DSSR-PyMOL cartoon-block schematics: PDB entry 1qes

PDB-id

1qes; SNAP-derived features in text and JSON formats

Class

RNA

Method

NMR

Summary

Tandem gu mismatches in RNA, NMR, 30 structures

Reference

McDowell JA, He L, Chen X, Turner DH (1997): "Investigation of the structural basis for thermodynamic stabilities of tandem GU wobble pairs: NMR structures of (rGGAGUUCC)2 and (rGGAUGUCC)2." Biochemistry, 36, 8030-8038. doi: 10.1021/bi970122c.

Abstract

The symmetric, tandem GU mismatch motifs, and , which only differ in the mismatch order, have an average difference in thermodynamic stability of 2 kcal/mol at 37 degrees C. Thermodynamic studies of duplexes containing these motifs indicate the effect is largely localized to the mismatches and adjacent base pairs. The three-dimensional structures of two representative duplexes, (rGGAGUUCC)2 and (rGGAUGUCC)2, were determined by two-dimensional NMR and a simulated annealing protocol. Local deviations are similar to other intrahelical GU mismatches with little effect on backbone torsion angles and a slight overtwisting between the base pair 5' of the G of the mismatch and the mismatch itself. Comparisons of the resulting stacking patterns along with electrostatic potential maps suggest that interactions between highly negative electrostatic regions between base pairs may play a role in the observed thermodynamic differences.