THE ORIENTATION AND DYNAMICS OF THE C2'-OH AND HYDRATION OF RNA AND DNA-RNA HYBRIDS

The stereochemical and dynamic properties of the C2' hydroxyl group in several DNA.RNA hybrids have been measured by NMR and compared with t he homologous RNA duplex. The C2'-OH NMR signals of the RNA strands we re identified, and numerous specific assignments were made. The rate c onstants for exchange of the hydroxyl protons with water were determin ed at 5 degrees C, and were found to depend on both the position withi n 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 similar to 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 t hat the OH proton points toward the H1' most of the time, and not towa rd the O3' of the same sugar. Evidence for significant hydration in bo th grooves of the DNA.RNA hybrids and the DNA duplex was found in ROES Y and NOESY experiments. On average, the minor groove of the DNA.RNA h ybrids showed more kinetically significant hydration than the DNA, whi ch can be attributed to the hydrophilic lining of hydroxyl groups in R NA.