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[[File:ADN animation.gif|thumb|220px|The structure of part of a DNA [[double helix]]]]
'''Deoxyribonucleic acid''' ('''DNA''') is a [[nucleic acid]] that contains the [[genetics|genetic]] instructions used in the development and functioning of all known living [[organism]]s and some [[virus]]es. The main role of DNA [[molecule]]s is the long-term storage of [[information]]. DNA is often compared to a set of [[blueprint]]s or a recipe, or a [[code]], since it contains the instructions needed to construct other components of [[cell (biology)|cells]], such as [[protein]]s and [[RNA]] molecules. The DNA segments that carry this genetic information are called [[gene]]s, but other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information.

Chemically, DNA consists of two long [[polymers]] of simple units called [[nucleotide]]s, with [[backbone chain|backbone]]s made of [[sugar]]s and [[phosphate]] groups joined by [[ester]] bonds. These two strands run in opposite directions to each other and are therefore [[antiparallel (biochemistry)|anti-parallel]]. Attached to each sugar is one of four types of molecules called [[nucleobase|bases]]. It is the sequence of these four bases along the backbone that encodes information. This information is read using the [[genetic code]], which specifies the sequence of the [[amino acid]]s within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA, in a process called [[transcription (genetics)|transcription]].

Within cells, DNA is organized into long structures called [[chromosome]]s. These chromosomes are duplicated before cells [[cell division|divide]], in a process called [[DNA replication]]. [[Eukaryote|Eukaryotic organisms]] ([[animal]]s, [[plant]]s, [[Fungus|fungi]], and [[protist]]s) store most of their DNA inside the [[cell nucleus]] and some of their DNA in [[organelle]]s, such as [[mitochondria]] or [[chloroplasts]].<ref>{{cite book | last = Russell | first = Peter | title = iGenetics | publisher = Benjamin Cummings | location = New York | date = 2001 | isbn = 0-805-34553-1 }}</ref> In contrast, [[prokaryote]]s ([[bacteria]] and [[archaea]]) store their DNA in the [[cytoplasm]]. Within the chromosomes, [[chromatin]] proteins such as [[histone]]s compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.

==Properties==
[[Image:DNA chemical structure.svg|right|thumb|350px|Chemical structure of DNA. [[Hydrogen bond]]s shown as dotted lines.]]

DNA is a long [[polymer]] made from repeating units called [[nucleotide]]s.<ref>{{cite book | last = Saenger | first = Wolfram | title = Principles of Nucleic Acid Structure | publisher = Springer-Verlag | location = New York | date = 1984 | isbn = 0387907629 }}</ref><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|year=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 |isbn=0-8153-3218-1 |oclc=145080076 48122761 57023651 69932405}}</ref><ref name=Butler>{{cite book | author=Butler, John M. | year=2001 | title=Forensic DNA Typing | publisher= Elsevier | isbn=978-0-12-147951-0 | oclc=223032110 45406517}} pp. 14–15.</ref> The DNA chain is 22 to 26&nbsp;[[Ångström]]s wide (2.2 to 2.6&nbsp;[[nanometre]]s), and one nucleotide unit is 3.3&nbsp;Å (0.33&nbsp;nm) long.<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 |pmid=7338906 |doi=10.1016/0022-2836(81)90099-1}}</ref> Although each individual repeating unit is very small, DNA polymers can be very large molecules containing millions of nucleotides. For instance, the largest [[human chromosome]], chromosome number 1, is approximately 220 million [[base pair]]s 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 |pmid=16710414 | doi = 10.1038/nature04727}}</ref>

In living organisms, DNA does not usually exist as a single molecule, but instead as a pair of molecules that are held tightly together.<ref name=FWPUB>{{cite journal| author = Watson J.D. and Crick F.H.C. | pmid=13054692 | doi = 10.1038/171737a0 | url= http://www.nature.com/nature/dna50/watsoncrick.pdf | title=A Structure for Deoxyribose Nucleic Acid | journal=Nature | volume=171 | pages=737–738 | year=1953 | access-date=4 May 2009|format=PDF}}</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 [[double helix]]. The nucleotide repeats contain both the segment of the backbone of the molecule, which holds the chain together, and a base, which interacts with the other DNA strand in the helix. 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 called 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 January 2006</ref>

The backbone of the DNA strand is made from alternating [[phosphate]] and [[carbohydrate|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 |pmid=12657780 |doi=10.1107/S0907444903003251}}</ref> The sugar in DNA is [[deoxyribose|2-deoxyribose]], which is a [[pentose]] (five-[[carbon]]) sugar. The sugars are joined together by phosphate groups that form [[phosphodiester bond]]s between the third and fifth carbon [[atom]]s of adjacent sugar rings. These asymmetric [[covalent bond|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: the strands are ''antiparallel''. The asymmetric ends of DNA strands are called the [[directionality (molecular biology)|5′]] (''five prime'') and [[directionality (molecular biology)|3′]] (''three prime'') ends, with the 5' end having a terminal phosphate group and the 3' end a terminal hydroxyl group. One major difference between DNA and RNA is the sugar, with the 2-deoxyribose in DNA being replaced by the alternative pentose sugar [[ribose]] in RNA.<ref name=berg/>

[[File:DNA orbit animated static thumb.png|thumb|right|250px|A section of DNA. The bases lie horizontally between the two spiraling strands.<ref>Created from [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1D65 PDB 1D65]</ref> Animated version at [[:File:DNA orbit animated.gif]].]]

The DNA double helix is stabilized 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 attached to the sugar/phosphate to form the complete nucleotide, as shown for [[adenosine monophosphate]].

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=berg/> A fifth pyrimidine base, called [[uracil]] (U), usually takes the place of thymine in RNA and differs from thymine by lacking a [[methyl group]] on its ring. Uracil is not usually found in DNA, occurring only as a breakdown product of cytosine. In addition to RNA and DNA, a large number of artificial [[nucleic acid analogues]] have also been created to study the proprieties of nucleic acids, or for use in biotechnology.<ref>{{cite journal |author=Verma S, Eckstein F |title=Modified oligonucleotides: synthesis and strategy for users |journal=Annu. Rev. Biochem. |volume=67 |issue= |pages=99–134 |year=1998 |pmid=9759484 |doi=10.1146/annurev.biochem.67.1.99}}</ref>

===Grooves===

Twin helical strands form the DNA backbone. Another double helix may be found by tracing the spaces, or grooves, between the strands. These voids are adjacent to the base pairs and may provide a [[binding site]]. As the strands are not directly opposite each other, the grooves are unequally sized. One groove, the major groove, is 22&nbsp;Å wide and the other, the minor groove, is 12&nbsp;Å 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 |pmid=7432492 |doi=10.1038/287755a0}}</ref> 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 make 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 |pages=293–321 |year=1984 |pmid=6236744 | doi = 10.1146/annurev.bi.53.070184.001453}}</ref> This situation varies in unusual conformations of DNA within the cell ''(see below)'', but the major and minor grooves are always named to reflect the differences in size that would be seen if the DNA is twisted back into the ordinary B form.

===Base pairing===
{{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 binding together across the double helix is called a base pair. 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 |pmc=1300792 |journal=Biophys J |volume=78 |issue=4 |pages=1997–2007 |year=2000 |pmid=10733978 |doi=10.1016/S0006-3495(00)76747-6}}</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/>
<div class="thumb tleft" style="background-color: #f9f9f9; border: 1px solid #CCCCCC; margin:0.5em;">
{|border="0" width=230 border="0" cellpadding="2" cellspacing="0" style="font-size: 85%; border: 1px solid #CCCCCC; margin: 0.3em;"
|[[Image:GC DNA base pair.svg|281px]]
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{|border="0" width=230 border="0" cellpadding="2" cellspacing="0" style="font-size: 85%; border: 1px solid #CCCCCC; margin: 0.3em;"
|[[Image:AT DNA base pair.svg|281px]]
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<div style="border: none; width:281px;"><div class="thumbcaption">Top, a '''GC''' base pair with three [[hydrogen bond]]s. Bottom, an '''AT''' base pair with two hydrogen bonds. Non-covalent hydrogen bonds between the pairs are shown as dashed lines.</div></div></div>
The two types of base pairs form different numbers of hydrogen bonds, AT forming two hydrogen bonds, and GC forming three hydrogen bonds (see figures, left). 
DNA with high [[GC-content]] is more stable than DNA with low GC-content, but contrary to popular belief, this is not due to the extra hydrogen bond of a GC basepair but rather the contribution of stacking interactions (hydrogen bonding merely provides specificity of the pairing, not stability).<ref name ="Yakovchuk2006">{{cite journal |author=Yakovchuk P, Protozanova E, Frank-Kamenetskii MD |title=Base-stacking and base-pairing contributions into thermal stability of the DNA double helix |journal=Nucleic Acids Res. |volume=34 |issue=2 |pages=564–74 |year=2006 |pmid=16449200 |pmc=1360284 |doi=10.1093/nar/gkj454 |url=http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=16449200}}</ref>
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 stronger-interacting strands, while short helices with high AT content have weaker-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 |pmc=22151 |journal=Proc Natl Acad Sci USA |volume=96 |issue=14 |pages=7853–8 |year=1999 |pmid=10393911 |doi=10.1073/pnas.96.14.7853}}</ref> In biology, parts of the DNA double helix that need to separate easily, such as the TATAAT [[Pribnow box]] in some [[promoter]]s, 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 |issue=5 |pages=817–24 |year=1995 |pmid=7476180 |doi=10.1111/j.1365-2958.1995.tb02309.x}}</ref> In the laboratory, the strength of this interaction can be measured by finding the temperature required to break the hydrogen bonds, their [[DNA melting|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 common 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 |pmid=15609994 | doi = 10.1021/bi048221v}}</ref>

===Sense and antisense===
{{further|[[Sense (molecular biology)]]}}

A DNA sequence is called "sense" if its sequence is the same as that of a [[messenger RNA]] copy that is translated into protein.<ref>[http://www.chem.qmul.ac.uk/iubmb/newsletter/misc/DNA.html Designation of the two strands of DNA] JCBN/NC-IUB Newsletter 1989, Accessed 07 May 2008</ref> The sequence on the opposite strand is called the "antisense" sequence. Both sense and antisense sequences can exist on different parts of the same strand of DNA (i.e. both strands contain both sense and antisense sequences). In both prokaryotes and eukaryotes, antisense RNA sequences are produced, but the functions of these RNAs are not entirely clear.<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 |pmid=15851066 |doi=10.1016/j.tig.2005.03.007}}</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 |pmid=15389973 | doi = 10.1002/jcb.20252}}</ref>

A few DNA sequences in prokaryotes and eukaryotes, and more in [[plasmid]]s and [[virus]]es, blur the distinction 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 |pmid=15680581 |doi=10.1016/j.compbiolchem.2004.12.006}}</ref> In these cases, some DNA sequences do double duty, encoding one protein when read along one strand, and a second protein when read in the opposite direction 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 |pmid=15520290 | doi = 10.1101/gr.2433104}}</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 |pmid=1771674}}</ref>

===Supercoiling===
{{Further|[[DNA supercoil]]}}
DNA can be twisted like a rope in a process called [[DNA supercoil]]ing. With DNA in its "relaxed" state, a 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= Annu Rev Biomed Eng |volume=7 |pages=21–53 |year=2005 |pmid=16004565 | doi = 10.1146/annurev.bioeng.6.062403.132016}}</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 [[enzyme]]s called [[topoisomerase]]s.<ref name=Champoux>{{cite journal |author=Champoux J |title=DNA topoisomerases: structure, function, and mechanism |journal=Annu Rev Biochem |volume=70 |pages=369–413 |year=2001 |pmid=11395412 | doi = 10.1146/annurev.biochem.70.1.369}}</ref> 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 |issue=6 |pages=430–40 |year=2002 |pmid=12042765 | doi = 10.1038/nrm831}}</ref>
[[Image:A-DNA, B-DNA and Z-DNA.png|thumb|right|290px|From left to right, the structures of A, B and Z DNA]]

===Alternate DNA structures===
{{Further|[[Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid|A Structure for DNA]], * [[Molecular models of DNA]], and [[DNA structure]]}}
DNA exists in many possible [[Conformational isomerism|conformations]] that include [[A-DNA]], B-DNA, and [[Z-DNA]] forms, although, only B-DNA and Z-DNA have been directly observed in functional organisms.<ref name=Ghosh/> The conformation that DNA adopts depends on the hydration level, DNA sequence, the amount and direction of supercoiling, chemical modifications of the bases, the type and concentration of metal [[ion]]s, as well as the presence of [[polyamine]]s in solution.<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 |pmid=2482766}}</ref>

The first published reports of A-DNA [[X-ray scattering techniques|X-ray diffraction patterns]]— and also B-DNA used analyses based on [[Patterson function|Patterson transforms]] that provided only a limited amount of structural information for oriented fibers of DNA.<ref>{{cite journal |author=Franklin RE, Gosling RG |title=The Structure of Sodium Thymonucleate Fibres I. The Influence of Water Content |journal=Acta Cryst |volume=6 |issue=8-9 |pages=673–7 |date=6 March 1953 |doi=10.1107/S0365110X53001939 |url=http://hekto.med.unc.edu:8080/CARTER/carter_WWW/Bioch_134/PDF_files/Franklin_Gossling.pdf}}<br/>{{cite journal |author=Franklin RE, Gosling RG |title=The structure of sodium thymonucleate fibres. II. The cylindrically symmetrical Patterson function |journal=Acta Cryst |volume=6 |issue=8-9 |pages=678–85 |year=1953 |month=September |doi=10.1107/S0365110X53001940 }}</ref><ref name=NatFranGos>{{cite journal| title=Molecular Configuration in Sodium Thymonucleate. Franklin R. and Gosling R.G| journal=Nature | volume= 171 | pages= 740–1 | year=1953 | url=http://www.nature.com/nature/dna50/franklingosling.pdf | pmid=13054694 | doi= 10.1038/171740a0| author=Franklin, Rosalind and Gosling, Raymond |format=PDF}}</ref> An alternate analysis was then proposed by Wilkins ''et al.'', in 1953, for the ''in vivo'' B-DNA X-ray diffraction/scattering patterns of highly hydrated DNA fibers in terms of squares of [[Bessel function]]s.<ref name=NatWilk>{{cite journal| title=Molecular Structure of Deoxypentose Nucleic Acids | author= Wilkins M.H.F., A.R. Stokes A.R. & Wilson, H.R. | journal=Nature | volume= 171 | pages= 738–740 | year=1953 | url=http://www.nature.com/nature/dna50/wilkins.pdf| pmid=13054693 | doi=10.1038/171738a0| format=PDF}}</ref> In the same journal, Watson and Crick presented their [[Molecular models of DNA|molecular modeling]] analysis of the DNA X-ray diffraction patterns to suggest that the structure was a double-helix.<ref name=FWPUB/> 

Although the `B-DNA form' is most common under the conditions found in cells,<ref>{{cite journal |author=Leslie AG, Arnott S, Chandrasekaran R, Ratliff RL |title=Polymorphism of DNA double helices |journal=J. Mol. Biol. |volume=143 |issue=1 |pages=49–72 |year=1980 |pmid=7441761 |doi=10.1016/0022-2836(80)90124-2}}</ref> it is not a well-defined conformation but a family of related DNA conformations<ref>{{cite journal |author=Baianu, I.C. |title=Structural Order and Partial Disorder in Biological systems|journal= Bull. Math. Biol. |volume= 42 |issue=4 |pages=137–141|year=1980}} http://cogprints.org/3822/</ref> that occur at the high hydration levels present in living cells. Their corresponding X-ray diffraction and scattering patterns are characteristic of molecular [[Paracrystalline|paracrystals]] with a significant degree of disorder.<ref>Hosemann R., Bagchi R.N., ''Direct analysis of diffraction by matter'', North-Holland Publs., Amsterdam – New York, 1962.</ref><ref>{{cite journal|author=Baianu, I.C. |title=X-ray scattering by partially disordered membrane systems.|journal=Acta Cryst., |volume=A34 |issue=5 |pages=751–753|year=1978|doi=10.1107/S0567739478001540}}</ref>

Compared to B-DNA, the A-DNA form is a wider right-handed spiral, with a shallow, wide minor groove and a narrower, deeper major groove. The A form occurs under non-physiological conditions in partially 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=Wahl M, Sundaralingam M |title=Crystal structures of A-DNA duplexes | journal=Biopolymers |volume=44 |issue=1 | pages=45–63 |year=1997 |pmid=9097733 | doi = 10.1002/(SICI)1097-0282(1997)44:1 |doi_brokendate=2009-03-14}}</ref><ref>{{cite journal |author=Lu XJ, Shakked Z, Olson WK |title=A-form conformational motifs in ligand-bound DNA structures |journal=J. Mol. Biol. |volume=300 |issue=4 |pages=819–40 |year=2000 |pmid=10891271 |doi=10.1006/jmbi.2000.3690}}</ref> Segments of DNA where the bases have been chemically modified by [[methylation]] 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, the opposite 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 | pages=286–98 |year=2001|pmid=12086319 |doi=10.1034/j.1600-065x.2001.1840125.x}}</ref> These unusual structures can be recognized by specific Z-DNA binding proteins and may be involved in the regulation of transcription.<ref>{{cite journal |author=Oh D, Kim Y, Rich A |title=Z-DNA-binding proteins can act as potent effectors of gene expression in vivo |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=99 |issue=26 |pages=16666–71 |year=2002 |pmid=12486233 |doi=10.1073/pnas.262672699 |pmc=139201 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=12486233}}</ref>

[[Image:Parallel telomere quadruple.png|thumb|left|260px|DNA quadruplex formed by [[telomere]] repeats. The looped conformation of the DNA backbone is very different from the typical DNA helix.<ref>Created from [http://ndbserver.rutgers.edu/atlas/xray/structures/U/ud0017/ud0017.html NDB UD0017]</ref>]]
===Quadruplex structures===
{{further|[[G-quadruplex]]}}

At the ends of the linear chromosomes 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 the enzymes that normally replicate DNA cannot copy the extreme 3′ ends of chromosomes.<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 |pmid=3907856 |doi=10.1016/0092-8674(85)90170-9}}</ref> These specialized chromosome caps also help protect the DNA ends, 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 |pmid=9553037 |doi=10.1101/gad.12.8.1073}}</ref> In [[List of distinct cell types in the adult human body|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 | journal=Genes Dev |volume=11 |issue=21 | pages=2801–9 |year=1997 |pmid=9353250 |doi=10.1101/gad.11.21.2801}}</ref>

These guanine-rich sequences may stabilize chromosome ends by forming structures of stacked sets of four-base units, rather than the usual base pairs found in other DNA molecules. Here, four guanine bases form a flat plate and these flat four-base units then stack on top of each other, to form a stable ''[[G-quadruplex]]'' structure.<ref name=Burge>{{cite journal |author=Burge S, Parkinson G, Hazel P, Todd A, Neidle S |title=Quadruplex DNA: sequence, topology and structure | journal=Nucleic Acids Res |volume=34 |issue=19 | pages=5402–15 |year=2006 |pmid=17012276 |pmc=1636468 | doi = 10.1093/nar/gkl655 |url=http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=17012276}}</ref> These structures are stabilized by hydrogen bonding between the edges of the bases and [[chelation]] of a metal ion in the centre of each four-base unit.<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 |pmid=12050675 | doi = 10.1038/nature755}}</ref> Other structures can also be formed, with the central set of four bases coming from either a single strand folded around the bases, or several different parallel strands, each contributing one base to the central structure.

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 long 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 |pmid=10338214 |doi=10.1016/S0092-8674(00)80760-6}}</ref> At 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 DNA|triple-stranded]] structure is called a displacement loop or [[D-loop]].<ref name=Burge/>

<div class="thumb tright" style="background-color: #f9f9f9; border: 1px solid #CCCCCC; margin:0.5em;">
{|border="0" width=200 border="0" cellpadding="2" cellspacing="0" style="font-size: 85%; border: 1px solid #CCCCCC; margin: 0.3em;"
|[[Image:Branch-dna.png|75px]]
|[[Image:Multi-branch-dna.png|95px]]
|-
|align=center|Single branch
|align=center|Multiple branches
|}
<div style="border: none; width:200px;font-size: 90%;"><div class="thumbcaption">[[Branched DNA]] can form networks containing multiple branches.</div></div></div>

===Branched DNA===
{{further|[[Branched DNA]] and [[DNA nanotechnology]]}}

In DNA [[DNA_end#Frayed_ends|fraying]] occurs when non-complementary regions exist at the end of an otherwise complementary double-strand of DNA. However, branched DNA can occur if a third strand of DNA is introduced and contains adjoining regions able to hybridize with the frayed regions of the pre-existing double-strand. Although the simplest example of branched DNA involves only three strands of DNA, complexes involving additional strands and multiple branches are also possible.<ref>{{cite journal |author=Seeman NC |title=DNA enables nanoscale control of the structure of matter |journal=Q. Rev. Biophys. |volume=38 |issue=4 |pages=363–71 |year=2005 |month=November |pmid=16515737 |doi=10.1017/S0033583505004087}}</ref> Branched DNA can be used in [[nanotechnology]] to construct geometric shapes, see the section on [[DNA#Uses_in_technology|uses in technology]] below.

==Chemical modifications==
<div class="thumb tright" style="background-color: #f9f9f9; border: 1px solid #CCCCCC; margin:0.5em;">
{|border="0" width=300 border="0" cellpadding="2" cellspacing="0" style="font-size: 85%; border: 1px solid #CCCCCC; margin: 0.3em;"
|[[file:Cytosin.svg|75px]]
|[[file:5-Methylcytosine.svg|95px]]
|[[file:Thymin.svg|97px]]
|-
|align=center|[[cytosine]]
|align=center|[[5-Methylcytosine|5-methylcytosine]]
|align=center|[[thymine]]
|}
<div style="border: none; width:300px;font-size: 90%;"><div class="thumbcaption">Structure of cytosine with and without the 5-methyl group. [[Deamination]] converts 5-methylcytosine into thymine.</div></div></div>

===Base modifications===
{{further|[[DNA methylation]]}}
The expression of genes is influenced by how the DNA is packaged in chromosomes, in a structure called [[chromatin]]. Base modifications can be involved in packaging, with regions that have low or no gene expression usually containing high levels of [[methylation]] of [[cytosine]] bases. For example, cytosine methylation, produces [[5-Methylcytosine|5-methylcytosine]], which is important for [[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 |pmid=16403636 |doi=10.1016/j.tibs.2005.12.008}}</ref> The average level of methylation varies between organisms - the worm ''[[Caenorhabditis elegans]]'' lacks cytosine methylation, while [[vertebrate]]s have higher levels, with up to 1% of their DNA containing 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 |pmid=11782440 |doi=10.1101/gad.947102}}</ref> Despite the importance of 5-methylcytosine, it can [[deamination|deaminate]] to leave a thymine base, methylated cytosines are therefore particularly prone to [[mutation]]s.<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=2006|pmid=16570853 |doi=10.1007/3-540-31390-7_11}}</ref> Other base modifications include adenine methylation in bacteria, the presence of [[5-hydroxymethylcytosine]] in the [[brain]],<ref>{{cite journal |author=Kriaucionis S, Heintz N |title=The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain |journal=Science |volume=324 |issue=5929 |pages=929–30 |year=2009 |month=May |pmid=19372393 |doi=10.1126/science.1169786}}</ref> 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 |pmid=16479578 | doi = 10.1002/bies.20342}}</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 |pmid=8261512 |doi=10.1016/0092-8674(93)90322-H}}</ref>

===Damage===
{{further|[[Mutation]]}}
[[Image:Benzopyrene DNA adduct 1JDG.png|thumb|right|250px|A [[covalent]] [[adduct]] between [[Benzo(a)pyrene|benzo[''a'']pyrene]], the major [[mutagen]] in [[tobacco smoking|tobacco smoke]], and DNA<ref>Created from [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1JDG PDB 1JDG]</ref>]]

DNA can be damaged by many sorts of [[mutagen]]s, which change the DNA sequence. Mutagens include [[oxidizing agent]]s, [[Alkylation|alkylating agents]] and also high-energy [[electromagnetic radiation]] such as [[ultraviolet]] light and [[X-ray]]s. The type of DNA damage produced depends on the type of mutagen. For example, UV light can damage DNA by producing [[thymine dimer]]s, which are cross-links between pyrimidine bases.<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 |pmid=12885257 | doi = 10.1021/bi034593c}},</ref> On the other hand, oxidants such as [[Radical (chemistry)|free radicals]] or [[hydrogen peroxide]] produce multiple forms of damage, including base modifications, particularly of guanosine, and 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 |pmid=10064846}}</ref> A typical human cell contains about 150,000 bases that have suffered oxidative damage.<ref>{{cite journal |author=Beckman KB, Ames BN |title=Oxidative decay of DNA |journal=J. Biol. Chem. |volume=272 |issue=32 |pages=19633–6 |year=1997 |month=August |pmid=9289489 |url=http://www.jbc.org/cgi/pmidlookup?view=long&pmid=9289489}}</ref> Of these oxidative lesions, the most dangerous are double-strand breaks, as these are difficult to repair and can produce [[point mutation]]s, [[Genetic insertion|insertions]] and [[Deletion (genetics)|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 |pmid=12947387 | doi = 10.1038/sj.onc.1206679}}</ref>

Many mutagens fit into the space between two adjacent base pairs, this is called [[intercalation (chemistry)|''intercalating'']]. Most intercalators are [[aromaticity|aromatic]] and planar molecules, and include [[Ethidium bromide]], [[Daunorubicin|daunomycin]], and [[doxorubicin]]. In order for an intercalator to fit between base pairs, the bases must separate, distorting the DNA strands by unwinding of the double helix. This inhibits both transcription and DNA replication, causing toxicity and mutations. As a result, DNA intercalators are often [[carcinogen]]s, and [[benzo(a)pyrene|Benzo[''a'']pyrene diol epoxide]], [[acridine]]s, [[aflatoxin]] and [[ethidium bromide]] are 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 |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 |pmid=3936066 |doi=10.1016/0163-7258(85)90013-0}}</ref><ref>{{cite journal |author=Stephens T, Bunde C, Fillmore B |title=Mechanism of action in thalidomide teratogenesis |journal=Biochem Pharmacol |volume=59 |issue=12 |pages=1489–99 |year=2000 |pmid=10799645 |doi=10.1016/S0006-2952(99)00388-3}}</ref> Nevertheless, due to their ability to inhibit DNA transcription and replication, other similar toxins are also used in [[chemotherapy]] to inhibit 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 |pmid=11562309 |doi=10.2174/1381612013397113}}</ref>

==Biological functions==
DNA usually occurs as linear [[chromosome]]s in eukaryotes, and circular chromosomes in prokaryotes. The set of chromosomes in a cell makes up its [[genome]]; the [[human genome]] has 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 |pmid=11181995 |doi=10.1126/science.1058040}}</ref> The information carried by DNA is held in the [[DNA sequence|sequence]] of pieces of DNA called [[gene]]s. [[Transmission (genetics)|Transmission]] of genetic information in genes is achieved via complementary base pairing. For example, in transcription, when a cell uses the information in a gene, the DNA sequence is copied into a complementary RNA sequence through the attraction between the DNA and the correct RNA nucleotides. Usually, this RNA copy is then used to make a matching [[Peptide sequence|protein sequence]] in a process called [[Translation (biology)|translation]] which depends on the same interaction between RNA nucleotides. 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 between DNA and other molecules that mediate the function of the genome.

===Genes and genomes===
{{further|[[Cell nucleus]], [[Chromatin]], [[Chromosome]], [[Gene]], [[Noncoding DNA]]}}
Genomic 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 |pmid=15988757 | doi = 10.1002/jcb.20519}}</ref> The genetic information in a genome is held within genes, and the complete set of this information in an organism is called its [[genotype]]. 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 transcription 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 [[exon]]s, 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 |pmid=11236998 | doi = 10.1038/35057000}}</ref> The reasons for the presence of so much [[noncoding DNA|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 |pmid=15596463 |doi=10.1093/aob/mci009}}</ref> However, DNA sequences that do not code protein may still encode functional [[non-coding RNA]] molecules, which are involved in the [[regulation of gene expression]].<ref>{{cite journal |author=The 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 |issue=7146 | pages =799–816 |year=2007 |doi=10.1038/nature05874}}</ref>
[[Image:T7 RNA polymerase at work.png|thumb|left|300px|[[T7 RNA polymerase]] (blue) producing a mRNA (green) from a DNA template (orange).<ref>Created from [http://www.rcsb.org/pdb/explore/explore.do?structureId=1MSW PDB 1MSW]</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 | pmc=1569473 | journal=Philos Trans R Soc Lond B Biol Sci |volume=360 |issue=1455 | pages=569–79 |year=2005 |pmid=15905142 | doi = 10.1098/rstb.2004.1611}}</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 |pmid=11827946 |doi=10.1101/gr.207102}}</ref> These sequences are usually just molecular [[fossil]]s, 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 |pmid=12083509 |doi=10.1016/S0022-2836(02)00109-2}}</ref>

===Transcription and translation===
{{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 one or more protein sequences. The relationship between the nucleotide sequences of genes and the [[amino acid|amino-acid]] sequences of proteins is determined by the rules of [[Translation (biology)|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]], giving most amino acids 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.

[[Image:DNA_replication_en.svg|thumb|450px|right|DNA replication. The double helix is unwound by a [[helicase]] and [[topoisomerase]]. Next, one [[DNA polymerase]] produces the [[Replication fork|leading strand]] copy. Another DNA polymerase binds to the [[Replication fork|lagging strand]]. This enzyme makes discontinuous segments (called [[Okazaki fragment]]s) before [[DNA ligase]] joins them together.]]

===Replication===
{{further|[[DNA replication]]}}

[[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 | journal=Genome Biol |volume=2 |issue=1 | pages=REVIEWS3002 |year=2001 |pmid=11178285 |pmc=150442 |url=http://genomebiology.com/1465-6906/2/REVIEWS3002 |doi=10.1186/gb-2001-2-1-reviews3002 |nopp=true}}</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.

==Interactions with proteins==
All the functions of DNA depend on interactions with proteins. These [[protein interactions]] can be non-specific, or the protein can bind specifically to a single 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.

===DNA-binding proteins===
{{further|[[DNA-binding protein]]}}
<div class="thumb tleft" style="background-color: #f9f9f9; border: 1px solid #CCCCCC; margin:0.5em;">
{|border="0" width=260 border="0" cellpadding="0" cellspacing="0" style="font-size: 85%; border: 1px solid #CCCCCC; margin: 0.3em;"
|[[Image:Nucleosome 2.jpg|260px]]
|-
|[[Image:Nucleosome (opposites attracts).JPG|260px]]
|}
<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 with 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 |pmid=9893710 |doi=10.1007/s000180050259}}</ref><ref>{{cite journal |author=Dame RT |title=The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin |journal=Mol. Microbiol. |volume=56 |issue=4 |pages=858–70 |year=2005 |pmid=15853876 |doi=10.1111/j.1365-2958.2005.04598.x}}</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 |pmid=9305837 | doi = 10.1038/38444}}</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 |pmid=11498575 |doi=10.1126/science.1063127}}</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 | pages=1–22 |pmid=12596902}}</ref> Other non-specific DNA-binding proteins in chromatin include the high-mobility group proteins, which bind 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 |pmid=11497996 |doi=10.1042/BST0290395}}</ref> These proteins are important in bending arrays of nucleosomes and arranging them into the larger structures that make up chromosomes.<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 |pmid=8178371 |doi=10.1016/0168-9525(94)90232-1}}</ref>

A distinct group of DNA-binding proteins are the DNA-binding proteins that specifically bind single-stranded DNA. In humans, replication [[protein A]] is the best-understood member of this family and is used in 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 |pmid=10473346 |doi=10.1080/10409239991209255}}</ref> These binding proteins seem to stabilize single-stranded DNA and protect it from forming [[stem-loop]]s or being degraded by [[nuclease]]s.

[[Image:Lambda repressor 1LMB.png|thumb|right|185px|The lambda repressor [[helix-turn-helix]] transcription factor bound to its DNA target<ref>Created from [http://www.rcsb.org/pdb/explore/explore.do?structureId=1LMB PDB 1LMB]</ref>]]
In contrast, other proteins have evolved to bind to particular DNA sequences. The most intensively studied of these are the various [[transcription factor]]s, which are proteins that regulate transcription. Each transcription factor binds to one particular set of DNA sequences and activates or inhibits the transcription of genes that have these sequences close to their promoters. 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 | pages=729–49 |year=2000 |pmid=10966474 | doi = 10.1146/annurev.biochem.69.1.729}}</ref> Alternatively, transcription factors can bind [[enzyme]]s 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 |pmid=15479634 |doi=10.1016/j.cell.2004.09.037}}</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 | journal=Proc Natl Acad Sci USA |volume=100 |issue=14 | pages=8164–9 |year=2003 |pmid=12808131 |pmc=166200 |doi=10.1073/pnas.1332764100 |url=http://www.pnas.org/cgi/pmidlookup?view=long&pmid=12808131}}</ref> Consequently, these proteins are often the targets of the [[signal transduction]] processes that control 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 | pages=293–321 |year=1984 |pmid=6236744 | doi = 10.1146/annurev.bi.53.070184.001453}}</ref>

[[Image:EcoRV 1RVA.png|thumb|left|255px|The [[restriction enzyme]] [[EcoRV]] (green) in a complex with its substrate DNA<ref>Created from [http://www.rcsb.org/pdb/explore/explore.do?structureId=1RVA PDB 1RVA]</ref>]]

===DNA-modifying enzymes===
====Nucleases and ligases====
[[Nuclease]]s 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 [[Bacteriophage|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 |pmc=372918 | journal=Microbiol Rev |volume=57 |issue=2 | pages=434–50 |year=1993 |pmid=8336674}}</ref> In technology, these sequence-specific nucleases are used in [[molecular cloning]] and [[Genetic fingerprinting|DNA fingerprinting]].

Enzymes called [[DNA ligase]]s can rejoin cut or broken DNA strands.<ref name=Doherty>{{cite journal |author=Doherty A, Suh S |title=Structural and mechanistic conservation in DNA ligases | journal=Nucleic Acids Res |volume=28 |issue=21 | pages=4051–8 |year=2000 |pmid=11058099 |pmc=113121 |doi=10.1093/nar/28.21.4051 |url=http://nar.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=11058099}}</ref> Ligases are particularly important in [[Replication fork|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/>

====Topoisomerases and helicases====
[[Topoisomerase]]s are enzymes with both nuclease and ligase activity. These proteins change the amount of [[DNA supercoil|supercoiling]] in DNA. Some of these enzymes 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 |pmid=16246147 |doi=10.1042/BST20051465}}</ref> Topoisomerases are required for many processes involving DNA, such as DNA replication and transcription.<ref name=Wang/>

[[Helicase]]s are proteins that 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 | doi= 10.1111/j.1432-1033.2004.04094.x | journal=Eur J Biochem |volume=271 |issue=10 | pages=1849–63 |year=2004 |pmid=15128295}}</ref> These enzymes are essential for most processes where enzymes need to access the DNA bases.

====Polymerases====
[[Polymerase]]s are [[enzyme]]s that synthesize polynucleotide chains from [[nucleoside triphosphate]]s. The sequence of their products are copies of existing polynucleotide chains - which are called ''templates''. These enzymes function by adding nucleotides onto the 3′ [[hydroxyl|hydroxyl group]] of the previous nucleotide in a DNA strand. Consequently, all polymerases work in a 5′ to 3′ direction.<ref name=Joyce>{{cite journal |author=Joyce C, Steitz T |title=Polymerase structures and function: variations on a theme? |pmc=177480 | journal=J Bacteriol |volume=177 |issue=22 | pages=6321–9 |year=1995 |pmid=7592405}}</ref> In the [[active site]] of these enzymes, the incoming nucleoside triphosphate base-pairs to the template: this allows polymerases to accurately synthesize the complementary strand of their template. Polymerases are classified according to the type of template that they use.

In DNA replication, a DNA-dependent [[DNA polymerase]] makes a copy of a DNA sequence. Accuracy is vital in this process, so many of these polymerases have a [[Proofreading (Biology)|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 | pages=133–63 |year=2002 |pmid=12045093 | doi = 10.1146/annurev.biochem.71.090501.150041}}</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 | pages=283–315 |year=2005 |pmid=15952889 | doi = 10.1146/annurev.biochem.73.011303.073859}}</ref>

RNA-dependent DNA polymerases are a specialized class of polymerases that copy the sequence of an 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 telomeres.<ref name=Greider/><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 |pmid=7514143 |month=May |day=01}}</ref> Telomerase is an unusual polymerase because it contains its own RNA template as part of its structure.<ref name=Nugent/>

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 |pmid=12516863 |doi=10.1023/A:1021258713850}}</ref>

==Genetic recombination==
<div class="thumb tright" style="background-color: #f9f9f9; border: 1px solid #CCCCCC; margin:0.5em;">
{|border="0" width=250 border="0" cellpadding="0" cellspacing="0" style="font-size: 85%; border: 1px solid #CCCCCC; margin: 0.3em;"
|[[Image:Holliday Junction cropped.png|250px]]
|-
|[[Image:Holliday junction coloured.png|250px]]
|}
<div style="border: none; width:250px;"><div class="thumbcaption">Structure of the [[Holliday junction]] intermediate in [[genetic recombination]]. The four separate DNA strands are coloured red, blue, green and yellow.<ref>Created from [http://www.rcsb.org/pdb/explore/explore.do?structureId=1M6G PDB 1M6G]</ref></div></div></div>
{{further|[[Genetic recombination]]}}
[[Image:Chromosomal Recombination.svg|thumb|250px|left|Recombination involves the breakage and rejoining of two chromosomes (M and F) to produce two re-arranged chromosomes (C1 and C2).]]

A DNA helix usually does not 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 |pmid=11283701 | doi = 10.1038/35066075}}</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 during [[chromosomal crossover]] when they [[genetic recombination|recombine]]. Chromosomal crossover is when two DNA helices break, swap a section and then rejoin.

Recombination allows chromosomes to exchange genetic information and produces new combinations of genes, which increases the efficiency of [[natural 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 |pmid=16619049 | doi = 10.1038/nrg1838}}</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 |pmid=16369571 | doi = 10.1038/nrg1746}}</ref>

The most common form of chromosomal crossover is [[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 [[RAD51]].<ref>{{cite journal |author=Vispé S, Defais M |title=Mammalian Rad51 protein: a RecA homologue with pleiotropic functions |journal=Biochimie |volume=79 |issue=9-10 |pages=587–92 |year=1997 |pmid=9466696 |doi=10.1016/S0300-9084(97)82007-X}}</ref> The first step in recombination is a double-stranded break either caused by an [[endonuclease]] or damage to the DNA.<ref>{{cite journal |author=Neale MJ, Keeney S |title=Clarifying the mechanics of DNA strand exchange in meiotic recombination |journal=Nature |volume=442 |issue=7099 |pages=153–8 |year=2006 |pmid=16838012 | doi = 10.1038/nature04885}}</ref> A series of steps catalyzed in part by the recombinase then leads to joining of the two helices by at least one [[Holliday junction]], in which a segment of a single strand in each helix is annealed to the complementary strand in the other helix. The Holliday junction is a tetrahedral junction structure that 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 |pmid=12423347 |doi=10.1046/j.1432-1033.2002.03250.x}}</ref>

==Evolution==
{{Further|[[RNA world hypothesis]]}}
DNA contains the genetic information that allows all modern living things to function, grow and reproduce. However, it is unclear how long in the 4-billion-year [[Timeline of evolution|history of life]] DNA has performed this function, as it has been proposed that the earliest forms of life may have used RNA as their genetic material.<ref name=Joyce>{{cite journal |author=Joyce G |title=The antiquity of RNA-based evolution |journal=Nature |volume=418 |issue=6894 |pages=214–21 |year=2002 |pmid=12110897 | doi = 10.1038/418214a}}</ref><ref>{{cite journal |author=Orgel L |title=Prebiotic chemistry and the origin of the RNA world | url=http://www.crbmb.com/cgi/reprint/39/2/99.pdf |journal=Crit Rev Biochem Mol Biol |volume=39 |issue=2 |pages=99–123 |pmid=15217990 | doi = 10.1080/10409230490460765|format=PDF |year=2004}}</ref> RNA may have acted as the central part of early [[cell metabolism]] as it can both transmit genetic information and carry out [[catalysis]] as part of [[ribozyme]]s.<ref>{{cite journal |author=Davenport R |title=Ribozymes. Making copies in the RNA world |journal=Science |volume=292 |issue=5520 |pages=1278 |year=2001 |pmid=11360970 | doi = 10.1126/science.292.5520.1278a}}</ref> This ancient [[RNA world hypothesis|RNA world]] where nucleic acid would have been used for both catalysis and genetics may have influenced the [[evolution]] of the current genetic code based on four nucleotide bases. This would occur since the number of unique bases in such an organism is a trade-off between a small number of bases increasing replication accuracy and a large number of bases increasing the catalytic efficiency of ribozymes.<ref>{{cite journal |author=Szathmáry E |title=What is the optimum size for the genetic alphabet? |url=http://www.pnas.org/cgi/reprint/89/7/2614.pdf |journal=Proc Natl Acad Sci USA |volume=89 |issue=7 |pages=2614–8 |year=1992 |pmid=1372984 |doi=10.1073/pnas.89.7.2614|format=PDF}}</ref>

Unfortunately, there is no direct evidence of ancient genetic systems, as recovery of DNA from most fossils is impossible. This is because DNA will survive in the environment for less than one million years and slowly degrades into short fragments in solution.<ref>{{cite journal |author=Lindahl T |title=Instability and decay of the primary structure of DNA |journal=Nature |volume=362 |issue=6422 |pages=709–15 |year=1993 |pmid=8469282 | doi = 10.1038/362709a0}}</ref> Claims for older DNA have been made, most notably a report of the isolation of a viable bacterium from a salt crystal 250-million years old,<ref>{{cite journal |author=Vreeland R, Rosenzweig W, Powers D |title=Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal |journal=Nature |volume=407 |issue=6806 |pages=897–900 |year=2000 |pmid=11057666 | doi = 10.1038/35038060}}</ref> but these claims are controversial.<ref>{{cite journal |author=Hebsgaard M, Phillips M, Willerslev E |title=Geologically ancient DNA: fact or artefact? |journal=Trends Microbiol |volume=13 |issue=5 |pages=212–20 |year=2005 |pmid=15866038 |doi=10.1016/j.tim.2005.03.010}}</ref><ref>{{cite journal |author=Nickle D, Learn G, Rain M, Mullins J, Mittler J |title=Curiously modern DNA for a "250 million-year-old" bacterium |journal=J Mol Evol |volume=54 |issue=1 |pages=134–7 |year=2002 |pmid=11734907 | doi = 10.1007/s00239-001-0025-x}}</ref>

==Uses in technology==
===Genetic engineering===
{{further|[[Molecular biology]], [[nucleic acid methods]] and [[genetic engineering]]}}

Methods have been developed to purify DNA from organisms, such as [[phenol-chloroform extraction]] and manipulate it in the laboratory, such as [[restriction digest]]s and the [[polymerase chain reaction]]. Modern [[biology]] and [[biochemistry]] make intensive use of these techniques in recombinant DNA technology. [[Recombinant DNA]] is a man-made DNA sequence that has been assembled from other DNA sequences. They can be [[transformation (genetics)|transformed]] into organisms in the form of [[plasmid]]s or in the appropriate format, by using a [[viral vector]].<ref>{{cite journal |author=Goff SP, Berg P |title=Construction of hybrid viruses containing SV40 and lambda phage DNA segments and their propagation in cultured monkey cells |journal=Cell |volume=9 |issue=4 PT 2 |pages=695–705 |year=1976 |pmid=189942 |doi=10.1016/0092-8674(76)90133-1}}</ref> The [[genetic engineering|genetically modified]] organisms produced can be used to produce products such as recombinant [[protein]]s, used in [[medical research]],<ref>{{cite journal |author=Houdebine L |title=Transgenic animal models in biomedical research |journal=Methods Mol Biol |volume=360 |pages=163–202 |pmid=17172731}}</ref> or be grown in [[agriculture]].<ref>{{cite journal |author=Daniell H, Dhingra A |title=Multigene engineering: dawn of an exciting new era in biotechnology |journal=Curr Opin Biotechnol |volume=13 |issue=2 |pages=136–41 |year=2002 |pmid=11950565 |doi=10.1016/S0958-1669(02)00297-5}}</ref><ref>{{cite journal |author=Job D |title=Plant biotechnology in agriculture |journal=Biochimie |volume=84 |issue=11 |pages=1105–10 |year=2002 |pmid=12595138 |doi=10.1016/S0300-9084(02)00013-5}}</ref>

===Forensics===
{{further|[[Genetic fingerprinting]]}}

[[Forensic science|Forensic scientists]] can use DNA in [[blood]], [[semen]], [[skin]], [[saliva]] or [[hair]] found at a [[crime scene]] to identify a matching DNA of an individual, such as 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 repeat]]s and [[minisatellite]]s, are compared between people. This method is usually an extremely reliable technique for identifying a matching DNA.<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 |issue=13 | pages=6007–11 |year=1994 |pmid=8016106 |doi=10.1073/pnas.91.13.6007|format=PDF}}</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 |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=1985|pmid=2989708 |doi=10.1038/316076a0}}</ref> and first used in forensic science to convict Colin Pitchfork in the 1988 [[Colin Pitchfork|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 December 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 |month=September | year=2006 |publisher=National Institute of Justice}}</ref> On the other hand, many convicted people have been released from prison on the basis of DNA techniques, which were not available when a crime had originally been committed.

===Bioinformatics===
{{further|[[Bioinformatics]]}}
[[Bioinformatics]] involves the manipulation, searching, and [[data mining]] of 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>{{citation | last1=Baldi|first1= Pierre|author1-link=Pierre Baldi|last2= Brunak|first2= Soren | title=Bioinformatics: The Machine Learning Approach | publisher= MIT Press | year=2001| isbn=978-0-262-02506-5 | oclc=45951728 57562233}}.</ref> String searching or matching algorithms, which find an occurrence of a sequence of letters inside a larger sequence of letters, were 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 |pmid=14734307 | doi = 10.1093/bioinformatics/bth021}}</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 prediction|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 | year = 2004 | isbn = 0879697121|oclc = 55106399|location=Cold Spring Harbor, NY}}</ref>

===DNA nanotechnology===
[[Image:DNA nanostructures.png|thumb|400px|The DNA structure at left (schematic shown) will self-assemble into the structure visualized by [[Atomic force microscope|atomic force microscopy]] at right. [[DNA nanotechnology]] is the field which seeks to design nanoscale structures using the [[molecular recognition]] properties of DNA molecules. Image from Strong, 2004.{{doi-inline|10.1371/journal.pbio.0020073}}]]

{{further|[[DNA nanotechnology]]}}
DNA nanotechnology uses the unique [[molecular recognition]] properties of DNA and other nucleic acids to create self-assembling branched DNA complexes with useful properties.<ref>{{cite journal |author=Rothemund PW |title=Folding DNA to create nanoscale shapes and patterns |journal=Nature |volume=440 |issue=7082 |pages=297–302 |year=2006 |month=March |pmid=16541064 |doi=10.1038/nature04586}}</ref> DNA is thus used as a structural material rather than as a carrier of biological information. This has led to the creation of two-dimensional periodic lattices (both tile-based as well as using the "[[DNA origami]]" method) as well as three-dimensional structures in the shapes of [[Polyhedron|polyhedra]].<ref>{{cite journal |author=Andersen ES, Dong M, Nielsen MM, ''et al.'' |title=Self-assembly of a nanoscale DNA box with a controllable lid |journal=Nature |volume=459 |issue=7243 |pages=73–6 |year=2009 |month=May |pmid=19424153 |doi=10.1038/nature07971}}</ref> [[DNA machine|Nanomechanical devices]] and [[DNA computing|algorithmic self-assembly]] have also been demonstrated,<ref>{{cite journal |author=Ishitsuka Y, Ha T |title=DNA nanotechnology: a nanomachine goes live |journal=Nat Nanotechnol |volume=4 |issue=5 |pages=281–2 |year=2009 |month=May |pmid=19421208 |doi=10.1038/nnano.2009.101}}</ref> and these DNA structures have been used to template the arrangement of other molecules such as [[Colloidal gold|gold nanoparticles]] and [[streptavidin]] proteins.<ref>{{cite journal |author=Aldaye FA, Palmer AL, Sleiman HF |title=Assembling materials with DNA as the guide |journal=Science |volume=321 |issue=5897 |pages=1795–9 |year=2008 |month=September |pmid=18818351 |doi=10.1126/science.1154533}}</ref>

===History and anthropology===
{{further|[[Phylogenetics]] and [[Genetic genealogy]]}}
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 [[Phylogenetics|phylogeny]].<ref>{{cite journal |author=Wray G |title=Dating branches on the tree of life using DNA | journal=Genome Biol |volume=3 |issue=1 | pages=REVIEWS0001 |year=2002 |pmid=11806830 |pmc=150454 |doi=10.1046/j.1525-142X.1999.99010.x |url=http://genomebiology.com/1465-6906/3/REVIEWS0001 |nopp=true}}</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|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 December 06</ref>

==History of DNA research==
{{further|[[History of molecular biology]]}}
DNA was first isolated by the [[Switzerland|Swiss]] physician [[Friedrich Miescher]] who, in 1869, discovered a microscopic substance in the [[pus]] of discarded surgical bandages. As it resided in the nuclei of cells, he called it "nuclein".<ref>{{cite journal |author=Dahm R |title=Discovering DNA: Friedrich Miescher and the early years of nucleic acid research |journal=Hum. Genet. |volume=122 |issue=6 |pages=565–81 |year=2008 |month=January |pmid=17901982 |doi=10.1007/s00439-007-0433-0}}</ref> In 1919, [[Phoebus Levene]] identified 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 |month=December |day=01}}</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 scattering techniques|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 1928, [[Frederick Griffith]] discovered that [[trait (biology)|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.<ref>{{cite journal |author=Lorenz MG, Wackernagel W |title=Bacterial gene transfer by natural genetic transformation in the environment |journal=Microbiol. Rev. |volume=58 |issue=3 |pages=563–602 |year=1994 |pmid=7968924 |pmc=372978 |url=http://mmbr.asm.org/cgi/pmidlookup?view=long&pmid=7968924 |month=September |day=01}}</ref> This system provided the first clear suggestion that DNA carried genetic information&mdash;the [[Avery-MacLeod-McCarty experiment]]&mdash;when [[Oswald Avery]], along with coworkers [[Colin Munro MacLeod|Colin MacLeod]] and [[Maclyn McCarty]], identified DNA as the [[Griffith's experiment|transforming principle]] in 1943.<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=79 |issue=2 | pages=137–158 |year=1944 |doi=10.1084/jem.79.2.137}}</ref> DNA's role in [[heredity]] was confirmed in 1952, when [[Alfred Hershey]] and [[Martha Chase]] in the [[Hershey-Chase experiment]] showed that DNA is the [[genetic material]] of the [[Enterobacteria phage T2|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 |pmid=12981234 |doi=10.1085/jgp.36.1.39|format=PDF}}</ref>
<center>
<gallery>
Image:JamesDWatson.jpg|[[James D. Watson]]
Image:Francis Crick.png|[[Francis Crick]]
Image:Rosalind Franklin.jpg|[[Rosalind Franklin]]
Image:Raymond Gosling.jpg|[[Raymond Gosling]]
Image:maurice_wilkins.jpg|[[Maurice Wilkins|Maurice F. Wilkins]]
Image:Erwin Chargaff.jpg|[[Erwin Chargaff]]
</gallery>
</center>
In 1953 James D. Watson and Francis Crick suggested what is now accepted as the first correct double-helix model of [[Molecular structure of Nucleic Acids|DNA structure]] in the journal [[Nature (journal)|''Nature'']].<ref name=FWPUB/> Their double-helix, molecular model of DNA was then based on a single [[Photo 51|X-ray diffraction image]] (labeled as "Photo 51")<ref>The B-DNA X-ray pattern [http://osulibrary.oregonstate.edu/specialcollections/coll/pauling/dna/pictures/sci9.001.5.html on the right of this linked image] was obtained by Rosalind Franklin and Raymond Gosling in May 1952 at high hydration levels of DNA and it has been labeled as "Photo 51"</ref> taken by Rosalind Franklin and Raymond Gosling in May 1952, as well as the information that the DNA bases were paired—also obtained through private communications from Erwin Chargaff in the previous years. [[Chargaff's rules]] played a very important role in establishing double-helix configurations for B-DNA as well as A-DNA.

Experimental evidence supporting the Watson and Crick model were published in a series of five articles in the same issue of ''Nature''.<ref name=NatureDNA50>Nature Archives [http://www.nature.com/nature/dna50/archive.html Double Helix of DNA: 50 Years]</ref> Of these, Franklin and Gosling's paper was the first publication of their own X-ray diffraction data and original analysis method that partially supported the [[Watson and Crick]] model<ref name=NatFranGos/><ref>[http://osulibrary.oregonstate.edu/specialcollections/coll/pauling/dna/pictures/franklin-typeBphoto.html Original X-ray diffraction image]</ref>; this issue also contained an article on DNA structure by Maurice Wilkins and two of his colleagues, whose analysis and ''in vivo'' B-DNA X-ray patterns also supported the presence ''in vivo'' of the double-helical DNA configurations as proposed by Crick and Watson for their double-helix molecular model of DNA in the previous two pages of ''Nature''.<ref name=NatWilk>{{cite journal| title=Molecular Structure of Deoxypentose Nucleic Acids | author= Wilkins M.H.F., A.R. Stokes A.R. & Wilson, H.R. | journal=Nature | volume= 171 | pages= 738–740 | year=1953 | url=http://www.nature.com/nature/dna50/wilkins.pdf| pmid=13054693 | doi=10.1038/171738a0|format=PDF}}</ref> In 1962, after Franklin's death, Watson, Crick, and Wilkins jointly received the [[Nobel Prize]] in [[Nobel Prize in Physiology or Medicine|Physiology or Medicine]].<ref>[http://nobelprize.org/nobel_prizes/medicine/laureates/1962/ The Nobel Prize in Physiology or Medicine 1962] Nobelprize .org Accessed 22 December 06</ref> Unfortunately, Nobel rules of the time allowed only living recipients, but a vigorous debate continues on who should receive credit for the discovery.<ref>{{cite journal | title=The double helix and the 'wronged heroine' | author= Brenda Maddox| journal= Nature | volume= 421 | pages= 407–408 | date=23 January 2003 | url=http://www.biomath.nyu.edu/index/course/hw_articles/nature4.pdf | pmid=12540909 | doi = 10.1038/nature01399 |format=PDF}}</ref>

In an influential presentation in 1957, Crick laid out the [[central dogma of molecular biology|"Central Dogma" of molecular biology]], 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 December 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 USA |volume=44 |issue=7 | pages=671–82 |year=1958 |pmid=16590258 |doi=10.1073/pnas.44.7.671}}</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 December 06</ref> These findings represent the birth of [[molecular biology]].

==See also==
<div style="-moz-column-count:2; column-count:2;">
* [[Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid]]
* [[Molecular models of DNA]]
* [[DNA microarray]]
* [[DNA sequencing]]
* [[Paracrystalline|Paracrystal model and theory]]
* [[X-ray scattering]]
* [[Crystallography]]
* [[X-ray crystallography]]
* [[Genetic disorder]]
* [[Junk DNA]]
* [[Nucleic acid analogues]]
* [[Nucleic acid methods]]
* [[List of nucleic acid simulation software|Nucleic acid modeling]]
* [[Nucleic Acid Notations]]
* [[Phosphoramidite]]
* [[Plasmid]]
* [[Polymerase chain reaction]]
* {{Proteopedia|DNA}}
* [[Southern blot]]
* [[Triple-stranded DNA]]
</div>

==References==
{{reflist|2}}

==Further reading==
*{{cite book |title=Understanding DNA: the molecule & how it works |author=Calladine, Chris R.; Drew, Horace R.; Luisi, Ben F. and Travers, Andrew A. |year=2003 |publisher=Elsevier Academic Press |location=Amsterdam |isbn=0-12-155089-3 }}
*{{cite book |author=Dennis, Carina; Julie Clayton |title=50 years of DNA |publisher=Palgrave Macmillan |location=Basingstoke |year=2003 |isbn=1-4039-1479-6 }} 
*{{cite book |author=Judson, Horace Freeland |title=The eighth day of creation: makers of the revolution in biology |publisher=CSHL Press |location=Plainview, N.Y |year=1996 |isbn=0-87969-478-5 }}
*{{cite book |author=Olby, Robert C. |authorlink=Robert Olby |title=The path to the double helix: the discovery of DNA |publisher=Dover Publications |location=New York |year=1994 |isbn=0-486-68117-3 }}, first published in October 1974 by MacMillan, with foreword by Francis Crick;the definitive DNA textbook,revised in 1994 with a 9 page postscript.
*{{cite book |author=Olby, Robert C. |title=Francis Crick: A Biography |publisher=Cold Spring Harbor Laboratory Press |location=Plainview, N.Y |year=2009 |isbn=0-87969-798-9 }}
*{{cite book |author=Ridley, Matt |authorlink=Matt Ridley |title=Francis Crick: discoverer of the genetic code |publisher=Eminent Lives, Atlas Books |location=[Ashland, OH |year=2006 |isbn=0-06-082333-X }}
*{{cite book |author=Berry, Andrew; Watson, James D. |title=DNA: the secret of life |publisher=Alfred A. Knopf |location=New York |year=2003 |isbn=0-375-41546-7 }}
*{{cite book |author=Stent, Gunther Siegmund; Watson, James D. |title=[[The Double Helix|The double helix: a personal account of the discovery of the structure of DNA]] |publisher=Norton |location=New York |year=1980 |isbn=0-393-95075-1 }}
*{{cite book |author=Wilkins, Maurice |title=The third man of the double helix the autobiography of Maurice Wilkins |publisher=University Press |location=Cambridge, Eng |year=2003 |isbn=0-19-860665-6 }}

==External links==
{{portalpar|Molecular and Cellular Biology|Portal.svg}}
{{Spoken Wikipedia|dna.ogg|2007-02-12}}
{{commonscat|DNA}}
* {{dmoz|Science/Biology/Biochemistry_and_Molecular_Biology/Biomolecules/Nucleic_Acids/DNA/|DNA}}
* [http://pipe.scs.fsu.edu/displar.html DNA binding site prediction on protein]
* [http://biostudio.com/c_%20education%20mac.htm DNA coiling to form chromosomes]
* [http://www.dnaftb.org/dnaftb/ DNA from the Beginning] Another DNA Learning Center site on DNA, genes, and heredity from Mendel to the human genome project.
* [http://ca.youtube.com/watch?v=iyb7fwduuGM DNA Lab, demonstrates how to extract DNA from wheat using readily available equipment and supplies.]
* [http://nobelprize.org/educational_games/medicine/dna_double_helix/ DNA the Double Helix Game] From the official Nobel Prize web site
* [http://www.fidelitysystems.com/Unlinked_DNA.html DNA under electron microscope]
* [http://www.dnalc.org/ Dolan DNA Learning Center]
* [http://www.nature.com/nature/dna50/archive.html Double Helix: 50 years of DNA], ''[[Nature (journal)|Nature]]''
* [http://www.ncbe.reading.ac.uk/DNA50/ Double Helix 1953–2003] National Centre for Biotechnology Education
* [http://www.bbc.co.uk/bbcfour/audiointerviews/profilepages/crickwatson1.shtml Francis Crick and James Watson talking on the BBC in 1962, 1972, and 1974]
* [http://www.genome.gov/10506718 Genetic Education Modules for Teachers] — ''DNA from the Beginning'' Study Guide
* [http://www.blackwellpublishing.com/trun/artwork/Animations/cloningexp/cloningexp.html Guide to DNA cloning]
* {{cite journal |author=Olby R |authorlink=Robert Olby |title=Quiet debut for the double helix |journal=Nature |volume=421 |issue=6921 |pages=402–5 |year=2003 |month=January |pmid=12540907 |doi=10.1038/nature01397 |url=http://chem-faculty.ucsd.edu/joseph/CHEM13/DNA1.pdf}}
* {{PDB Molecule of the Month|pdb23_1}}
* [http://mason.gmu.edu/~emoody/rfranklin.html Rosalind Franklin's contributions to the study of DNA]
* [http://orpheus.ucsd.edu/speccoll/testing/html/mss0660a.html#abstract The Register of Francis Crick Personal Papers 1938 - 2007] at Mandeville Special Collections Library, Geisel Library, [[University of California, San Diego]]
* [http://www.genome.gov/10506367 U.S. National DNA Day] — watch videos and participate in real-time chat with top scientists
* {{cite news |title=Clue to chemistry of heredity found |work=The New York Times |date=Saturday, June 13, 1953 |url=http://www.nytimes.com/packages/pdf/science/dna-article.pdf}} The first American newspaper coverage of the discovery of the DNA structure.
* [http://hopes.stanford.edu/basics/dna/b0.html An Introduction to DNA and Chromosomes] from [[HOPES]]: Huntington's Disease Outreach Project for Education at Stanford

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