Solution structure of a RNA decamer duplex, containing 9-[2-O-(β-D- ribofuranosyl)-β-D-ribofuranosyl]adenine, a special residue in lower eukaryotic initiator tRNAs
Luyten I., Esnouf RM., Mikhailov SN., Efimtseva EV., Michiels P., Heus HA., Hilbers CW., Herdewijn P.
The solution structure of the self-complementary deca-ribonucleotide 5'- r(GCGA*AUUCGC)-3' containing 9-[2-O-(β-D-ribofuranosyl)-β-D- ribofuranosyl]adenine (A*), a modified nucleotide that occurs in lower eukaryotic methionine initiator tRNAs (tRNAs(i)(Met)), was determined by NMR spectroscopy. Unexpectedly, 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 agreement with its position in tRNAs(i)(Met) as determined by X- ray crystallography. Molecular-dynamics simulations on the RNA duplex in H 2 O show that the position of the extra ribofuranose moiety seems to be stabilized by bridged H-bonds (mediated by two H 2 O molecules) to the backbone of the complementary chain.