Abstract
The solution structure and hydration of a DNA•RNA hybrid chimeric duplex [d(CGC)r(a m a m a m )d(TTTGCG)] 2 in which the RNA adenines were substituted by 2′-O-methylated riboadenines was determined using two-dimensional NMR, simulated annealing, and restrained molecular dynamics. Only DNA residue 7T in the 2′-OMe-RNA•DNA junction adopted an O4′-endo sugar conformation, while the other DNA residues including 3C in the DNA•2′-OMe-RNA junction, adopted C1′-exo or C2′-endo conformations. The observed NOE intensity of 2′-O-methyl group to H1′ proton of 4a m at the DNA•2′-OMe-RNA junction is much weaker than those of 5a m and 6a m . The 2′-O-methyl group of 4a m was found to orient towards the minor groove in the trans domain while the 2′-O-methyl groups of 5a m and 6a m were found to be in the gauche (+) domain. In contrast to the long-lived water molecules found close to the RNA adenine H2 and H1′ protons and the methyl group of 7T in the RNA-DNA junction of [d(CGC)r(aaa)d(TTTGCG)] 2 , there were no long-lived water molecules found in [d(CGC)r(a m a m a m )d(TTTGCG)] 2 . This is probably due to the hydrophobic environment created by the 2′-O-methylated riboadenines in the minor groove or due to the wider minor groove width in the middle of the structure. In addition, the 2′-O-methylation of riboadenines in pure chimeric duplex increses its melting temperature from 48.5°C to 51.9°C. The characteristic structural features and hydration patterns of this chimeric duplex provide a molecular basis for further therapeutic applications of DNA•RNA hybrid and chimeric duplexes with 2′-modified RNA residues.