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词条 A-DNA
释义

  1. Structure

  2. Comparison geometries of the most common DNA forms

  3. Biological function

  4. See also

  5. References

  6. External links

A-DNA is one of the possible double helical structures which DNA can adopt. A-DNA is thought to be one of three biologically active double helical structures along with B-DNA and Z-DNA. It is a right-handed double helix fairly similar to the more common B-DNA form, but with a shorter, more compact helical structure whose base pairs are not perpendicular to the helix-axis as in B-DNA. It was discovered by Rosalind Franklin, who also named the A and B forms. She showed that DNA is driven into the A form when under dehydrating conditions. Such conditions are commonly used to form crystals, and many DNA crystal structures are in the A form.[1] The same helical conformation occurs in double-stranded RNAs, and in DNA-RNA hybrid double helices.

Structure

A-DNA is fairly similar to B-DNA given that it 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 (resulting in a smaller twist angle), and smaller rise per base pair (making A-DNA 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 apparently more compressed along its axis than B-DNA.[2]

Comparison geometries of the most common DNA forms

Geometry attribute:A-formB-formZ-form
Helix sense right-handedright-handedleft-handed
Repeating unit 1 bp1 bp2 bp
Rotation/bp 32.7°34.3°60°/2
Mean bp/turn 1110.512
Inclination of bp to axis +19°−1.2°−9°
Rise/bp along axis 2.6 Å (0.26 nm)3.4 Å (0.34 nm)3.7 Å (0.37 nm)
Rise/turn of helix 28.6 Å (2.86 nm)35.7 Å (3.57 nm)45.6 Å (4.56 nm)
Mean propeller twist +18°+16°0°
Glycosyl angle antiantipyrimidine: anti,
purine: syn
Nucleotide phosphate to phosphate distance 5.9 Å7.0 ÅC: 5.7 Å,
G: 6.1 Å
Sugar pucker C3'-endoC2'-endoC: C2'-endo,
G: C3'-endo
Diameter 23 Å (2.3 nm)20 Å (2.0 nm)18 Å (1.8 nm)

Biological function

Dehydration of DNA drives it into the A form, and this apparently protects DNA under conditions such as the extreme desiccation of bacteria.[3] Protein binding can also strip solvent off of DNA and convert it to the A form, as revealed by the structure of a rod-shaped virus.[4]

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.[5] 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.[6][7] 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.

See also

  • Mechanical properties of DNA
  • DNA
  • B-DNA
  • Z-DNA
  • C-DNA

References

1. ^{{Cite journal|last=Rosalind|first=Franklin|date=1953|title=The Structure of Sodium Thymonucleate Fibres. I. The Influence of Water Content|url=http://journals.iucr.org/q/issues/1953/08-09/00/a00979/a00979.pdf|journal=Acta Crystallographica|volume=6|issue=8|pages=673–677|via=|doi=10.1107/s0365110x53001939}}
2. ^{{Cite book|last=Dickerson|first=Richard E.|date=1992|title=DNA Structure From A to Z|url=https://ac.els-cdn.com/0076687992110076/1-s2.0-0076687992110076-main.pdf?_tid=53e46970-aa00-11e7-8a59-00000aacb361&acdnat=1507230584_5ff12415fca4b560400edc52c588d063|journal=Methods in Enzymology|volume=211|pages=67–111|via=Elsevier Science Direct|doi=10.1016/0076-6879(92)11007-6|pmid=1406328|isbn=9780121821128}}
3. ^{{cite journal |vauthors=Whelan DR, etal |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}}
4. ^{{cite journal |vauthors=Di Maio F, Egelman EH, etal |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}}
5. ^{{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}}
6. ^{{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 }}
7. ^{{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 }}

External links

  • [https://web.archive.org/web/20061219121357/http://www.tulane.edu/~biochem/nolan/lectures/rna/bzcomp2.htm Cornell Comparison of DNA structures]
  • Nucleic Acid Nomenclature
{{Nucleic acids}}

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