Structure of the Trinucleotide D-acp³U-A with Coordinated Mg²⁺Demonstrates that Modified Nucleosides Contribute to Regional Conformations of RNA

Abstract

Abstract 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 (acp3U) occurs in the tRNA sequence D-acp3U-A. CD spectra indicated that D-acp3U-A and U-acp3U-A bind Mg2+, whereas acp3U, D-acp3U, DUA and UUA do not. Ion dependent changes in chemical shifts and paramagnetic broadening of 1H signals indicated that Mg2+ coordination involved the acp3U side chain and the ribose of A. The Mg2+-bound structure was modeled with simulated annealing, molecular mechanics and NMR restraints. Acp3U contributed to local charge density that facilitated Mg2+ coordination. #Present addresses: W. W. S., NMR Facility University of California, Davis, CA; B. F., School of Medicine, University of North Carolina, Chapel Hill, NC; B. N., Lab for Biochemistry, University of Bayreuth, Bayreuth, Germany. Notes #Present addresses: W. W. S., NMR Facility University of California, Davis, CA; B. F., School of Medicine, University of North Carolina, Chapel Hill, NC; B. N., Lab for Biochemistry, University of Bayreuth, Bayreuth, Germany.