Effects of flanking G.cntdot.C base pairs on internal Watson-Crick, G.cntdot.U and nonbonded base pairs within a short RNA duplex

Abstract

A series of pentaribonucleotides, ApGpXpGpU (where X identical to A, G, C, or U), was synthesized to investigate the effects of flanking G . C pairs on internal Watson-Crick, G . U, and nonbonded base pairs. Sequences ApGpApCpU (Tm = 26 degrees C) and ApGpCpCpU (Tm = 25 degrees C) were each found to form a duplex with non-base-paired internal residues that stacked with the rest of the sequence but were not looped out. ApGpGpCpU also forms a duplex (Tm = 30 degrees C) but with dangling terminal nonbonded adenosines rather than internal nonbonded guanosines. ApGpUpCpU prefers a stacked single-strand conformation. In addition, contribution to duplex stability from an internal A . U or G . C base pair is enhanced by 6 degrees C when flanked by G . C base pairs as compared to A . U base pairs. G . C base pairs flanking an internal G . U base pair were found to be more tolerant to the altered conformation of a G . U pair and result in an increase to stability comparable with that found for an internal A . U base pair.

The structure of an RNA dodecamer shows how tandem U–U base pairs increase the range of stable RNA structures and the diversity of recognition sites

“…The dodecamer examined in this study, GGCGCUUGCGUC ('CUUG'), provides an example of a tandem U-U base pair, that is, two consecutive U-U base pairs. Single U-U base pairs destabilize a helix [7,12], but with the right combination of flanking base pairs, tandem U-U base pairs can stabilize a duplex [5]. Consistent with the thermodynamic stabilization, NMR data show evidence that the CUUG duplex forms U-U base pairs [13].…”

“…2b). The bottom region, (residues 1-5 and 20-24), shows a striking swinging motion while the top region, (8)(9)(10)(11)(12)(13)(14)(15)(16)(17), shows much less of a swinging motion. Both top and bottom stem regions are compressed relative to A-form RNA; they have an average helical rise of 2.4 Å, while the A-form has an average helical rise of 2.8 Å.…”

“…Solvent molecules make an additional 11 interactions in the first contact and nine in the second. While 2′ OH are (8)(9)(10)(11)(12)(13)(14)(15)(16)(17) for the second six base pairs. The base step parameters reported for the base step between U6-U19 and U7-U18 were averaged from the results for the two stems.…”

Conformational Transitions in Viroids and Virusoids: Comparison of Results from Energy Minimization Algorithm and from Experimental Data

“…In the parameter set of Gralla and Crothers it is assumed that the thermodyanmic properties of G:U pairs are identical to those of A:U pairs. This assumption is also used in this work: it is supported by experimental results from oligonucleotide binding to tRNA (20,21,22), NMR-studies on G:U containing RNA-double helices (23,24,25,26), and calculations on the stability of G:U containing tRNAs.…”

Nuclear Overhauser effect study of yeast tRNAVal1: evidence for uridine-pseudouridine base pairing

“…Nonstandard pairing in RNA pentamer duplexes has also been studied by NMR. 16 The significance of this first observation of a pyrimidine-pyrimidine-8303 pair in tRNA extends beyond the study of tRNA structure. The observation lends support to the model for wobble interactions proposed by Grosjean et al17 and to the proposed scheme for mitochondrial codon-anticodon base-pairing,18 both of which include the possibility of U-U base pairs.…”