STRUCTURE OF THE TRINUCLEOTIDE D-ACP(3)U-A WITH COORDINATED MG2+ DEMONSTRATES THAT MODIFIED NUCLEOSIDES CONTRIBUTE TO REGIONAL CONFORMATIONS OF RNA

In tRNA crystal structures, the only nonaromatic ribonucleoside, dihyd rouridine (D) and 3'-adjacent nucleotides adopt the infrequent 2'-endo conformation. Analysis of D, DUA and UUA by circular dichroism (CD) a nd NMR confirmed that D produces the 2'-endo conformation of the trime r and is responsible for the same in tRNA. The nucleoside, 3-[3-(S)-am ino-3-carboxypropyl]uridine (acp(3)U) occurs in the tRNA sequence D-ac p(3)U-A. CD spectra indicated that D-acp(3)U-A and U-acp(3)U-A bind Mg 2+, whereas acp(3)U, D-acp(3)U, DUA and UUA do not. Ion dependent chan ges in chemical shifts and paramagnetic broadening of H-1 signals indi cated that Mg2+ coordination involved the acp(3)U side chain and the r ibose of A. The Mg2+-bound structure was modeled with simulated anneal ing, molecular mechanics and NMR restraints. Acp(3)U contributed to lo cal charge density that facilitated Mg2+ coordination.