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Simulation of conformational possibilities of DNA via calculation of nonbonded interactions of complementary dinucleoside phosphate complexes
Author(s) -
Poltev V. I.,
Milova L. A.,
Zhorov B. S.,
Govyrin V. A.
Publication year - 1981
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/bip.1981.360200102
Subject(s) - dihedral angle , chemistry , molecule , crystallography , bond length , molecular geometry , base (topology) , computational chemistry , dna , chemical physics , hydrogen bond , crystal structure , organic chemistry , mathematical analysis , biochemistry , mathematics
Using 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.