title: Folding kinetics of large RNAs.
abstract: We introduce here a heuristic approach to kinetic RNA folding that constructs secondary structures by stepwise combination of building blocks. These blocks correspond to subsequences and their thermodynamically optimal structures. These are determined by the standard dynamic programming approach to RNA folding. Folding trajectories are modeled at base-pair resolution using the Morgan-Higgs heuristic and a barrier tree-based heuristic to connect combinations of the local building blocks. Implemented in the program Kinwalker, the algorithm allows co-transcriptional folding and can be used to fold sequences of up to about 1500 nucleotides in length. A detailed comparison with several well-studied examples from the literature, including the delayed folding of bacteriophage cloverleaf structures, the adenine sensing riboswitch, and the hok RNA, shows an excellent agreement of predicted trajectories and experimental evidence. The software is available as part of the ViennaRNA Package.
authors.affiliation: Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany. michael@bioinf.uni-leipzig.de
authors.forename: Michael
authors.initials: M
authors.lastname: Geis
authors.forename: Christoph
authors.initials: C
authors.lastname: Flamm
authors.forename: Michael T
authors.initials: MT
authors.lastname: Wolfinger
authors.forename: Andrea
authors.initials: A
authors.lastname: Tanzer
authors.forename: Ivo L
authors.initials: IL
authors.lastname: Hofacker
authors.forename: Martin
authors.initials: M
authors.lastname: Middendorf
authors.forename: Christian
authors.initials: C
authors.lastname: Mandl
authors.forename: Peter F
authors.initials: PF
authors.lastname: Stadler
authors.forename: Caroline
authors.initials: C
authors.lastname: Thurner
mesh_terms: D000225:Adenine / Q000737:chemistry; D001483:Base Sequence; D007700:Kinetics; D017909:Levivirus / Q000235:genetics; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry*; D012984:Software; D014158:Transcription, Genetic
chemical_list: D012313:RNA; D000225:Adenine