Biophysical and Conformational Properties of Modified Nucleosides in RNA (Nuclear Magnetic Resonance Studies)

Abstract

The location and identity of a large number of the modified nucleosides found in tRNA are highly conserved across diverse species and between tRNA isoacceptors. Conserved modification patterns in rRNAs and small nuclear RNAs also suggest that particular modified nucleosides have critical roles, although these functions are not well described compared to modifications found in tRNA. The nuclear magnetic resonance (NMR) determined biophysical properties have also provided an explanation for changes in important functions of tRNA during protein synthesis such as codon-anticodon recognition. This chapter talks about NMR determination of nucleoside conformation. The use of the percentage of 3'-endo sugar conformation as a measure of base stacking originated from NMR investigations on ribonucleotide dimers and trimers. Nucleoside modification in either the base or sugar can have significant effects on the sugar conformation, the glycosyl conformation, and base stacking. The 3'-gauche effect is mechanistically related to the anomeric effect in that it arises due to a geometrically dependent overlap between σ* and n lone pair molecular orbitals. Nucleoside bases that are in a stacked geometry generally have aromatic NMR proton shifts that are upfield of the positions seen in the absence of significant stacking. The chapter also focuses on conformational and thermodynamic effects of specific nucleoside modifications. Our knowledge of the fundamental biophysical properties of modified nucleosides will be critical to understanding how modification has been used throughout biology to optimize the function of biochemically critical processes involving RNA.