Investigation of the structural basis for thermodynamic stabilities of tandem GU wobble pairs: NMR structures of (rGGAGUUCC)2 and (rGGAUGUCC)2.
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.
McDowell
J A
JA
Department of Chemistry, University of Rochester, Rochester, New York 14627-0216, USA.
He
L
L
Chen
X
X
Turner
D H
DH
D001482:Base Composition; D004355:Drug Stability; D006147:Guanine / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*; D012091:Repetitive Sequences, Nucleic Acid; D013816:Thermodynamics; D014498:Uracil / Q000737:chemistry*
D009841:Oligonucleotides; D014498:Uracil; D006147:Guanine; D012313:RNA