| The effect of coaxial stacking of helixes on the prediction of RNA secondary structure and the thermodynamics of coaxial stacking with intervening GA and CC mismatches were studied. Coaxial stacking of helixes was added to a program, EFN2, which recalculates the free energies of the structures generated by the Zuker folding algorithm, MFOLD. The accuracy of the predictions increased from 63% (Jaeger, J. A., Turner, D. H., and Zuker, M. (1989) Proc. Natl. Acad. Sci. USA 86, 7706-7710) to 76% of known helixes. This is the largest single increase in prediction accuracy since the complete nearest neighbor parameters for helix propagation by Watson-Crick pairs were measured.; Coaxial stacking with intervening GA mismatches is shown to stabilize helixes. The range in free energy increments is from {dollar}-{dollar}1.8 to {dollar}-{dollar}2.4 kcal/mol. These interfaces show little sequence dependence on the closing base pair, whether the break in the phosphodiester backbone is 5{dollar}spprime{dollar} or 3{dollar}spprime{dollar} to the mismatch, or whether the chains are extended beyond the helix-helix interface. Surprisingly, coaxial stacking with CC mismatches stabilize helixes, with free energy increments of about {dollar}-{dollar}1.4 kcal/mol.; NMR studies were attempted on several oligoribonucleotide models containing a GA mismatch between helixes in order to elucidate the conformation of the GA mismatch. The GA mismatch may be either in the imino hydrogen bonded or sheared conformation. 1D NOE and 2D WATERGATE NOESY experiments were conducted on a model sequence. All the imino exchangeable protons could not be assigned definitively. However, the NMR data suggest that the GA mismatch between the helixes in the model system is in the sheared conformation. |
