title: Conformational flexibility of dinucleoside dimers during unwinding from the B-form to an intercalation structure.
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.
mesh_terms: D001482:Base Composition; D001483:Base Sequence; D002151:Calorimetry; D055598:Chemical Phenomena; D002621:Chemistry; D004247:DNA; D009690:Nucleic Acid Conformation; D009705:Nucleosides; D013329:Structure-Activity Relationship; D013816:Thermodynamics
chemical_list: D009705:Nucleosides; C028270:dinucleoside dimers; D004247:DNA