Speaker: Sebastian Doniach, Stanford University

“Forces Stabilizing Tertiary Structure Formation in RNA: Measurements and Computer Simulations”

In recent years the function of relatively small RNA molecules has been found to have a broad scope, as enzymes (ribozymes) and as parts of the control machinery for gene expression, in addition to the traditional role of RNA as messenger for translation of the genetic code. Understanding the tertiary self-assembly of functional RNA molecules is complicated by the very large coulomb forces arising because of its highly charged nature. We have been using small angle x-ray scattering (SAXS) to study the folding process of small RNAs and the nature of the atmosphere of counter-ions needed in the self-assembly process. In the course of these studies we have found significant deviation from non-linear Poisson-Boltzmann theory in the dependence of the counter-ion induced forces on ion size and charge. We will present a modified form of Poisson-Boltzmann theory, incorporating effects of excluded volume, which goes part of the way to representing the dependence of the screening forces on ion size.