Solution structure of a RNA decamer duplex, containing 9-[2-O-(beta-D-ribofuranosyl)-beta-D-ribofuranosyl]adenine, a special residue in lower eukaryotic initiator tRNAs

The solution structure of the selt-complementary deca-ribenueleotide 5'-r(G CGA*AUUCGC)-3' containing 9-[2-O-(beta-D-ribofuranosyl)-beta-D-ribofuranosy l]adenine (A*),a modified nucleotide that occurs in lower eukaryotic methio nine initiator tRNAs (tRNAs(i)(Met)),was determined by NMR spectroscopy. Un expectedly, the modification has no effect on the thermal stability of the duplex. However, the extra ribose moiety is in the C(3')-endo conformation and takes up a well-defined position in the minor groove, which is in agree ment with its position in tRNAs(i)(Met) as determined by X-ray crystallogra phy. Molecular-dynamics simulations on the RNA duplex in H2O show that the position of the extra ribofuranose moiety seems to be stabilized by bridged H-bonds (mediated by two H2O molecules) to the backbone of the complementa ry chain.