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

, : The orientation and dynamics of the C2'-OH and hydration of RNA and DNAcntdotRNA hybrids. Nucleic Acids Research 26(13): 3104-3110, July 1

The stereochemical and dynamic properties of the C2' hydroxyl group in several DNAcntdotRNA 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 5degreeC, 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 rRcntdotdY, and fastest for the RNA duplex, with an overall range of apprx10-50/s. In the DNAcntdotRNA 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 DNAcntdotRNA hybrids and the DNA duplex was found in ROESY and NOESY experiments. On average, the minor groove of the DNAcntdotRNA hybrids showed more kinetically significant hydration than the DNA, which can be attributed to the hydrophilic lining of hydroxyl groups in RNA.

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