DNA: Ìyàtọ̀ láàrin àwọn àtúnyẹ̀wò

[[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]].]]

 

 

 

[[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]].]]

 

 

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|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.

 

 

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/>

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_m'' 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>

 

{{Further|[[Sense (molecular biology)]]}}

 

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>

 

{{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]]

 

{{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>

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>

 

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.

 

{{Further|[[G-quadruplex]]}}

 

<div style="border: none; width:200px;font-size: 90%;"><div class="thumbcaption">[[Branched DNA]] can form networks containing multiple branches.</div></div></div>

 

{{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.

 

 

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>