Structural investigations on small RNA molecules using different force field methods

The structures of two kinds of small RNA hairpin loops were investigated. As an example of four-membered loops the family of GNNA-loops was chosen, and the influence of a variation of the two middle bases on the rather uncommon G-A base pair was examined. Comparison of the resulting structures showed surprisingly little dependence on the sequence for the overall structure and for the G-A base pair geometry. As an example of three-membered loops a systematic investigation on the loop-sequences UUU, AUU, UUA, GUU, UUG was carried out. Here, not only the loop sequence but also the influence of the closing pair was examined. Again the structural variation with different sequences was very small. Both calculations were used to compare the amber 4.0 and the jumna iv force field programs. Though both programs show a quite different approach to modeling RNA structures the resulting geometries are comparable.