Analyzing Secondary Structure Transition Paths of DNA/RNA Molecules

Abstract

Analysis of secondary structure transition is important for designing bistable DNA/RNA molecules. To make reliable molecular machines out of such molecules, it is necessary to estimate the height of the energy barrier to the structure transition. This paper suggests three kinds of optimized transition path: the locally optimized direct path, the globally optimized direct path, and the globally optimized path. These paths can be used as criteria for evaluating structure transitions. Then, we introduce algorithms to obtain or approximate these optimized paths. The algorithm that Morgan and Higgs used to obtain the globally optimized direct path is analyzed and improved as an algorithm on a bipartite graph. The algorithms are implemented as a C language program.