1D80

CRYSTAL STRUCTURE OF AN OLIGONUCLEOTIDE DUPLEX CONTAINING G.G BASE-PAIRS: THE INFLUENCE OF MISPAIRING ON DNA BACKBONE CONFORMATION

Summary for 1D80

• Entry DOI: 10.2210/pdb1d80/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*GP*GP*CP*G)-3') (2 entities in total)
• Functional Keywords: b-dna, double helix, mismatched, dna
• Total number of polymer chains: 2
• Total formula weight: 7406.83

Authors

Skelly, J.V.,Edwards, K.J.,Jenkins, T.C.,Neidle, S. (deposition date: 1992-06-17, release date: 1993-07-15, Last modification date: 2024-02-07)

Primary citation

Skelly, J.V.,Edwards, K.J.,Jenkins, T.C.,Neidle, S.
Crystal structure of an oligonucleotide duplex containing G.G base pairs: influence of mispairing on DNA backbone conformation.
Proc.Natl.Acad.Sci.USA, 90:804-808, 1993

PubMed Abstract: The structure of the G.G mispaired dodecanucleotide d(CGCGAATTGGCG)2 has been solved by x-ray crystallography and refined to an R factor of 18.8% at 2.2 A resolution for 3513 reflections. The dodecamer crystallizes as a B-type DNA double helix. It contains two G(anti).G(syn) base pairs--i.e., G-4/G-16(anti).G-21/G-9(syn). The Hoogsteen base pairing involves atoms O-6 and N-7 of the guanine in the syn conformation with atoms N-1 and N-2 of the anti-paired purine. One G.G base pair has a bifurcated hydrogen bond between G-4(N-1)...G-21(N-7) and G-4(N-1)...G-21(O-6). There is little overall structural distortion of the double helix induced as a consequence of the mispairing. The helical width is significantly increased by comparison with the structure of the native duplex, and the minor groove width in the 5'-AATT region is decreased. The G.G base pairing induces high-BII phosphate conformations at residues G-9 and T-20 in addition to more normal BII conformations at G-10 and G-22. It is suggested that these backbone aberrations provide signals for the facile repairability of G.G mispairs in DNA.

PubMed: 8430089
DOI: 10.1073/pnas.90.3.804

Experimental method

X-RAY DIFFRACTION (2.2 Å)