Hydration of [d(CGC)r(aaa)d(TTTGCG)](2)

We have studied the hydration and dynamics of RNA C2'-OH in a DNA.RNA hybri d chimeric duplex [d(CGC)r(aaa)d(TTTGCG)](2). Long-lived water molecules wi th correlation time tau(c) larger than 0.3 ns were found close to the RNA a denine H2 and H1' protons in the hybrid segment. A possible long-lived wate r molecule was also detected close to the methyl group of 7T in the RNA-DNA junction but not to the other two thymine bases (8T and 9T). This result c orrelates with the structural studies that only DNA residue 7T in the RNA-D NA junction adopts an O4'-endo sugar conformation (intermediate between B-f orm and A-form), while the other DNA residues including 3C in the DNA-RNA j unction, adopt C1'-exo or C2'-endo conformations (in the B-form domain). Ba sed on the NOE cross-peak patterns, we have found that RNA C2'-OH tends to orient toward the O3' direction, forming a possible hydrogen bond with the 3'-phosphate group. The exchange rates for RNA C2'-OH were found to be arou nd 5-20 s(-1), compared to 26.7(+/-13.8)s(-1) reported previously for the o ther DNA RNA hybrid duplex. This slow exchange rate may be due to the narro w minor groove width of [d (CGC)r(aaa) d(TTTGCG)](2), which may trap the wa ter molecules and restrict the dynamic motion of hydroxyl protons. The dist inct hydration patterns of the RNA adenine H2 and H1' protons and the DNA 7 T methyl group in the hybrid segment, as well as the orientation and dynami cs of the RNA C2'-OH protons, may provide a molecular basis for further und erstanding the structure and recognition of DNA.RNA hybrid and chimeric dup lexes. (C) 2000 Academic Press.