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Nucleic Acids Research, 1980, Vol. 8, No. 22 5289-5304
© 1980

CHEMISTRY

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

D. Malhotra and A.J. Hopfinger

Department of Macromolecular Science, Case Western Reserve University Cleveland, OH 44106, USA

Received August 21, 1980. Intra-dinucleoside diner 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 structure 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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