A-DNA

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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.

Contents

Structure

Like the more common B-DNA, A-DNA 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. This results in a smaller twist angle, and smaller rise per base pair, so that A-DNA is 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 more compressed along its axis than B-DNA. [2] [3]

The identifiable characteristic of A-DNA X-ray crystallography is the hole in the center. [2] A-DNA has a C3'-endo pucker, which refers to the C3' carbon in the furanose ring being below the sugar plane.

Comparison geometries of the most common DNA forms

Side and top view of A-, B-, and Z-DNA conformations. Dnaconformations.png
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. B&Z&A DNA formula.svg
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-formB-formZ-form
Helix senseright-handedright-handedleft-handed
Repeating unit1 bp1 bp2 bp
Rotation/bp32.7°34.3°60°/2
Mean bp/turn111012
Inclination of bp to axis+19°−1.2°−9°
Rise/bp along axis2.6 Å (0.26 nm)3.4 Å (0.34 nm)3.7 Å (0.37 nm)
Rise/turn of helix28.6 Å (2.86 nm)35.7 Å (3.57 nm)45.6 Å (4.56 nm)
Mean propeller twist+18°+16°0°
Glycosyl angleantiantipyrimidine: anti,
purine: syn
Nucleotide phosphate to phosphate distance5.9 Å7.0 ÅC: 5.7 Å,
G: 6.1 Å
Sugar puckerC3'-endoC2'-endoC: C2'-endo,
G: C3'-endo
Diameter23 Å (2.3 nm)20 Å (2.0 nm)18 Å (1.8 nm)

A/B intermediates

Research also indicates that A-form DNA can hybridize with the more common B-DNA. These A-B intermediate forms adopt the sugar pucker properties and/or the base conformation of both DNA forms. In one study, the characteristic C3'-endo pucker is found on the first three sugars of the DNA strand, while the last three sugars have a C2'-endo pucker, like B-DNA. [2] These intermediates can form in aqueous solutions when the cytosine bases are methylated or brominated, altering the conformation. Alternatively, guanine and cytosine rich fragments have been shown to be easily converted from B to A-form in aqueous solutions. [4]

Biological function

A-DNA can be derived from a few processes, including dehydration and protein binding. Dehydration of DNA drives it into the A form, which has been shown to protect DNA under conditions such as the extreme desiccation of bacteria. [5] [1] 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. These viruses include rod-shaped rudiviruses SIRV2 [6] and SSRV1, [7] enveloped filamentous lipothrixviruses AFV1, [8] SFV1 [9] and SIFV, [7] tristromavirus PFV2 [10] as well as icosahedral portoglobovirus SPV1. [11] 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. [12] 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. [13] [14] 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

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References

  1. 1 2 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. 1 2 3 Dickerson, Richard E. (1992). "DNA structure from a tkjko Z". DNA Structures Part A: Synthesis and Physical Analysis of DNA. Methods in Enzymology. Vol. 211. pp. 67–111. doi:10.1016/0076-6879(92)11007-6. ISBN   9780121821128. PMID   1406328.
  3. ↑ Cox, Michael M. (2015). Molecular biology : principles and practice. Jennifer A. Doudna, Michael O'Donnell (Second ed.). New York. ISBN   978-1-4641-2614-7. OCLC   905380069.
  4. ↑ Trantı́rek, Lukáš; Štefl, Richard; Vorlı́čková, Michaela; Koča, Jaroslav; Sklenářář, Vladimı́r; Kypr, Jaroslav (2000-04-07). "An A-type double helix of DNA having B-type puckering of the deoxyribose rings11Edited by I. Tinoco". Journal of Molecular Biology. 297 (4): 907–922. doi:10.1006/jmbi.2000.3592. ISSN   0022-2836. PMID   10736226.
  5. ↑ 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.
  6. ↑ Di Maio F, Egelman EH, et al. (2015). "A virus that infects a hyperthermophile encapsidates A-form DNA". Science. 348 (6237): 914–917. Bibcode:2015Sci...348..914D. doi:10.1126/science.aaa4181. PMC   5512286 . PMID   25999507.
  7. 1 2 Wang, F; Baquero, DP; Beltran, LC; Su, Z; Osinski, T; Zheng, W; Prangishvili, D; Krupovic, M; Egelman, EH (5 August 2020). "Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments". Proceedings of the National Academy of Sciences of the United States of America. 117 (33): 19643–19652. doi: 10.1073/pnas.2011125117 . PMC   7443925 . PMID   32759221.
  8. ↑ Kasson, P; DiMaio, F; Yu, X; Lucas-Staat, S; Krupovic, M; Schouten, S; Prangishvili, D; Egelman, EH (2017). "Model for a novel membrane envelope in a filamentous hyperthermophilic virus". eLife. 6: e26268. doi:10.7554/eLife.26268. PMC   5517147 . PMID   28639939.
  9. ↑ Liu, Y; Osinski, T; Wang, F; Krupovic, M; Schouten, S; Kasson, P; Prangishvili, D; Egelman, EH (2018). "Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile". Nature Communications. 9 (1): 3360. Bibcode:2018NatCo...9.3360L. doi:10.1038/s41467-018-05684-6. PMC   6105669 . PMID   30135568.
  10. ↑ Wang, F; Baquero, DP; Su, Z; Osinski, T; Prangishvili, D; Egelman, EH; Krupovic, M (2020). "Structure of a filamentous virus uncovers familial ties within the archaeal virosphere". Virus Evolution. 6 (1): veaa023. doi:10.1093/ve/veaa023. PMC   7189273 . PMID   32368353.
  11. ↑ Wang, F; Liu, Y; Su, Z; Osinski, T; de Oliveira, GAP; Conway, JF; Schouten, S; Krupovic, M; Prangishvili, D; Egelman, EH (2019). "A packing for A-form DNA in an icosahedral virus". Proceedings of the National Academy of Sciences of the United States of America. 116 (45): 22591–22597. doi: 10.1073/pnas.1908242116 . PMC   6842630 . PMID   31636205.
  12. ↑ 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.
  13. ↑ 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.
  14. ↑ 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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