SOLUTION STRUCTURE OF AN RNA-CENTER-DOT-2'-O-METHYLATED RNA HYBRID DUPLEX CONTAINING AN RNA-CENTER-DOT-DNA HYBRID SEGMENT AT THE CENTER

The solution structure of an RNA . 2'-O-methylated RNA hybrid duplex c ontaining an RNA . DNA hybrid segment at its center, (ggagaugac).(G(m) U(m)C(m)ATCTC(m)C(m)), where lowercase letters, capital letters, and c apital letters with the subscript m are RNA, DNA, and 2'-O-methylated RNA residues, respectively, was determined by observing the NMR spectr a and performing the full relaxation matrix refinement. The 2'-O-methy lation gives several characteristic features to oligoribonucleotides. In addition, this hybrid duplex is cleaved at a specific position by E scherichia coli ribonuclease HI, and so the role of the tertiary struc ture during the substrate recognition by the enzyme is of interest. Th e NOE connectivities among the proton resonances revealed that the dup lex was a right handed helix. The 2'-O-methylated RNA segments had a t ypical C3'-endo conformation, and the 2'-O-methyl groups were directed to the minor groove of this duplex, taking the torsion angles phi (C1 '-C2'-O2'-CH3) that were all gauche(+). The DNA residues in the centra l RNA . DNA hybrid duplex formed the C3'-endo conformation, except for the middle thymine residue. No remarkable structural discontinuities were observed around the junction sites at either the 5'- or 3'-end of the DNA. The overall structure was close to the typical A-form duplex .