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

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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.

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