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. 1980 Nov 25;8(22):5289–5304. doi: 10.1093/nar/8.22.5289

Conformational flexibility of dinucleoside dimers during unwinding from the B-form to an intercalation structure.

D Malhotra, A J Hopfinger
PMCID: PMC324302  PMID: 7465414

Abstract

Intra-dinucleoside dimer conformational energy calculations were performed on a series of conformations corresponding to the unwinding of a dinucleoside dimer from the B-form type structure. Conformational states were characterized in terms of the distance, d, between parallel bases. All 16 possible sequences for (G) and (C) and/or (A) and (T) bases were considered. Both free space, and free space plus aqueous solvation energies were computed. It was found that the B-form like conformer is the most stable structures in free space and in an aqueous medium. However, the energy as function of d is base pair sequence dependent. This sequence dependence suggests a possible inherent specificity for intercalation of the dinucleoside dimer with a drug molecule.

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Selected References

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