Branch and bound algorithm for nonenzymatic RNA degradation

A stability of individual phosphodiester bonds is an important factor affecting biological properties of large RNA molecules. One or more unstable bonds can control the rate of RNA decay and consequently, regulate its activity in vivo. Earlier in vitro studies on the mechanism of the spontaneous RNA degradation revealed that it is structure dependent process. Here, we present a mathematical formulation of a new problem of nonenzymatic spontaneous RNA degradation and a branch and bound algorithm for finding the solution of the problem. We also show the experimental data that enable to verify the results of the algorithm.