NEAREST-NEIGHBOR PARAMETERS FOR G.U MISMATCHES - 5'GU3'/3'UG5' IS DESTABILIZING IN THE CONTEXTS CGUG..GUGC, UGUA..AUGU, AND AGUU..UUGU BUT STABILIZING IN GGUC..CUGG

Thermodynamic parameters derived from optical melting studies are reported for duplex formation by a series of oligoribonucleotides containing G.U mismatches. The results are used to determine nearest-neighbor parameters for helix propagation by G.U mismatches. Surprisingly, the 3'UG5'(5'GU3') nearest-neighbor free energy increment is unfavorable in the contexts GUGC(CGUC), AUGU(UGUA), and UUGA(AGUU) but favorable in the context CUGG(GGUC). This is a non-nearest-neighbor effect. In contrast, the 3'GU5'(5'UG3') free energy increment is favorable and independent of context. Circular dichroism and imino proton NMR spectra of several sequences do not reveal an obvious structural basis for this dichotomy. For example, all the G.U mismatches have two slowly exchanging imino protons. The imino resonances for the G-U mismatches in GGAGUUCC, GUCGUGAC, and CCUGUAGG, however, broaden at lower temperature than the imino resonances for the interior Watson-Crick base pairs. In contrast, the imino resonances for the G-U mismatches in GGAUGUCC remain sharp at high temperature. The improved parameters for G.U mismatches should improve predictions of RNA structure from sequence.