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Minimum energy conformations of DNA dimeric subunits: Potential energy calculations for dGpdC, dApdA, dCpdC, dGpdG, and dTpdT
Author(s) -
Broyde S.,
Wartell R. M.,
Stellman S. D.,
Hingerty B.
Publication year - 1978
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.1978.360170608
Subject(s) - conformational isomerism , chemistry , dihedral angle , crystallography , alkane stereochemistry , energy minimization , potential energy , dna , stereochemistry , computational chemistry , molecule , atomic physics , hydrogen bond , crystal structure , physics , biochemistry , organic chemistry
Minimum energy conformations have been calculated for the deoxydinucleoside phosphates dGpdC, dApdA, dCpdC, dGpdG, and dTpdT. In these potential energy calculations the eight diheldral angles and the sugar pucker were flexible parameters. A substantial survey of conformation space was made in which all staggred combination ofthe dihedral angles ω′,ω, and ψ, in conjuction with C(2′)‐ endo puker, were used as starting conformers for the energy minimization. The most important conformations in the C(3′)‐ endo ‐puckering domain have ψ = g + ; ω′,ω = g − , g − (A‐form), g + , g + , and g − ,t. With C(2′)‐ endo ‐type puker the most important conformations have ψ = g + ; ω′,ω = g _ , g _ (B‐form) and g + ,t; and ψ =t; ω′,ω = g _ ,t(Watson‐Crick from) and t, g + (skewed). Stacked bases are a persistent feature of the low‐energy conformations, the g + conformer being an exception. Freeing the suger puker allowed this conformation to become low energy, with C(3′)‐ exo puker. It also caused other low‐energy forms, such and the Waston‐Crick conformation, to become more favourable. Conformation flexibility in the sugar puker and in ψ, as well as the ω′,ω angle pair, is indicated for the dimeric subunits of DNA.