This study will investigate the interaction of divalent metal ions, specifically Mg ion with RNA. Crystal structures of RNA show an intimate association of the folded RNA structure with metal ions. The metal ions often are found associated with non- base paired regions of the RNA. The interactions of Mg ion with small RNA oligomers containing these metal-binding motifs will be explored. These studies will include both experimental and computer simulations. Optical melting of the RNA oligomers will be conducted to determine the role of Mg on the thermal stability of RNA secondary structure. Equilibrium dialysis will determine the number of metal ions bound and the binding affinity of Mg for the RNA motifs. Brownian-dynamics simulations will predict the metal ion binding sites in the RNA motifs. Optical melting of the td group I intron and several mutant RNAs will elucidate the role of metal ions on long range tertiary RNA interactions.
|Serra, Martin J; Baird, John D; Dale, Taraka et al. (2002) Effects of magnesium ions on the stabilization of RNA oligomers of defined structures. RNA 8:307-23|