3D structure stability of RNA hairpin controlled by loop size

摘要

The thermodynamic stability of RNAs, which is important for unravelling structure-function relationships for RNAs, can be controlled by loops. To predict RNA 3D structure and stability, we have previously proposed a three-bead coarse-grained model. In this work, we further employ the model to predict the stability of RNA hairpins with different lengths of hairpin loops in monovalent/divalent ion solutions. The melting temperatures for the hairpins predicted by the present model are in correspondence with the extensive experiments. Our results suggest that RNA hairpin stability decreases with the length of hairpin loops, and the change is slowed down gradually as the increases of ion concentration and loop-size.