Direct Revelation of Multiple Conformations in RNA by Femtosecond Dynamics

摘要

The intrinsic dynamics of RNA structures occur on a wide range of length and time scales, implying structural flexibility or heterogeneity. The role of conformational dynamics in molecular recognition and functions, however, is not well understood. Despite significant advances in traditional and new spectroscopic methodologies, it is still difficult to extract information on both the exact nature of the heterogeneous conformations and their quantitative distributions. Here we demonstrate a femtosecond dynamics approach for probing the multiple conformations coexisting in RNAs. We focus primarily on mapping the base stacking patterns. The observed base stacking/ unstacking rates in the single strand are typically in the range of 100—500 ns. This means that, for a time window much shorter than the nanosecond regime, the distributions of stacking patterns are static and can potentially be analyzed by ultrafast spectroscopy.