Spatial configuration of polynucleotide chains. II. Conformational energies and the average dimensions of polyribonucleotides

Abstract

AbstractConformational energies are calculated for pairs of successive bond rotations within an internal residue of a polyribonucleotide chain. Contributions to these energies include bond torsional strain, van der Waals repulsions, London attractions, electrostatic interactions, and inductive interactions between nonbonded atoms in the nucleotide repeat unit. The average dimensions of unperturbed random‐coil polyribonucleotide chains are then evaluated on the basis of energies thus estimated, using for this purpose the previously developed virtual bond treatment. The characteristic ratio \documentclass{article}\pagestyle{empty}\begin{document}$ C_\infty = \mathop {{\rm lim}}\limits_{n \to \infty } (\langle r^2 \rangle_0/nl^2) $\end{document} of the mean‐square end‐to‐end distance calculated for polyribonucleotide chains in which all pentose rings are fixed in a C3′‐endo conformation is ≈9; for chains consisting exclusively of C2′‐endo units it is ≈25. These values are considerably greater than those obtained by giving equal weight to all conformations judged to be sterically allowed. Satisfactory agreement between the calculations here and experimental values from viscosity and light‐scattering studies is achieved by treating the chain as a random copolymer of C3′‐endo and C2′‐endo conformational isomers. The critical dependence of the characteristic ratio on the rotation about bond C3′–O3′ in the C2′‐endo chain, however, obscures the interpretation of chain dimensions. The chain is also treated in higher approximation as a sequence of independent repeat units, each of which consists of six chemical bonds. The characteristic ratio obtained in this manner is 6.5 for the C3′‐endo chain and 18.5 for the C2′‐endo chain. Finally, the effects of partially stacked conformations in polyribonucleotides are investigated using the virtual bond treatment. Chain dimensions are calculated for random coil poly rA chains in which stacking is introduced by both noncooperative and cooperative processes.