1VJ4

SEQUENCE-DEPENDENT CONFORMATION OF AN A-DNA DOUBLE HELIX: THE CRYSTAL STRUCTURE OF THE OCTAMER D(G-G-T-A-T-A-C-C)

Summary for 1VJ4

• Entry DOI: 10.2210/pdb1vj4/pdb
• Descriptor: 5'-D(*GP*GP*TP*AP*TP*AP*CP*C)-3' (1 entity in total)
• Functional Keywords: a-dna, double helix, dna
• Total number of polymer chains: 2
• Total formula weight: 4853.23

Authors

Shakked, Z.,Rabinovich, D.,Kennard, O.,Cruse, W.B.,Salisbury, S.A.,Viswamitra, M.A. (deposition date: 1989-01-11, release date: 1989-01-11, Last modification date: 2024-02-14)

Primary citation

Shakked, Z.,Rabinovich, D.,Kennard, O.,Cruse, W.B.,Salisbury, S.A.,Viswamitra, M.A.
Sequence-dependent conformation of an A-DNA double helix: The crystal structure of the octamer d(G-G-T-A-T-A-C-C)
J.Mol.Biol., 166:183-201, 1983

PubMed Abstract: The crystal structures of the synthetic self-complementary octamer d(G-G-T-A-T-A-C-C) and its 5-bromouracil-containing analogue have been refined to R values of 20% and 14% at resolutions of 1.8 and 2.25 A, respectively. The molecules adopt and A-DNA type double-helical conformation, which is minimally affected by crystal forces. A detailed analysis of the structure shows a considerable influence of the nucleotide sequence on the base-pair stacking patterns. In particular, the electrostatic stacking interactions between adjacent guanine and thymine bases produce symmetric bending of the double helix and a major-groove widening. The sugar-phosphate backbone appears to be only slightly affected by the base sequence. The local variations in the base-pair orientation are brought about by correlated adjustments in the backbone torsion angles and the glycosidic orientation. Sequence-dependent conformational variations of the type observed here may contribute to the specificity of certain protein-DNA interactions.

PubMed: 6854642
DOI: 10.1016/S0022-2836(83)80005-9

Experimental method

X-RAY DIFFRACTION (1.8 Å)