A-DNA
A-DNA is one of the possible double helical structures which DNA can adopt. ADNA 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.
Contents
Structure
Comparison geometries of the most common DNA forms
Biological function
Play media
The A-DNA structure.
See also
References
External links
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 BDNA.[2]
Comparison geometries of the most common DNA forms
Geometry attribute:
Helix sense
Repeating unit
A-form
B-form
Z-form
righthanded
righthanded
lefthanded
1 bp
1 bp
2 bp
32.7°
34.3°
60°/2
11
10.5
12
+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)
+18°
+16°
0°
Rotation/bp
Mean bp/turn
Inclination of bp to axis
Mean propeller twist
Glycosyl angle
Nucleotide phosphate to
phosphate distance
Sugar pucker
anti
anti
pyrimidine:
anti,
purine:
syn
5.9 Å
7.0 Å
C: 5.7 Å,
G: 6.1 Å
C2'-endo
C: C2'endo,
G: C3'endo
C3'-endo
Diameter
23 Å
(2.3 nm)
20 Å
(2.0 nm)
Side and top view of A-, B-, and ZDNA conformations.
18 Å
(1.8 nm)
Biological function
Yellow dots represent the location of the
helical axis of A-, B-, and Z-DNA with
respect to a Guanine-Cytosine base pair.
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. Rosalind, Franklin (1953). "The Structure of Sodium Thymonucleate Fibres. I. The Influence of Water Content" (h
ttp://journals.iucr.org/q/issues/1953/08-09/00/a00979/a00979.pdf) (PDF). Acta Crystallographica. 6 (8): 673–677.
doi:10.1107/s0365110x53001939 (https://doi.org/10.1107%2Fs0365110x53001939).
2. Dickerson, Richard E. (1992). DNA Structure From A to Z (https://ac.els-cdn.com/0076687992110076/1-s2.0-007
6687992110076-main.pdf?_tid=53e46970-aa00-11e7-8a59-00000aacb361&acdnat=1507230584_5ff12415fca4b
560400edc52c588d063) (PDF). Methods in Enzymology. 211. pp. 67–111. doi:10.1016/0076-6879(92)11007-6
(https://doi.org/10.1016%2F0076-6879%2892%2911007-6). ISBN 9780121821128. PMID 1406328 (https://www.
ncbi.nlm.nih.gov/pubmed/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" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4208382). J R Soc
Interface. 11 (97): 20140454. doi:10.1098/rsif.2014.0454 (https://doi.org/10.1098%2Frsif.2014.0454).
PMC 4208382 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4208382). PMID 24898023 (https://www.ncbi.nlm.
nih.gov/pubmed/24898023).
4. Di Maio F, Egelman EH, et al. (2015). "A virus that infects a hyperthermophile encapsidates A-form DNA" (https://
www.ncbi.nlm.nih.gov/pmc/articles/PMC5512286). Science. 348 (6237): 914–917. doi:10.1126/science.aaa4181
(https://doi.org/10.1126%2Fscience.aaa4181). PMC 5512286 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC55
12286). PMID 25999507 (https://www.ncbi.nlm.nih.gov/pubmed/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" (https://www.ncbi.nlm.nih.gov/pmc/articles/
PMC4357361). Journal of Structural Biology. 189 (1): 1–8. doi:10.1016/j.jsb.2014.11.012 (https://doi.org/10.101
6%2Fj.jsb.2014.11.012). PMC 4357361 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4357361).
PMID 25486612 (https://www.ncbi.nlm.nih.gov/pubmed/25486612).
6. Oram, M (2008). "Modulation of the packaging reaction of bacteriophage t4 terminase by DNA structure" (https://
www.ncbi.nlm.nih.gov/pmc/articles/PMC2528301). J Mol Biol. 381 (1): 61–72. doi:10.1016/j.jmb.2008.05.074 (htt
ps://doi.org/10.1016%2Fj.jmb.2008.05.074). PMC 2528301 (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2528
301). PMID 18586272 (https://www.ncbi.nlm.nih.gov/pubmed/18586272).
7. Ray, K (2010). "DNA crunching by a viral packaging motor: Compression of a procapsid-portal stalled Y-DNA
substrate" (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2824061). Virology. 398 (2): 224–232.
doi:10.1016/j.virol.2009.11.047 (https://doi.org/10.1016%2Fj.virol.2009.11.047). PMC 2824061 (https://www.ncbi.
nlm.nih.gov/pmc/articles/PMC2824061). PMID 20060554 (https://www.ncbi.nlm.nih.gov/pubmed/20060554).
External links
Cornell Comparison of DNA structures (https://web.archive.org/web/20061219121357/http://www.tulane.edu/~bio
chem/nolan/lectures/rna/bzcomp2.htm)
Nucleic Acid Nomenclature (http://jenalib.fli-leibniz.de/ImgLibDoc/nana/IMAGE_NANA.html)
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