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The Info List - A-DNA


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A- DNA
DNA
is one of the possible double helical structures which DNA
DNA
can adopt. A- DNA
DNA
is thought to be one of three biologically active double helical structures along with B- DNA
DNA
and Z- DNA
DNA
. It is a right-handed double helix fairly similar to the more common B- DNA
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
DNA
is driven into the A form when under dehydrating conditions. Such conditions are commonly used to form crystals, and many DNA
DNA
crystal structures are in the A form. The same helical conformation occurs in double-stranded RNAs, and in DNA- RNA
RNA
hybrid double helices.

CONTENTS

* 1 Structure * 2 Comparison geometries of the most common DNA
DNA
forms * 3 Biological function * 4 See also * 5 References * 6 External links

STRUCTURE

A- DNA
DNA
is fairly similar to B- DNA
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
DNA
20-25% shorter than B-DNA). The major groove of A- DNA
DNA
is deep and narrow, while the minor groove is wide and shallow.

COMPARISON GEOMETRIES OF THE MOST COMMON DNA
DNA
FORMS

Side and top view of A-, B-, and Z- DNA
DNA
conformations. Yellow dots represent the location of the helical axis of A-, B-, and Z- DNA
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 10.5 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° 0°

Glycosyl angle anti anti pyrimidine: anti, purine: syn

Nucleotide
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 FUNCTION

Dehydration of DNA
DNA
drives it into the A form, and this apparently protects DNA
DNA
under conditions such as the extreme desiccation of bacteria. Protein binding can also strip solvent off of DNA
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
DNA
is shorter than B-DNA, and that conformational changes in the DNA
DNA
itself are the source of the large forces generated by these motors. Experimental evidence for A- DNA
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
DNA
shortening/lengthening cycle is coupled to a protein-DNA grip/release cycle to generate the forward motion that moves DNA
DNA
into the capsid.

SEE ALSO

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

REFERENCES

* ^ Whelan DR, et al. (2014). "Detection of an en masse and reversible B- to A- DNA
DNA
conformational transition in prokaryotes in response to desiccation" . J R Soc Interface. 11: 20140454. PMC 4208382  . PMID 24898023 . doi :10.1098/rsif.2014.0454 . * ^ Di Maio F, Egelman EH, et al. (2015). "A virus that infects a hyperthermophile encapsidates A-form DNA". Science. 348: 914–917. PMID 25999507 . doi :10.1126/science.aaa4181 . * ^ Harvey, SC (2015). "The scrunchworm hypothesis: Transitions between A- DNA