The orientation and dynamics of the C2'-OH and hydration of RNA and DNA RNA hybrids

Abstract

The stereochemical and dynamic properties of the C2' hydroxyl group in several DNA RNA hybrids have been measured by NMR and compared with the homologous RNA duplex. The C2'-OH NMR signals of the RNA strands were identified, and numerous specific assignments were made. The rate constants for exchange of the hydroxyl protons with water were determined at 5°C, and were found to depend on both the position within a particular sequence and the nature of the duplex. On average, the exchange rate constants were slowest for the hybrids of composition rR dY, and fastest for the RNA duplex, with an overall range of ~ 10-50/s. In the DNA RNA hybrids, strong NOEs and ROEs were observed between the OH and the H1' of the same sugar, unambiguously showing that the OH proton points toward the H1' most of the time, and not toward the O3' of the same sugar. Evidence for significant hydration in both grooves of the DNA RNA hybrids and the DNA duplex was found in ROESY and NOESY experiments. On average, the minor groove of the DNA RNA hybrids showed more kinetically significant hydration than the DNA, which can be attributed to the hydrophilic lining of hydroxyl groups in RNA.