A-DNA
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. 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 per turn, and smaller rise per base pair. 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.Comparison geometries of the most common DNA forms
| 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 | 3.4 Å | 3.7 Å |
| Rise/turn of helix | 28.6 Å | 35.7 Å | 45.6 Å |
| Mean propeller twist | +18° | +16° | 0° |
| 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 | 20 Å | 18 Å |
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. 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, including rod-shaped rudivirus SIRV2, enveloped filamentous lipothrixviruses AFV1 and SFV1, tristromavirus PFV2 as well as icosahedral portoglobovirus SPV1. 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. 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 A-form intermediate. 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.