1D75

CONFORMATION OF THE GUANINE.8-OXOADENINE BASE PAIRS IN THE CRYSTAL STRUCTURE OF D(CGCGAATT(O8A)GCG)

Summary for 1D75

• Entry DOI: 10.2210/pdb1d75/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*(A38)P*GP*CP*G)-3') (2 entities in total)
• Functional Keywords: b-dna, double helix, modified, mismatched, dna
• Total number of polymer chains: 2
• Total formula weight: 7406.83

Authors

Leonard, G.A.,Guy, A.,Brown, T.,Teoule, R.,Hunter, W.N. (deposition date: 1992-05-07, release date: 1993-01-15, Last modification date: 2024-02-07)

Primary citation

Leonard, G.A.,Guy, A.,Brown, T.,Teoule, R.,Hunter, W.N.
Conformation of guanine-8-oxoadenine base pairs in the crystal structure of d(CGCGAATT(O8A)GCG).
Biochemistry, 31:8415-8420, 1992

PubMed Abstract: The structure of the synthetic deoxydodecamer d(CGCGAATT(O8A)GCG)2 (O8A = 8-oxoadenine) has been determined by single-crystal X-ray diffraction techniques. The oligonucleotide crystallizes in the orthorhombic space group P2(1)2(1)2(1) with cell dimensions of a = 25.48 A, b = 41.84 A, and c = 64.91 A. The refinement has converged with an R-factor of 0.151 for 1119 reflections in the resolution range 8.0-2.25 A. Sixty-seven solvent molecules were located during the course of the refinement. The B-DNA helix consists of ten Watson-Crick base pairs and two guanine-8-oxoadenine (G.O8A) base pairs. In order to achieve hydrogen-bonding complementarity between the two bases, an unusual G(anti).O8A-(syn) wobble conformation is adopted. It is proposed that the G.O8A mispairs are held together by a network of four interbase hydrogen bonds which are the result of the formation of two reverse three-center hydrogen-bonding systems. These involve one carbonyl oxygen lone pair interacting with two hydrogen atoms. In a departure from previous observations of the characteristics of purine-purine anti-syn base pairs, lambda 1 and lambda 2, the angles between the glycosidic bonds and the C1'-C1' vector, are symmetric. A reassessment of the other purine-purine mispairs suggests that similar three-center hydrogen bonds may occur and make a contribution to stabilizing other base pairings.

PubMed: 1390625
DOI: 10.1021/bi00151a004

Experimental method

X-RAY DIFFRACTION (2.8 Å)