Loop stereochemistry and dynamics in transfer RNA

Journal of Biomolecular Structure & Dynamics
E WesthofD Moras

Abstract

The stereochemistry and the dynamics of two loops of yeast tRNA-asp, the thymine loop and the anticodon loop, are compared in the hope of a better understanding of the relationships between loop sequence and loop topology. Both loops are seven residues long and both present sharp turns after the second residue, U33 and psi 55, stabilized by hydrogen bonds between N3-H of the pyrimidine and the phosphates of C36 and A58 and stacking interactions of the pyrimidine ring with the phosphates of U35 and A57, respectively. In the thymine loop, the two purines following C56, A57 and A58, open up to leave space for the intercalation of the first invariant guanine residue of the D-loop, while the two pyrimidine bases, which follow A58, turn away from the stacking pattern of the thymine arm and stack instead with the last base pair of the dihydrouridine arm A15-U48. In the anticodon loop, however, the bases G34 to C38 form an helical stack in continuity with the anticodon stem on the 3'-end. At the same time C36 forms Watson-Crick hydrogen bonds with G34 of a twofold symmetrically related molecule. The anticodon-anticodon base pairing interactions between symmetrically-related molecules are stabilized by stacking with the modified base G3...Continue Reading

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Citations

Jan 1, 1986·Bio Systems·R CedergrenB Larue
Feb 1, 1986·Proceedings of the National Academy of Sciences of the United States of America·D MorasR Giegé
Feb 1, 1986·Journal of Biomolecular Structure & Dynamics·O KennardD Rabinovich
Oct 1, 1989·Journal of Biomolecular Structure & Dynamics·G StrikerM C Vega-Martin
Jan 11, 1994·Nucleic Acids Research·K WatanabeK Miura
May 12, 2006·Nucleic Acids Research·Guillaume GabantJean Armengaud
Jul 28, 2016·Nucleic Acids Research·Henri Grosjean, Eric Westhof
Jul 5, 1985·Journal of Molecular Biology·E WesthofD Moras
Mar 18, 2006·Nucleosides, Nucleotides & Nucleic Acids·Wayne DawsonKenji Yamamoto
Dec 1, 1987·Journal of Biomolecular Structure & Dynamics·P RombyR Giegé

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