Conformational statistics of short RNA chains

The conformational statistics of short ribonucleic acid (RNA) chains have been investigated by a Monte Carlo approach that includes effects due to base-base stacking interations. Using oligoadenylate chains up to ten residues in length as a model, we have determined the dependence of the radial distribution functions and its second moments 〈R_N ²〉 and 〈S_N2〉, the mean square end-to-end distance and radius of gyration respectively, on temperature, due to these stacking interactions. Assuming a helical geometry for stacked residues and different possible coil geometries corresponding to unstacked residues, we find that when stacking is present at low temperatures, the chains are severely non-Gaussian for N ≤ 10, while at high temperatures where stacking interactions diminish, chains are substantially Gaussian for N ≥ 5 residues. Distribution functions for chains with termini constrained to fixed distances have been estimated, in order to permit evaluation of the probability for loop closure of different kinds in short chains. The results are in reasonable agreement with experimental values for short hairpin RNA structures, and predict enthalpic contributions arising from stacking interactions in the process of forming loops from small chains.