DNA: Ìyàtọ̀ láàrin àwọn àtúnyẹ̀wò
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[[File:DNA orbit animated static thumb.png|thumb|upright|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]].]]
Alopo emeji DNA double helix je gbigbero pelu ipa meji: awon [[hydrogen bond|ide haidrojin]] larin awon nukleotidi ati awon ibasepo [[Stacking (chemistry)|ipele ipile]] larin awon ipilenukleu [[aromatic|oloorundidun]].<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 }}</ref> Ninu ayika olomi ahamo, awon [[Pi bond|ide π]] adarapo awon ipile nukleotidi
The nucleobases are classified into two types: the [[purine]]s, A and G, being fused five- and six-membered [[heterocyclic compound]]s, and the [[pyrimidine]]s, the six-membered rings C and T.<ref name=berg/> A fifth pyrimidine nucleobase, [[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 |pages=99–134 |year=1998 |pmid=9759484 |doi=10.1146/annurev.biochem.67.1.99}}</ref>
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[[File:DNA-ligand-by-Abalone.png|left|thumb|Major and minor grooves of DNA. Minor groove is a binding site for the dye [[Hoechst stain|Hoechst 33258]].]]
===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 Å wide and the other, the minor groove, is 12 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|bibcode = 1980Natur.287..755W }}</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 name="Pabo1984">{{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]]}}
In a DNA double helix, each type of nucleobase on one strand normally interacts with just one type of nucleobase 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 |bibcode=2000BpJ....78.1997C}}</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/>
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<div style="border: none; width:282px;"><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. Although it is often stated that this is due to the added stability of an additional hydrogen bond, this is incorrect.{{source?|date=October 2011}} DNA with high GC-content is more stable due to intra-strand base stacking interactions.{{cn|date=November 2011}}
As noted above, most DNA molecules are actually two polymer strands, bound together in a helical fashion by noncovalent bonds; this double stranded structure (dsDNA) is maintained largely by the intrastrand base stacking interactions, which are strongest for G,C stacks. The two strands can come apart – a process known as melting – to form two ss DNA molecules. Melting occurs when conditions favor ssDNA; such conditions are high temperature, low salt and high pH (low pH also melts DNA, but since DNA is unstable due to acid depurination, low pH is rarely used).
The stability of the dsDNA form depends not only on the GC-content (% G,C basepairs) but also on sequence (since stacking is sequence specific) and also length (longer molecules are more stable). The stability can be measured in various ways; a common way is the "melting temperature", which is the temperature at which 50% of the ds molecules are converted to ss molecules; melting temperature is dependent on ionic strength and the concentration of DNA.
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|bibcode = 1999PNAS...96.7853C }}</ref> In biology, parts of the DNA double helix that need to separate easily, such as the TATAAT [[Pribnow box]] in some [[promoter (biology)|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 {{Anchor|ssDNA}}single-stranded DNA molecules (''ssDNA'') 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 |pmc=525685}}</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>
[[File:A-DNA, B-DNA and Z-DNA.png|thumb|right|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]], [[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 Crystallogr |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 Crystallogr |volume=6 |issue=8–9 |pages=678–85 |year=1953|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| issue=4356 | bibcode=1953Natur.171..740F}}</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| issue=4356 | bibcode=1953Natur.171..738W}}</ref> In the same journal, [[James D. Watson]] and [[Francis 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 Crystallogr A |volume=34 |issue=5 |pages=751–753|year=1978|doi=10.1107/S0567739478001540|bibcode = 1978AcCrA..34..751B }}</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<45::AID-BIP4>3.0.CO;2-# }}</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 |bibcode = 2002PNAS...9916666O }}</ref>
===Alternate DNA chemistry===
For a number of years exobiologists have proposed the existence of a [[shadow biosphere]], a postulated microbial biosphere of Earth that uses radically different biochemical and molecular processes than currently known life. One of the proposals was the existence of lifeforms that use [[Arsenic DNA|arsenic instead of phosphorus in DNA]].
A December 2010 [[NASA]] press conference stated that the [[bacterium]] [[GFAJ-1]], which has evolved in an arsenic-rich environment, is the first terrestrial lifeform found which may have this ability. The bacterium was found in [[Mono Lake]], east of [[Yosemite National Park]]. GFAJ-1 is a [[Rod-shaped bacteria|rod]]-shaped [[extremophile]] bacterium in the family [[Halomonadaceae]] that, when starved of [[phosphorus]], may be capable of incorporating the usually poisonous element [[arsenic]] in its DNA.<ref name='arsenic extremophile'>{{cite news | first = Jason Palmer | title = Arsenic-loving bacteria may help in hunt for alien life | date = December 2, 2010 | url = http://www.bbc.co.uk/news/science-environment-11886943 | work = BBC News | accessdate = 2010-12-02}}</ref> This discovery may lend weight to the long-standing idea that [[life on other planets|extraterrestrial life]] could have a [[Hypothetical types of biochemistry|different chemical makeup]] from life on [[Earth]].<ref name='arsenic extremophile'/><ref name=Space>{{cite news | last = Bortman | first = Henry | title = Arsenic-Eating Bacteria Opens New Possibilities for Alien Life | date = 2010-12-02 | publisher = Space.com | url = http://www.space.com/scienceastronomy/arsenic-bacteria-alien-life-101202.html | work = [http://www.space.com/ Space.Com web site] | accessdate = 2010-12-02}}</ref> The research was carried out by a team led by [[Felisa Wolfe-Simon]], a [[geomicrobiologist]] and geobiochemist, a Postdoctoral Fellow of the [[NASA Astrobiology Institute]] with [[Arizona State University]]. This finding has, however, faced strong criticism from the scientific community; scientists have argued that there is no evidence that arsenic is actually incorporated into biomolecules.<ref name="Space"/><ref>{{cite news | first = Alla Katsnelson | title = Arsenic-eating microbe may redefine chemistry of life | date = 2 December 2010 | url = http://www.nature.com/news/2010/101202/full/news.2010.645.html | work = Nature News | accessdate = 2010-12-02}}</ref> Independent conformation of this finding has also not yet been possible.
===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 | 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 | journal=Genes Dev |volume=11 |issue=21 | pages=2801–9 |year=1997 |pmid=9353250 |doi=10.1101/gad.11.21.2801 |pmc=316649}}</ref>
[[File:Parallel telomere quadruple.png|thumb|right|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>]]
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}}</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/>
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<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|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.
===Vibration===
DNA may carry out [[Low-frequency collective motion in proteins and DNA|low-frequency]] collective motion as observed by the [[Raman spectroscopy]]<ref name="pmid7115900">{{cite journal | author = Painter PC, Mosher LE, Rhoads C | title = Low-frequency modes in the Raman spectra of proteins | journal = Biopolymers | volume = 21 | issue = 7 | pages = 1469–72 | year = 1982 | pmid = 7115900 | doi = 10.1002/bip.360210715}}</ref><ref name="Urabe_1983">{{cite journal | author = Urabe H, Tominaga Y, Kubota K | title = Experimental evidence of collective vibrations in DNA double helix (Raman spectroscopy) | journal = Journal of Chemical Physics | year=1983 | volume = 78 | pages = 5937–5939 | doi = 10.1063/1.444600|bibcode = 1983JChPh..78.5937U | issue = 10 }}</ref> and analyzed with a quasi-continuum model.<ref name="pmid6466317">{{cite journal | author = Chou KC | title = Low-frequency vibrations of DNA molecules | journal = Biochem. J. | volume = 221 | issue = 1 | pages = 27–31 | year = 1984| pmid = 6466317 | pmc = 1143999}}</ref><ref name="pmid2775828">{{cite journal | author = Chou KC, Maggiora GM, Mao B | title = Quasi-continuum models of twist-like and accordion-like low-frequency motions in DNA | journal = Biophys. J. | volume = 56 | issue = 2 | pages = 295–305 | year = 1989| pmid = 2775828 | pmc = 1280479 | doi = 10.1016/S0006-3495(89)82676-1 | bibcode=1989BpJ....56..295C}}</ref>
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