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The A-DNA structure.

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.


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 formsEdit

Side and top view of A-, B-, and Z-DNA conformations.
Yellow dots represent the location of the helical axis of A-, B-, and Z-DNA with respect to a Guanine-Cytosine base pair.
Geometry attribute: A-form B-form Z-form
Helix sense right-handed right-handed left-handed
Repeating unit 1 bp 1 bp 2 bp
Rotation/bp 32.7° 34.3° 60°/2
Mean bp/turn 11 10 12
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°
Glycosyl angle anti anti pyrimidine: anti,
purine: syn
Nucleotide phosphate to phosphate distance 5.9 Å 7.0 Å C: 5.7 Å,
G: 6.1 Å
Sugar pucker C3'-endo C2'-endo C: C2'-endo,
G: C3'-endo
Diameter 23 Å (2.3 nm) 20 Å (2.0 nm) 18 Å (1.8 nm)

Biological functionEdit

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 alsoEdit


  1. ^ Rosalind, Franklin (1953). "The Structure of Sodium Thymonucleate Fibres. I. The Influence of Water Content" (PDF). Acta Crystallographica. 6 (8): 673–677. doi:10.1107/s0365110x53001939.
  2. ^ Dickerson, Richard E. (1992). DNA Structure From A to Z (PDF). Methods in Enzymology. 211. pp. 67–111. doi:10.1016/0076-6879(92)11007-6. ISBN 9780121821128. PMID 1406328 – via Elsevier Science Direct.
  3. ^ Whelan DR, et al. (2014). "Detection of an en masse and reversible B- to A-DNA conformational transition in prokaryotes in response to desiccation". J R Soc Interface. 11 (97): 20140454. doi:10.1098/rsif.2014.0454. PMC 4208382. PMID 24898023.
  4. ^ Di Maio F, Egelman EH, et al. (2015). "A virus that infects a hyperthermophile encapsidates A-form DNA". Science. 348 (6237): 914–917. doi:10.1126/science.aaa4181. PMC 5512286. PMID 25999507.
  5. ^ Harvey, SC (2015). "The scrunchworm hypothesis: Transitions between A-DNA and B-DNA provide the driving force for genome packaging in double-stranded DNA bacteriophages". Journal of Structural Biology. 189 (1): 1–8. doi:10.1016/j.jsb.2014.11.012. PMC 4357361. PMID 25486612.
  6. ^ Oram, M (2008). "Modulation of the packaging reaction of bacteriophage t4 terminase by DNA structure". J Mol Biol. 381 (1): 61–72. doi:10.1016/j.jmb.2008.05.074. PMC 2528301. PMID 18586272.
  7. ^ Ray, K (2010). "DNA crunching by a viral packaging motor: Compression of a procapsid-portal stalled Y-DNA substrate". Virology. 398 (2): 224–232. doi:10.1016/j.virol.2009.11.047. PMC 2824061. PMID 20060554.

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