Serra 9707940 The goal of this project is to determine the effect of sequence and divalent ions on the stability of RNA. This project has four specific goals: 1) to test the limits of a model for the prediction of RNA hairpin stability, 2) to provide the thermodynamics parameters for the prediction of RNA bulge loop stability from sequence, 3) to determine the effect of metal ions on the stability of RNA secondary structural motifs, and 4) to determine the stoichiometry and affinity for metal ion binding to RNA secondary structural motifs. RNA oligomers will be prepared by chemical synthesis. The structural stability of the RNA oligomers will be determined by Van't Hoff analysis of optical melting curves of the synthetic oligomers. Interaction of metal ions (Mg2+ and Zn2+) with RNA will be determined by observing their effect on the thermal stability of RNA oligomers in optical melting studies. The stoichiometry and affinity of the metal ion binding will be determined by equilibrium dialysis. The overall goal of this research is to determine the effect of sequence on the structural stability of RNA oligomers and to understand the molecular forces responsible for their stability and to provide thermodynamic parameters for the prediction of those stabilities. ***
