Sequence dependence of stability for coaxial stacking of RNA helixes with Watson-Crick base paired interfaces

Thermodynamic parameters from UV melting studies are reported for the helix-helix interfaces of coaxially stacked helixes in RNA. The model system consists of a short oligomer binding to a four-nucleotide overhang at the end of a hairpin stem, creating the helix-helix interface. Interfaces containing Watson-Crick base pairs are approximately 1 kcal/mol more stable than the corresponding nearest neighbor interaction in an uninterrupted helix. Thus the sequence dependence of stability for coaxially stacked interfaces is similar to that for regular helixes. This provides experimental evidence for an assumption that has been shown to improve predictions of RNA secondary structure [Walter, A. E., Turner, D. H., Kim, J., Lyttle, M. H., Muller, P., Mathews, D. H., & Zuker, M. (1994) Proc. Natl. Acad. Sci. U.S.A. (in press)]. The results should also be useful for modeling three-dimensional structures of RNA.