B-DNA

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Side and top views of A, B, and Z DNA

B-DNA is one of the possible double helix - structures of DNA .

properties

B-DNA is a right-handed double-stranded DNA double helix, which is more relaxed than the A-form and whose nucleobases are oriented orthogonally to the helix axis. B-DNA is the form of double-stranded DNA that is typically present under physiological conditions, e.g. B. in chromosomes in cells . Other DNA structures are e.g. B. A-DNA , Z-DNA , hairpin, triplex, cruciform, left-handed Z-form, tetraplex and A-motif . Due to the more relaxed shape, B-DNA has a smaller number of nucleobases per turn of the helix, a shallower large groove, a deeper small groove and is about 30% longer per turn than A-DNA.

Double-stranded DNA structures (dsDNA)

B-DNA
Helix axis (yellow dots) in relation to guanidine - cytidine base pairings in A, B and Z DNA
Base pair geometries
geometry A shape B shape Z shape
Helix direction of rotation right-handed right-handed left-handed
Repetition unit 1 bp 1 bp 2 bp
Rotation / bp 33.6 ° 34.6 ° 60 ° / 2
bp / turn 11 10.4 12
Inclination of the bp to the axis + 19 ° −1.2 ° −9 °
Length / bp along the axis 2.4 Å (0.24 nm) 3.4 Å (0.34 nm) 3.7 Å (0.37 nm)
Length / turn 24.6 Å (2.46 nm) 33.2 Å (3.32 nm) 45.6 Å (4.56 nm)
Bend (propeller twist) + 18 ° + 16 ° 0 °
Glycosyl angle anti anti Pyrimidine: anti,
purine: syn
Phosphate spacing 5.9 Å 7.0 Å C: 5.7 Å,
G: 6.1 Å
Glycosyl flexibility (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)

literature

  • E. Girard, T. Prangé, AC Dhaussy, E. Migianu-Griffoni, M. Lecouvey, JC Chervin, M. Mezouar, R. Kahn, R. Fourme: Adaptation of the base-paired double-helix molecular architecture to extreme pressure . In: Nucleic acids research. Volume 35, number 14, 2007, pp. 4800-4808, doi: 10.1093 / nar / gkm511 , PMID 17617642 , PMC 1950552 (free full text).
  • P. Cysewski: The post-SCF quantum chemistry characteristics of inter- and intra-strand stacking interactions in d (CpG) and d (GpC) steps found in B-DNA, A-DNA and Z-DNA crystals. In: Journal of molecular modeling. Volume 15, Number 6, June 2009, pp. 597-606, doi: 10.1007 / s00894-008-0378-9 , PMID 19039609 .

Web links

Individual evidence

  1. ↑ DL Beveridge, TE Cheatham, M. Mezei: The ABCs of molecular dynamics simulations on B-DNA, circa 2012. In: Journal of biosciences. Volume 37, Number 3, July 2012, pp. 379-397, PMID 22750978 , PMC 4029509 (free full text).
  2. ↑ AS Boyer, S. Grgurevic, C. Cazaux, JS Hoffmann: The human specialized DNA polymerases and non-B DNA: vital relationships to preserve genome integrity. In: Journal of molecular biology. Volume 425, number 23, November 2013, pp. 4767-4781, doi: 10.1016 / j.jmb.2013.09.022 , PMID 24095858 .
  3. ↑ J. Choi, T. Majima: Conformational changes of non-B DNA. In: Chemical Society reviews. Volume 40, Number 12, December 2011, pp. 5893-5909, doi: 10.1039 / c1cs15153c , PMID 21901191 .
  4. ↑ MC election, M. Sundaralingam: Crystal structures of A-DNA duplexes. In: Biopolymers. Volume 44, Number 1, 1997, pp. 45-63, PMID 9097733 , doi : 10.1002 / (SICI) 1097-0282 (1997) 44: 1 <45 :: AID-BIP4> 3.0.CO; 2- # .