Density of States, Metastable States, and Saddle Points Exploring the Energy Landscape of an RNA Molecule

Detailed knowledge of the energy landscape of a biopolymer molecule is a prerequisite for understanding its folding kinetics and its final spatial structure. In the case of RNA we consider the energy landscape defined on the set of all secondary structures that can be formed by a given sequence. We show that the exploration of this energy landscapes is computationally feasible. For this prurpose we present a recursive algorithm for computing the complete density of states and discuss its application to tRNA sequences. For shorter sequences a more detailed analysis of the energy surface is possible using a complete list of all secondary structures. In this case we identify metastable states and the saddle points that connect them. The Density of States The density of states (d.o.s.), i.e. the energy distribution of suboptimal secondary structures, is of utmost importance for an understanding of the structural versatility of RNA molecules (Higgs 1995). For short RNA chains it is possibl..