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, dihydrouridine (D) and 3'-adjacent nucleotides adopt the infrequent 2'-endo conformation. Analysis of D, DUA and UUA by circular dichroism (CD) and NMR confirmed that D produces the 2'-endo conformation of the trimer and is responsible for the same in tRNA. The nucleoside, 3-[3-(S)-amino-3-carboxypropyl]uridine (acp(3)U) occurs in the tRNA sequence D-acp(3)U-A. CD spectra indicated that D-acp(3)U-A and U-acp(3)U-A bind Mg2+, whereas acp(3)U, D-acp(3)U, DUA and UUA do not. Ion dependent changes in chemical shifts and paramagnetic broadening of H-1 signals indicated that Mg2+ coordination involved the acp(3)U side chain and the ribose of A. The Mg2+-bound structure was modeled with simulated annealing, molecular mechanics and NMR restraints. Acp(3)U contributed to local charge density that facilitated Mg2+ coordination.