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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. 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.[1] 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[edit] 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. A- DNA
DNA
is broader and apparently more compressed along its axis than B-DNA.[2] Comparison geometries of the most common DNA
DNA
forms[edit]

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[edit] 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.[3] 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.[4] 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.[5] Experimental evidence for A- DNA
DNA
as an intermediate in viral biomotor packing comes from double dye Förster resonance energy transfer
Förster resonance energy transfer
measurements showing that B- DNA
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
DNA
shortening/lengthening cycle is coupled to a protein- DNA
DNA
grip/release cycle to generate the forward motion that moves DNA
DNA
into the capsid. See also[edit]

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

References[edit]

^ Rosalind, Franklin (1953). "The Structure of Sodium Thymonucleate Fibres. I. The Influence of Water Content" (PDF). Acta Crystallographica. 6: 673–677. doi:10.1107/s0365110x53001939.  ^ Dickerson, Richard E. (1992). " DNA
DNA
Structure From A to Z" (PDF). Methods in Enzymology. 211: 67–111 – via Elsevier Science Direct.  ^ 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. doi:10.1098/rsif.2014.0454. PMC 4208382 . PMID 24898023.  ^ Di Maio F, Egelman EH, et al. (2015). "A virus that infects a hyperthermophile encapsidates A-form DNA". Science. 348: 914–917. doi:10.1126/science.aaa4181. PMC 5512286 . PMID 25999507.  ^ Harvey, SC (2015). "The scrunchworm hypothesis: Transitions between A- DNA
DNA
and B- DNA
DNA
provide the driving force for genome packaging in double-stranded DNA
DNA
bacteriophages". Journal of Structural Biology. 189: 1–8. doi:10.1016/j.jsb.2014.11.012. PMC 4357361 . PMID 25486612.  ^ Oram, M (2008). "Modulation of the packaging reaction of bacteriophage t4 terminase by DNA
DNA
structure". J Mol Biol. 381: 61–72. doi:10.1016/j.jmb.2008.05.074.  ^ Ray, K (2010). " DNA
DNA
crunching by a viral packaging motor: Compression of a procapsid-portal stalled Y- DNA
DNA
substrate". Virology. 398: 224–232. doi:10.1016/j.virol.2009.11.047. 

External links[edit]

Cornell Comparison of DNA
DNA
structures Nucleic Acid Nomenclature

v t e

Types of nucleic acids

Constituents

Nucleobases Nucleosides Nucleotides Deoxynucleotides

Ribonucleic acids (coding, non-coding)

Translational

Messenger

precursor, heterogenous nuclear

Transfer Ribosomal Transfer-messenger

Regulatory

Interferential

Micro Small interfering Piwi-interacting

Antisense Processual

Small nuclear Small nucleolar Small Cajal Body RNAs Y RNA

Enhancer RNAs

Others

Guide Ribozyme Small hairpin Small temporal Trans-acting small interfering Subgenomic messenger

Deoxyribonucleic acids

Complementary Chloroplast Deoxyribozyme Genomic Multicopy single-stranded Mitochondrial

Analogues

Xeno

Glycol Threose Hexose

Locked Peptide Morpholino

Cloning vectors

Phagemid Plasmid Lambda phage Cosmid Fosmid Artificial chromosomes

P1-derived Bac

.