title: Prediction of RNA multiloop and pseudoknot conformations from a lattice-based, coarse-grain tertiary structure model.
abstract: We present a semiquantitative lattice model of RNA folding, which is able to reproduce complex folded structures such as multiloops and pseudoknots without relying on the frequently employed ad hoc generalization of the Jacobson-Stockmayer loop entropy. We derive the model parameters from the Turner description of simple secondary structural elements and pay particular attention to the unification of mismatch and coaxial stacking parameters as well as of border and nonlocal loop parameters, resulting in a reduced, unified parameter set for simple loops of arbitrary type and size. For elementary structures, the predictive power of the model is comparable to the standard secondary structure approaches, from which its parameters are derived. For complex structures, our approach offers a systematic treatment of generic effects of chain connectivity as well as of excluded volume or attractive interactions between and within all elements of the secondary structure. We reproduce the native structures of tRNA multiloops and of viral frameshift signal pseudoknots.
authors.affiliation: Laboratoire de Physique and Centre Blaise Pascal of the Ecole Normale Supérieure de Lyon, Université de Lyon, CNRS UMR 5672, 46 allée d'Italie, 69364 Lyon Cedex 07, France. daniel.jost@ens-lyon.fr
authors.forename: Daniel
authors.initials: D
authors.lastname: Jost
authors.forename: Ralf
authors.initials: R
authors.lastname: Everaers
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry* / Q000648:ultrastructure*
chemical_list: D012313:RNA