CONFORMATIONAL CHARACTERISTICS OF THE TRINUCLEOSIDE DIPHOSPHATE-D (APAPA) FROM ENERGY-MINIMIZATION STUDIES

Energy‐minimization studies were carried out on the trinucleoside diphosphate d(ApApA). The potential energy contributions from nonbonded, electrostatic, hydrogen‐bonding, and torsional interactions were minimized by treating the 13 relevant dihedral angles as simultaneous variables. For the C(3′)‐endo trimer, 14 low‐energy conformations are within 10 kcal/mol above the lowest energy found, compared to only 3 in the case of the C(2′)‐endo trimer. This result shows the flexible character of the C(3′)‐endo unit. The hairpin‐type, loop‐promoting conformer with (ω′,ω) = (101°, 59°) was found to be the most favored structure at the 3′‐terminus of d(ApApA). The predicted U‐ and L‐type bend conformers were found to lie within 5 kcal/mol, compared to the lowest energy B‐DNA structure. The A‐DNA and Watson‐Crick DNA types of helical conformers also lie within very small energy barriers. The phosphate group at the 5′‐end of the nucleotide residue has a definite influence on the base of the corresponding nucleotide, keeping it in the normal anti‐region, and hence on the base‐stacking property. The results are compared with the presently available experimental data, mainly with the tRNAPhe crystal. Copyright © 1979 John Wiley & Sons, Inc.