Contribution of a G·U base pair to the stability of a short RNA helix

Abstract

Variable temperature lH n.m.r. spectroscopic studies have shown that the contribution of an internal G-U base pair approximates that of an A.U base pair in the stability of a short RNA helix, THE existence of G-U base pairs was first proposed in the wobble hypothesis of Crick1 to explain the codon-anticodon interactions between mRNA and tRNA. This base pair has since been included in the proposed secondary structures of several native R N A S ~~~~Q despite the fact that several physical studies on the existence of G-U base pairs were inconcl~sive.~ v6 Substantial evidence for the presence of a G-U interaction has recently been provided by the X-ray crystal structure of yeast tRNAPhe2 and the n.m.r. spectrum of polyd(GpT).' In order to study both the formation and relative stability of a G*U base pair in a short RNA helix flanked by normal Watson-Crick base-pairs, we have synthesized the pentaribonucleotides, CAGUG and CAUUG,? by the phosphotriester method.8 We have examined the duplex formation of these complementary sequences by lH n.m.r. spectroscopy.

NMR evidence for dynamic secondary structure in helixes II and III of the 5S RNA of Escherichia coli

“…There is no NOE evidence for a second GU base pair in the spectrum to account for G18-U65 in Figure 1. Given that Watson-Crick base pairs at helix termini are often difficult to observe due to exchange broadening [e.g., see Chou et al (1984)] and that GU's are believed to be no stronger than AU Watson-Crick pairs (Romaniuk et al, 1979), the absence of NOE evidence for another GU is not surprising.…”

Principles of Nucleic Acid Structure

“…It probably accounts for the stability of the poly(G)·poly(V) double helix (582) and was found to approximate, in a complementary double-helical oligonucleotide, an A-V base-pair in stabilizing efficiency (583). As for the long A-I base-pair, it could be verified in the all-purine double-helix poly(A)'poly(I) (Chapter 13).…”

Free energy contributions of G.cntdot.U and other terminal mismatches to helix stability

“…though there are limited studies on the effect of internal G-U mismatches on duplex stability (Uhlenbeck et al, 1971;Lomant & Fresco, 1975;Romaniuk et al, 1979a,b; Alkema et al, 1982), no experiments have been reported on the effect of terminal G-U mismatches on oligonucleotide stability. We report below thermodynamic parameters of helix formation for four oligoribonucleotides containing terminal G-U mismatches.…”