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Titel:
Design of Multi-Stable RNA Molecules
Author(s):
Christoph Flamm,
Ivo L. Hofacker,
Sebastian Maurer-Stroh,
Peter F. Stadler,
Martin Zehl
Appeared in:
RNA, 7, 254-265 (2001)
Abstract:
We show that the problem of designing RNA sequences that can fold into
multiple stable secondary structures can be transformed into a
combinatorial optimization problem that can be solved by means of simple
heuristics. Hence it is feasible to design RNA switches with prescribed
structural alternatives. We discuss the theoretical background and present
an efficient tool that allows the design of various types of switches. We
argue that both the general properties of the sequence structure map of
RNA secondary structures and the ease with which our design tool finds
bistable RNAs strongly indicates that RNA switches are easily accessible
in evolution. Thus conformational switches are yet another function for
which RNA can be employed.
Keywords:
RNA switches,
sequence design,
RNA folding,
RNA secondary structure prediction
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