Nucleic Acids Research: VOLUME 37 ISSUE 7 2009

Structural features of mismatched base pairs were studied on four nonamer hybrid duplexes formed between the 50-d(GTGATATGC)-30 complement and its 50-r(GCAUNUCAC)-30 (N 1⁄4 A, C, G, U) counterparts. This oligonucleotide set is considered a model molecular system for future systematic studies of various modifications of internucleotide linkages with respect to their impact on the structure of mismatched base pairs. Raman spectra, measured at 158C, revealed the prevailing A-like structure of the RNA strand and mixed A-like and B-like characteristics for the DNA strand. All three mismatches disturb only weakly the overall conformation of the hybrid duplex in contrast to analogous mismatched DNA duplexes. In particular, the dT rG mismatch influences the global hybrid duplex geometry almost negligibly. The dT rC and dT rU mismatches induce somewhat more pronounced distortions of the backbone structure and of the thymine position, the latter being expressed by a change of the surrounding methylene group without effect on the carbonyl’s vibrations. Structural effects of the mismatches correlate well with the duplex thermodynamic stabilities obtained by ultraviolet (UV) absorption, i.e., the dT rG mismatch decreases the hybrid duplex stability very weakly while the effect of both pyrimidine–pyrimidine mismatches is considerable. # 2005 Wiley Periodicals, Inc. Biopolymers 79: 1–8, 2005 This article was originally published online as an accepted preprint. The ‘‘Published Online’’date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com