TBI-Preprint 07-11-001
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Titel:
Folding Kinetics of Large RNAs.
Authors:
Michael Geis,
Christoph Flamm,
Michael T. Wolfinger,
Ivo L. Hofacker,
Martin Middendorf,
Christian Mandl,
Peter F. Stadler,
Caroline Thurner
Submitted to:
JMB (2007)
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 sub-sequences 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 ASR riboswitch, and the Hok RNA,
shows an excellent agreement of predicted trajectories and experimental
evidence. The software is available as part of the Vienna RNA
Package
.
Keywords:
RNA folding kinetics,
Co-transcriptional folding,
Folding pathway,
Metastable structure,
Folding Trajectories
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Last modified: 2008-02-26 18:45:53 xtof