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

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.