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.
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.
Comparison geometries of the most common DNA forms
|Repeating unit||1 bp||1 bp||2 bp|
|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||anti||anti||pyrimidine: anti,|
|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,|
|Diameter||23 Å (2.3 nm)||20 Å (2.0 nm)||18 Å (1.8 nm)|
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 a rod-shaped virus.
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 ("crunched") 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.
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