Nucleic Acids Research, Vol 26, Issue 13 3104-3110, Copyright © 1998 by Oxford University Press
JI Gyi, AN Lane, GL Conn and T Brown
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
degrees 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 approximately 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.
ARTICLES
The orientation and dynamics of the C2'-OH and hydration of RNA and DNA.RNA hybrids
Division of Molecular Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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