverse transcriptase, which is a viral enzyme involved in the infection of cells by retroviruses; another example is telomerase, which is required for the replication of telomeres.[75][43] Telomerase is an unusual polymerase because it contains its own RNA template as part of its structure.[76]

Transcription is carried out by a RNA polymerase that copies a DNA sequence into RNA. The enzyme binds to a promoter and separates the DNA strands. It then copies the gene sequence into a mRNA transcript until it reaches a region of DNA called the terminator, where it halts and detaches from the DNA. RNA polymerase II, which transcribes most of the genes in the human genome, operates as part of a large protein complex with multiple regulatory and accessory subunits.[77]

Genetic recombination

A DNA helix does not usually interact with other segments of DNA, and in human cells the different chromosomes even occupy different regions of the nucleus (called "chromosome territories").[78] This physical separation of chromosomes is important for the ability of DNA to function as a stable repository for information, as one of the few times chromosomes interact is when they recombine. Recombination is when two DNA helices break, swap a section and then rejoin. In eukaryotes, this usually occurs during meiosis, when two chromatids are paired together in the center of the cell. This allows chromosomes to exchange genetic information and produces new combinations of genes.[79] Genetic recombination can also be involved in DNA repair.[80] The most common form of recombination is homologous recombination, where the two chromosomes involved share very similar sequences. However, recombination can also damage cells, by producing chromosomal translocations and genetic abnormalities. Recombination reactions are catalyzed by recombinases,[81] which have a DNA-dependent ATPase activity. The recombinase makes a 'nick' in one strand of a DNA double helix, allowing the nicked strand to separate from its complementary strand and anneal to one strand of the double helix on the opposite chromatid. A second nick allows the strand in the second chromatid to separate and anneal to the strand in the first helix, forming a cross-strand exchange (also called a Holliday junction). The Holliday junction is a tetrahedral junction structure which can be moved along the pair of chromosomes, swapping one strand for another. The recombination is then halted by cleavage of the junction and re-ligation of the released DNA.[82]

DNA and molecular evolution

As well as being susceptible to largely random mutations (that usually affect just a single base), some regions of DNA are specialised to undergo dramatic, rapid, non-random rearrangements, or to undergo more subtle changes at a high frequency so that the expression of a gene is dramatically altered. Such rearrangements include various versions of site-specific recombination. This depends on enzymes that recognise particular sites on DNA and create novel structures such as insertions, deletions and inversions. For instance, DNA regions in the small genome of the bacterial virus P1 can invert, enabling different versions of tail fibers to be expressed in different viruses. Similarly, site-specific recombinase enzymes are responsible for mating type variation in yeast, and for flagellum type (phase) changes in the bacterium Salmonella enterica Typhimurium.

More subtle mutations can occur in micro-satellite repeats (also called homopolymeric tracts of DNA). An example of such a structure are short DNA intervals where the same base is tandemly repeated, as in 5'-gcAAAAAAAAAAAttg-3', or a dinucleotide or even a triplet as in 5'- ATGATGATGATGATGATGATG-3'. DNA polymerase III is prone to make 'stuttering errors' at such repeats. As a consequence, changes in repeat number occur quite often during cell replication, and when they appear at a position where the spacing of nucleotide residues is critical for gene function, they can cause changes to the phenotype.

The stomach ulcer bacterium Helicobacter pylori is a good example of how homopolymeric tracts can enable quasi-directed evolution of particular genes. H. pylori has 46 genes that contain homopolymeric runs of nucleotides or dinucleotide repeats that are prone to frequent length changes as a consequence of stuttering errors during replication. These changes can lead to frequent reversible inactivation of these genes, or to changed gene transcription if the repeat is located in a regulatory sequence. This generates highly diverse populations of H. pylori in an individual human host, and this diversity helps the bacterium evade the immune system.[83]

Triplet repeats behave similarly, but are particularly suited to evolution of proteins with differing characteristics. In the clock-like period gene of the fruit fly, triplet repeats 'fine tune' an insect's biological clock in response to changes in environmental temperatures. Triplet repeats are widely distributed in genomes, and their high frequency of mutation is responsible for several genetically determined disorders in humans.[84]

Uses in technology

Forensics

Forensic scientists can use DNA in blood, semen, skin, saliva or hair to match samples collected at a crime scene to samples taken from possible suspects. This process is called genetic fingerprinting or more formally, DNA profiling. In DNA profiling, the lengths of variable sections of repetitive DNA (such as short tandem repeats and minisatellites) are compared between people. This is usually very reliable for identifying the source of a sample,[85] but identification can be complicated if the samples that are collected include DNA from several people.[86] DNA profiling was developed in 1984 by British geneticist Sir Alec Jeffreys,[87] and first used in forensic science to convict Colin Pitchfork (and to clear the prime suspect) in the 1988 Enderby murders case.[88] People convicted of certain types of crimes may be required to provide a sample of DNA for a database. This has helped investigators solve old cases where only a DNA sample was obtained from the scene. DNA profiling can also be used to identify victims of mass casualty incidents.[89]

Bioinformatics

Bioinformatics involves the analysis of DNA sequence data; DNA from hundreds of different organisms has now been partially sequenced, and this information is stored in massive databases. The development of techniques to store and search DNA sequences has led to many applications in computer science.[90] String-searching or 'matching' algorithms, which identify a given sequence of letters inside a larger sequence of letters, are used to search for specific sequences of nucleotides. The related problem of sequence alignment aims to identify homologous sequences; these are sequences that are very similar but not identical. When two different genes in an organism have very similar sequences, this is evidence that, at some stage in evolution, a single gene was duplicated, and the sequences subsequently diverged (under different selection pressures) by incorporating different mutations. Identifying such holologies can give valuable clues about the likely function of novel genes. Similarly, identifying homologies between genes in different organisms can be used to reconstruct the evolutionary relationships between organisms.[91] Data sets representing entire genomes' worth of DNA sequences, such as those produced by the Human Genome Project, are difficult to use without annotations, which label the locations of genes and regulatory elements on each chromosome. Regions of DNA sequence that have patterns that are characteristic of protein- or RNA-coding genes can be identified by gene finding algorithms, allowing researchers to predict the presence of particular gene products in an organism.[92]

Molecular cloning

The small chromosomes of bacteria have proved extraordinarily useful for analysing genetic mechanisms and genome structure in many organisms, including humans. This utility arose because of several important discoveries made by microbiologists in the 1950-70's that provided new laboratory tools for directly manipulating genes. The principal laboratory tools and techniques discovered in this period were:

  • Compact circular plasmid molecules such as ColE1 that were relatively easy to extract and purify from bacterial cells, and when inserted back inside living bacterial cells could serve as genetically stable carriers (vectors) of novel DNA fragments. These vectors were propagated in bacterial cell lines termed "clones". Since each plasmid vector in these clones carried a single DNA molecular fragment, these could be considered to be 'molecular clones'.
  • Convenient methods for extracting plasmid DNA from cells, physical analysis of this DNA, and reinsertion of circular plasmid DNA back inside living cells. The main method for DNA re-insertion is termed DNA transformation - that is, direct uptake of naked DNA molecules by cells. One technique that assisted DNA transformation was the use of selectable genetic markers, and plasmid-borne bacterial antibiotic resistance provided such markers in the form of traits like ampicillin resistance and tetracycline resistance.
  • Restriction endonucleases such as the enzymes EcoRI or HindIII, were found to be useful for specifically digesting DNA at particular sites and creating novel combinations of DNA fragments in the laboratory.
  • Restriction enzymes enabled re-annealing different DNA fragments, such as circular plasmid DNA which had been linearised at a single EcoRI restriction endonuclease target site together with another fragment, say an EcoRI generated fragment of a human chromosome. By sealing together two such fragments with the enzyme DNA ligase, novel hybrid-plasmid molecules could be created in which "foreign" DNA inserts were carried in a chimeric or hybrid plasmid, often called a recombinant DNA molecule.

After the mid-1970's, re-insertion of recombinant DNA plasmids into living bacterial cells, such as those of Escherichia coli opened up many new approaches in biotechnology. These made it possible to manufacture, for example, human hormones such as insulin in microbial cell-based protein factories. When combined with other genetic techniques, the field of "recombinant DNA technology" opened up the possibility of decoding the gene sequence of whole genomes. This latter area is now usually referred to as genomics, and includes the Human Genome Project.

References

  1. 1.0 1.1 Venter J et al. (2001). "The sequence of the human genome". Science 291: 1304–51. PMID 11181995.
  2. Pollard KS et al. (2006) Forces shaping the fastest evolving regions in the human genome. PLoS Genet 2(10):e168 PMID 17040131
  3. Thanbichler M et al. (2005). "The bacterial nucleoid: a highly organized and dynamic structure". J Cell Biochem 96: 506–21. PMID 15988757.
  4. Human Genome Project Information [1]
  5. The C. elegans Sequencing Consortium (1998)Genome Sequence of the Nematode C. elegans: A Platform for Investigating Biology. Science 282: 2012-8 [2]
  6. Wolfsberg T et al. (2001). "Guide to the draft human genome". Nature 409: 824-6. PMID 11236998.
  7. See Sydney Brenner's Nobel lecture (2002) [3]
  8. 8.0 8.1 Wright W et al. (1997). "Normal human chromosomes have long, G-rich telomeric overhangs at one end". Genes Dev 11: 2801-9. PMID 9353250.
  9. Pidoux A, Allshire R (2005). "The role of heterochromatin in centromere function". Philos Trans R Soc Lond B 360: 569-79. PMID 15905142.
  10. Harrison P et al. (2002). "Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22". Genome Res 12: 272-80. PMID 11827946.
  11. Harrison P, Gerstein M (2002). "Studying genomes through the aeons: protein families, pseudogenes and proteome evolution". J Mol Biol 318: 1155-74. PMID 12083509.
  12. Weinstock GM (2007). "ENCODE: More genomic empowerment". Genome Research 17: 667-668. PMID 17567987.
  13. 13.0 13.1 ENCODE Project Consortium (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature 447: 799-816. PMID 17571346.
  14. Albà M (2001). "Replicative DNA polymerases". Genome Biol 2: REVIEWS3002. PMID 11178285.
  15. 15.0 15.1 Alberts, Bruce; Alexander Johnson, Julian Lewis, Martin Raff, Keith Roberts, and Peter Walters (2002). Molecular Biology of the Cell; Fourth Edition. New York and London: Garland Science. ISBN 0-8153-3218-1. 
  16. Mandelkern M et al. (1981). "The dimensions of DNA in solution". J Mol Biol 152: 153-61. PMID 7338906.
  17. Gregory S et al. (2006). "The DNA sequence and biological annotation of human chromosome 1". Nature 441: 315-21. PMID 16710414.
  18. Watson J, Crick F (1953). "Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid". Nature 171: 737-8. PMID 13054692.
  19. 19.0 19.1 Berg J et al. (2002) Biochemistry. WH Freeman and Co. ISBN 0-7167-4955-6
  20. 20.0 20.1 Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents IUPAC-IUB Commission on Biochemical Nomenclature (CBN) Accessed 03 Jan 2006
  21. Ghosh A, Bansal M (2003). "A glossary of DNA structures from A to Z". Acta Crystallogr D Biol Crystallogr 59: 620-6. PMID 12657780.
  22. Takahashi I, Marmur J (1963). "Replacement of thymidylic acid by deoxyuridylic acid in the deoxyribonucleic acid of a transducing phage for Bacillus subtilis". Nature 197: 794-5. PMID 13980287.
  23. Agris P (2004). "Decoding the genome: a modified view". Nucleic Acids Res 32: 223 – 38. PMID 14715921.
  24. Wing R et al. (1980). "Crystal structure analysis of a complete turn of B-DNA". Nature 287: 755 – 8. PMID 7432492.
  25. 25.0 25.1 Pabo C, Sauer R. "Protein-DNA recognition". Ann Rev Biochem 53: 293-321. PMID 6236744.
  26. Ponnuswamy P, Gromiha M (1994). "On the conformational stability of oligonucleotide duplexes and tRNA molecules". J Theor Biol 169: 419-32. PMID 7526075.
  27. Clausen-Schaumann H et al. (2000). "Mechanical stability of single DNA molecules". Biophys J 78: 1997-2007. PMID 10733978.
  28. Chalikian T et al. (1999). "A more unified picture for the thermodynamics of nucleic acid duplex melting: a characterization by calorimetric and volumetric techniques". Proc Natl Acad Sci USA 96: 7853-8. PMID 10393911.
  29. deHaseth P, Helmann J (1995). "Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase-induced strand separation of double helical DNA". Mol Microbiol 16: 817-24. PMID 7476180.
  30. 30.0 30.1 Joyce C, Steitz T (1995). "Polymerase structures and function: variations on a theme?". J Bacteriol 177: 6321-9. PMID 7592405.
  31. Hüttenhofer A et al. (2005). "Non-coding RNAs: hope or hype?". Trends Genet 21: 289-97. PMID 15851066.
  32. Munroe S (2004). "Diversity of antisense regulation in eukaryotes: multiple mechanisms, emerging patterns". J Cell Biochem 93: 664-71. PMID 15389973.
  33. Makalowska I et al. (2005). "Overlapping genes in vertebrate genomes". Comput Biol Chem 29: 1–12. PMID 15680581.
  34. 34.0 34.1 Johnson Z, Chisholm S (2004). "Properties of overlapping genes are conserved across microbial genomes". Genome Res 14: 2268–72. PMID 15520290.
  35. Lamb R, Horvath C (1991). "Diversity of coding strategies in influenza viruses". Trends Genet 7: 261–6. PMID 1771674.
  36. Davies J, Stanley J (1989). "Geminivirus genes and vectors". Trends Genet 5: 77–81. PMID 2660364.
  37. Benham C, Mielke S. "DNA mechanics". Ann Rev Biomed Eng 7: 21–53. PMID 16004565.
  38. 38.0 38.1 Wang J (2002). "Cellular roles of DNA topoisomerases: a molecular perspective". Nat Rev Mol Cell Biol 3: 430–40. PMID 12042765.
  39. Basu H et al. (1988). "Recognition of Z-RNA and Z-DNA determinants by polyamines in solution: experimental and theoretical studies". J Biomol Struct Dyn 6: 299-309. PMID 2482766.
  40. Lu XJ et al. (2000). "A-form conformational motifs in ligand-bound DNA structures". J Mol Biol 300: 819-40. PMID 10891271.
  41. Rothenburg S et al.. "DNA methylation and Z-DNA formation as mediators of quantitative differences in the expression of alleles". Immunol Rev 184: 286–98. PMID 12086319.
  42. Oh D et al. (2002). "Z-DNA-binding proteins can act as potent effectors of gene expression in vivo". Proc Natl Acad Sci USA 99: 16666-71. PMID 12486233.
  43. 43.0 43.1 Greider C, Blackburn E (1985). "Identification of a specific telomere terminal transferase activity in Tetrahymena extracts". Cell 43: 405-13. PMID 3907856.
  44. Burge S et al. (2006). "Quadruplex DNA: sequence, topology and structure". Nucleic Acids Res 34: 5402-15. PMID 17012276.
  45. Griffith J et al. (1999). "Mammalian telomeres end in a large duplex loop". Cell 97: 503-14. PMID 10338214.
  46. For example, cytosine methylation, to produce 5-methylcytosine, is important for X-chromosome inactivation. Klose R, Bird A (2006). "Genomic DNA methylation: the mark and its mediators". Trends Biochem Sci 31: 89–97. PMID 16403636.
  47. Adrian Bird (2007). "Perceptions of epigenetics". Nature 447: 396-398. PMID 17522671
  48. V.L. Chandler (2007). "Paramutation: From Maize to Mice". Cell 128: 641-645.
  49. Bird A (2002). "DNA methylation patterns and epigenetic memory". Genes Dev 16: 6–21. PMID 11782440.
  50. Walsh C, Xu G. "Cytosine methylation and DNA repair". Curr Top Microbiol Immunol 301: 283–315. PMID 16570853.
  51. Ratel D et al. (2006). "N6-methyladenine: the other methylated base of DNA". Bioessays 28: 309–15. PMID 16479578.
  52. Gommers-Ampt J et al. (1993). "beta-D-glucosyl-hydroxymethyluracil: a novel modified base present in the DNA of the parasitic protozoan T. brucei". Cell 75: 1129–36. PMID 8261512.
  53. Douki T et al. (2003). "Bipyrimidine photoproducts rather than oxidative lesions are the main type of DNA damage involved in the genotoxic effect of solar ultraviolet radiation". Biochemistry 42: 9221-6. PMID 12885257.
  54. Cadet J et al. (1999). "Hydroxyl radicals and DNA base damage". Mutat Res 424 (1-2): 9-21. PMID 10064846.
  55. Shigenaga M et al. (1989). "Urinary 8-hydroxy-2'-deoxyguanosine as a biological marker of in vivo oxidative DNA damage". Proc Natl Acad Sci USA 86: 9697-701. PMID 2602371.
  56. Cathcart R et al. (1984). "Thymine glycol and thymidine glycol in human and rat urine: a possible assay for oxidative DNA damage". Proc Natl Acad Sci USA 81: 5633-7. PMID 6592579.
  57. Valerie K, Povirk L (2003). "Regulation and mechanisms of mammalian double-strand break repair". Oncogene 22: 5792-812. PMID 12947387.
  58. 58.0 58.1 Braña M et al. (2001). "Intercalators as anticancer drugs". Curr Pharm Des 7: 1745-80. PMID 11562309.
  59. Sandman K et al. (1998). "Diversity of prokaryotic chromosomal proteins and the origin of the nucleosome". Cell Mol Life Sci 54: 1350-64. PMID 9893710.
  60. Luger K et al. (1997). "Crystal structure of the nucleosome core particle at 2.8 A resolution". Nature 389: 251-60. PMID 9305837.
  61. Jenuwein T, Allis C (2001). "Translating the histone code". Science 293: 1074-80. PMID 11498575.
  62. Ito T. "Nucleosome assembly and remodelling". Curr Top Microbiol Immunol 274: 1-22. PMID 12596902.
  63. Thomas J (2001). "HMG1 and 2: architectural DNA-binding proteins". Biochem Soc Trans 29: 395-401. PMID 11497996.
  64. Grosschedl R et al. (1994). "HMG domain proteins: architectural elements in the assembly of nucleoprotein structures". Trends Genet 10: 94-100. PMID 8178371.
  65. Iftode C et al. (1999). "Replication protein A (RPA): the eukaryotic SSB". Crit Rev Biochem Mol Biol 34: 141-80. PMID 10473346.
  66. Myers L, Kornberg R. "Mediator of transcriptional regulation". Ann Rev Biochem 69: 729-49. PMID 10966474.
  67. Spiegelman B, Heinrich R (2004). "Biological control through regulated transcriptional coactivators". Cell 119: 157-67. PMID 15479634.
  68. Li Z et al. (2003). "A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells". Proc Natl Acad Sci USA 100: 8164-9. PMID 12808131.
  69. Bickle T, Krüger D (1993). "Biology of DNA restriction". Microbiol Rev 57: 434–50. PMID 8336674.
  70. Doherty A, Suh S (2000). "Structural and mechanistic conservation in DNA ligases.". Nucleic Acids Res 28: 4051–8. PMID 11058099.
  71. Champoux J. "DNA topoisomerases: structure, function, and mechanism". Ann Rev Biochem 70: 369–413. PMID 11395412.
  72. Schoeffler A, Berger J (2005). "Recent advances in understanding structure-function relationships in the type II topoisomerase mechanism". Biochem Soc Trans 33: 1465–70. PMID 16246147.
  73. Tuteja N, Tuteja R (2004). "Unraveling DNA helicases. Motif, structure, mechanism and function". Eur J Biochem 271: 1849–63. PMID 15128295.
  74. Hubscher U et al.. "Eukaryotic DNA polymerases". Annu Rev Biochem 71: 133–63. PMID 12045093.
  75. Tarrago-Litvak L et al. (1994). "The reverse transcriptase of HIV-1: from enzymology to therapeutic intervention". FASEB J 8: 497–503. PMID 7514143.
  76. Nugent C, Lundblad V (1998). "The telomerase reverse transcriptase: components and regulation". Genes Dev 12 (8): 1073–85. PMID 9553037.
  77. Martinez E (2002). "Multi-protein complexes in eukaryotic gene transcription". Plant Mol Biol 50: 925–47. PMID 12516863.
  78. Cremer T, Cremer C (2001). "Chromosome territories, nuclear architecture and gene regulation in mammalian cells". Nat Rev Genet 2: 292-301. PMID 11283701.
  79. Pál C et al. (2006). "An integrated view of protein evolution". Nat Rev Genet 7: 337-48. PMID 16619049.
  80. O'Driscoll M, Jeggo P (2006). "The role of double-strand break repair - insights from human genetics". Nat Rev Genet 7: 45-54. PMID 16369571.
  81. Sung P et al. (2003). "Rad51 recombinase and recombination mediators". J Biol Chem 278: 42729-32. PMID 12912992.
  82. Dickman M et al. (2002). "The RuvABC resolvasome". Eur J Biochem 269: 5492-501. PMID 12423347.
  83. Suerbaum S, Josenhans C (2007) Helicobacter pylori evolution and phenotypic diversification in a changing host. Nat Rev Microbiol 5:441-52 PMID 17505524
  84. Christopher Wills discusses the evolutionary significance of these concepts in The Runaway Brain: The Evolution of Human Uniqueness ISBN 0-00-654672-2 (1995)
  85. Collins A, Morton N (1994). "Likelihood ratios for DNA identification". Proc Natl Acad Sci USA 91: 6007-11. PMID 8016106.
  86. Weir B et al. (1997). "Interpreting DNA mixtures". J Forensic Sci 42: 213-22. PMID 9068179.
  87. Jeffreys A et al. (1985). "Individual-specific 'fingerprints' of human DNA.". Nature 316: 76-9. PMID 2989708.
  88. Colin Pitchfork - first murder conviction on DNA evidence also clears the prime suspect Forensic Science Service Accessed 23 Dec 2006
  89. DNA Identification in Mass Fatality Incidents. National Institute of Justice (September 2006).
  90. Baldi, Pierre. Brunak, Soren. Bioinformatics: The Machine Learning Approach MIT Press (2001) ISBN 978-0-262-02506-5
  91. Sjölander K (2004). "Phylogenomic inference of protein molecular function: advances and challenges". Bioinformatics 20: 170-9. PMID 14734307.
  92. Mount DM (2004). Bioinformatics: Sequence and Genome Analysis, 2. Cold Spring Harbor Laboratory Press. ISBN 0879697121.