A-DNA

Like the more common B-DNA, A-DNA is a right-handed double helix with major and minor grooves. However, as shown in the comparison table below, there is a slight increase in the number of base pairs (bp) per turn. This results in a smaller twist angle, and smaller rise per base pair, so that A-DNA is 20-25% shorter than B-DNA. The major groove of A-DNA is deep and narrow, while the minor groove is wide and shallow. A-DNA is broader and more compressed along its axis than B-DNA.{{Cite book |chapter-url=https://archive.org/details/dnastructures0000unse/page/67 |doi=10.1016/0076-6879(92)11007-6 |pmid=1406328 |isbn=9780121821128|chapter=DNA structure from a tkjko Z |title=DNA Structures Part A: Synthesis and Physical Analysis of DNA |series=Methods in Enzymology |year=1992 |last1=Dickerson |first1=Richard E. |volume=211 |pages=67–111 }}{{Cite book |last=Cox |first=Michael M. |url=https://www.worldcat.org/oclc/905380069 |title=Molecular biology : principles and practice |date=2015 |others=Jennifer A. Doudna, Michael O'Donnell |isbn=978-1-4641-2614-7 |edition=Second |location=New York |oclc=905380069}}

The identifiable characteristic of A-DNA X-ray crystallography is the hole in the center. A-DNA has a C3'-endo pucker, which refers to the C3' carbon in the furanose ring being below the sugar plane.

Image:Dnaconformations.png

Image:B&Z&A DNA formula.svg

Research also indicates that A-form DNA can hybridize with the more common B-DNA. These A-B intermediate forms adopt the sugar pucker properties and/or the base conformation of both DNA forms. In one study, the characteristic C3'-endo pucker is found on the first three sugars of the DNA strand, while the last three sugars have a C2'-endo pucker, like B-DNA. These intermediates can form in aqueous solutions when the cytosine bases are methylated or brominated, altering the conformation. Alternatively, guanine and cytosine rich fragments have been shown to be easily converted from B to A-form in aqueous solutions.{{Cite journal |last1=Trantı́rek |first1=Lukáš |last2=Štefl |first2=Richard |last3=Vorlı́čková |first3=Michaela |last4=Koča |first4=Jaroslav |last5=Sklenářář |first5=Vladimı́r |last6=Kypr |first6=Jaroslav |date=2000-04-07 |title=An A-type double helix of DNA having B-type puckering of the deoxyribose rings11Edited by I. Tinoco |url=https://www.sciencedirect.com/science/article/pii/S0022283600935927 |journal=Journal of Molecular Biology |language=en |volume=297 |issue=4 |pages=907–922 |doi=10.1006/jmbi.2000.3592 |pmid=10736226 |issn=0022-2836}}

A-DNA can be derived from a few processes, including dehydration and protein binding. Dehydration of DNA drives it into the A form, which has been shown to protect DNA under conditions such as the extreme desiccation of bacteria.{{cite journal |vauthors=Whelan DR, et al. |title=Detection of an en masse and reversible B- to A-DNA conformational transition in prokaryotes in response to desiccation |journal=J R Soc Interface |volume=11 |issue=97 |pages=20140454 |year=2014 |pmid=24898023 |doi=10.1098/rsif.2014.0454 |pmc=4208382}} Protein binding can also strip solvent off of DNA and convert it to the A form, as revealed by the structure of several hyperthermophilic archaeal viruses. These viruses include rod-shaped rudiviruses SIRV2 {{cite journal |vauthors=Di Maio F, Egelman EH, et al. |title=A virus that infects a hyperthermophile encapsidates A-form DNA |journal=Science |volume=348 |issue=6237 |pages=914–917 |year=2015 |pmid=25999507 |doi=10.1126/science.aaa4181|pmc=5512286|bibcode=2015Sci...348..914D }} and SSRV1,{{cite journal |last1=Wang |first1=F |last2=Baquero |first2=DP |last3=Beltran |first3=LC |last4=Su |first4=Z |last5=Osinski |first5=T |last6=Zheng |first6=W |last7=Prangishvili |first7=D |last8=Krupovic |first8=M |last9=Egelman |first9=EH |title=Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments |journal=Proceedings of the National Academy of Sciences of the United States of America |date=5 August 2020 |volume=117 |issue=33 |pages=19643–19652 |doi=10.1073/pnas.2011125117 |pmid=32759221|pmc=7443925 |bibcode=2020PNAS..11719643W |doi-access=free }} enveloped filamentous lipothrixviruses AFV1,{{cite journal |last1=Kasson |first1=P |last2=DiMaio |first2=F |last3=Yu |first3=X |last4=Lucas-Staat |first4=S |last5=Krupovic |first5=M |last6=Schouten |first6=S |last7=Prangishvili |first7=D |last8=Egelman |first8=EH |title=Model for a novel membrane envelope in a filamentous hyperthermophilic virus |journal=eLife |date=2017 |volume=6 |pages=e26268 |doi=10.7554/eLife.26268 |pmid=28639939|pmc=5517147 |doi-access=free }} SFV1 {{cite journal |last1=Liu |first1=Y |last2=Osinski |first2=T |last3=Wang |first3=F |last4=Krupovic |first4=M |last5=Schouten |first5=S |last6=Kasson |first6=P |last7=Prangishvili |first7=D |last8=Egelman |first8=EH |title=Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile |journal=Nature Communications |date=2018 |volume=9 |issue=1 |pages=3360 |doi=10.1038/s41467-018-05684-6 |pmid=30135568|pmc=6105669 |bibcode=2018NatCo...9.3360L }} and SIFV, tristromavirus PFV2 {{cite journal |last1=Wang |first1=F |last2=Baquero |first2=DP |last3=Su |first3=Z |last4=Osinski |first4=T |last5=Prangishvili |first5=D |last6=Egelman |first6=EH |last7=Krupovic |first7=M |title=Structure of a filamentous virus uncovers familial ties within the archaeal virosphere |journal=Virus Evolution |date=2020 |volume=6 |issue=1 |pages=veaa023 |doi=10.1093/ve/veaa023 |pmid=32368353|pmc=7189273 }} as well as icosahedral portoglobovirus SPV1.{{cite journal |last1=Wang |first1=F |last2=Liu |first2=Y |last3=Su |first3=Z |last4=Osinski |first4=T |last5=de Oliveira |first5=GAP |last6=Conway |first6=JF |last7=Schouten |first7=S |last8=Krupovic |first8=M |last9=Prangishvili |first9=D |last10=Egelman |first10=EH |title=A packing for A-form DNA in an icosahedral virus |journal=Proceedings of the National Academy of Sciences of the United States of America |date=2019 |volume=116 |issue=45 |pages=22591–22597 |doi=10.1073/pnas.1908242116 |pmid=31636205|pmc=6842630 |bibcode=2019PNAS..11622591W |doi-access=free }} A-form DNA is believed to be one of the adaptations of hyperthermophilic archaeal viruses to harsh environmental conditions in which these viruses thrive.

It has been proposed that the motors that package double-stranded DNA in bacteriophages exploit the fact that A-DNA is shorter than B-DNA, and that conformational changes in the DNA itself are the source of the large forces generated by these motors.{{cite journal |author=Harvey, SC |title=The scrunchworm hypothesis: Transitions between A-DNA and B-DNA provide the driving force for genome packaging in double-stranded DNA bacteriophages |journal=Journal of Structural Biology |volume=189 |issue=1 |pages=1–8 |year=2015 |pmid=25486612 |doi=10.1016/j.jsb.2014.11.012 |pmc=4357361}} Experimental evidence for A-DNA as an intermediate in viral biomotor packing comes from double dye Förster resonance energy transfer measurements showing that B-DNA is shortened by 24% in a stalled ("crunched") A-form intermediate.{{cite journal |author=Oram, M |title=Modulation of the packaging reaction of bacteriophage t4 terminase by DNA structure |journal=J Mol Biol |volume=381 |issue=1 |pages=61–72 |year=2008 |doi=10.1016/j.jmb.2008.05.074|pmid=18586272 |pmc=2528301 }}{{cite journal |author=Ray, K |title=DNA crunching by a viral packaging motor: Compression of a procapsid-portal stalled Y-DNA substrate |journal=Virology |volume=398 |issue=2 |pages=224–232 |year=2010 |doi=10.1016/j.virol.2009.11.047|pmid=20060554 |pmc=2824061 }} In this model, ATP hydrolysis is used to drive protein conformational changes that alternatively dehydrate and rehydrate the DNA, and the DNA shortening/lengthening cycle is coupled to a protein-DNA grip/release cycle to generate the forward motion that moves DNA into the capsid.

• Nucleic acid tertiary structure
• DNA
• B-DNA
• Z-DNA
• C-DNA

{{reflist}}

• [https://web.archive.org/web/20061219121357/http://www.tulane.edu/~biochem/nolan/lectures/rna/bzcomp2.htm Cornell Comparison of DNA structures]
• [http://jenalib.fli-leibniz.de/ImgLibDoc/nana/IMAGE_NANA.html Nucleic Acid Nomenclature]

{{Nucleic acids}}

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