Modeling RNA folding paths with pseudoknots: Application to hepatitis delta virus ribozyme

摘要: A quantitative understanding of nucleic acid hybridization is essential to many aspects biotechnology, such as DNA microarrays, well the structure and folding kinetics RNA. However, predictions secondary structures have long been impeded by presence helices interior loops, so-called pseudoknots, which impose complex three-dimensional conformational constraints. In this paper we compute pseudoknot free energies analytically in terms known standard parameters, show how results can be included a kinetic Monte Carlo code follow succession during quenched or sequential folding. For hepatitis delta virus ribozyme, predict several nonnative stems on path, characterize kinetically trapped state, interpret experimentally characterized mutations suggest with other parts genome inactivates newly formed ribozyme.