Simulation of conformational possibilities of DNA via calculation of nonbonded interactions of complementary dinucleoside phosphate complexes

Abstract

SynopsisUsing classical potential functions, we carried out potential-energy calculations on the complementary deoxydinucleoside phosphate complexes dApdA:dUpdU, dUpdA:dUpdA, and dApdU:dApdU. All dihedral and bond angles, except those of the nitrogen bases, were varied. The resulting minimum-energy conformations of the complexes are close to DNA A-and B-family conformations, with a typical arrangement of the nitrogen bases. The dihedral and bond angles of one of the molecules forming the complex can thereby differ by several degrees from those of the other molecule. For different base sequences, some dihedral and bond angles may vary over a range of several degrees without appreciably changing the total energy of the complex. Some low-energy conformations of the complexes corresponding to other regions of the conformational space are also found. The biological consequences of possible changes in dihedral and bond angles, occurring on interaction with other molecules, are discussed.

Use of a 3D structure data base for understanding sequence-dependent conformational aspects of DNA

“…The electropolarization of the base-pairs has been analyzed but the conclusions are not totally consistent (Stewart, 1970;Ornstein et al, 1978;Zhurkin et al, 1980;Kollman et al, 1981;Poltev et al, 1981;Weiner et al, 1984;Hunter & Sanders 1990;Pearlman & Kim, 1990;Sponer et al, 1996a). Hunter (1993) has concluded that the electrostatic interactions between the neighboring base-pairs would stabilize the stacking in vacuum, while Friedman & Honig (1995) have concluded otherwise in aqueous solution mainly because the stacking would prevent favorable base-solvent electrostatic interactions.…”

A Complete Conformational Map for RNA

“…The relevance of this approach is limited by the completeness of the database used. Other attempts have tried to improve the quality of the conformational maps by including various energy terms (Lakshminarayanan & Sasisekharan, 1969;Sasisekharan & Lakshminarayanan, 1969;Govil & Saran, 1971a,b;Saran & Govil, 1971;Kim et al, 1973;Newton, 1973;Saran et al, 1973a,b;Yathindra & Sundaralingam, 1973;Perahia et al, 1974a,b;Tewari 1974;Govil, 1976;Levitt & Warshel, 1978;Srinivasan et al, 1980;Poltev et al, 1981;Tosi & Lipari, 1981;Pattabiraman & Langridge, 1985;Pearlman & Kim, 1985, 1986b, 1988Gabb & Harvey, 1993;Girlado et al, 1998). Computational limitations continue to prevent comprehensive searching using energy criteria, limiting the signi®cance of the constructed maps to special cases or to model compounds.…”

Possible conformations of double-helical polynucleotides containing incorrect base pairs

“…Within these regions different mutual positions of the base pairs at rather close values of dihedral angles of the sugar-phosphate backbone are possible (8). On the other hand, a search for low-energy conformations of complexes of dinucleoside phosphates has shown that considerable deviations of the double-stranded structure from regularity are, possible without noticeable energy increase (9). This conformational freedom permitted us to hope that incorporation of incorrect base pairs in normal tautomeric forms into the double helix is possible without any considerable distortion of the sugar-phosphate backbone.…”