Abstract

RNA secondary structures provide a suitable model system for studying the thermodynamics and kinetics of biopolymer folding. In contrast to models of protein folding of comparable complexity, the ground state structure as well as most thermodynamic quantities of interest, such as partition function and density of states can be calculated by efficient algorithms in polynomial time. For small RNA molecules, up to as few hundred bases, the kinetics of folding can be studied in Monte Carlo type simulations. As an example application, we consider the effect of modified bases in tRNA molecules.

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