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Design of multistable RNA molecules

Published online by Cambridge University Press:  07 February 2001

CHRISTOPH FLAMM
Affiliation:
Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, A-1090 Wien, Austria
IVO L. HOFACKER
Affiliation:
Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, A-1090 Wien, Austria
SEBASTIAN MAURER-STROH
Affiliation:
Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, A-1090 Wien, Austria
PETER F. STADLER
Affiliation:
Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, A-1090 Wien, Austria The Santa Fe Institute, Santa Fe, New Mexico 87501, USA
MARTIN ZEHL
Affiliation:
Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, A-1090 Wien, Austria
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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.

Type
Research Article
Copyright
2001 RNA Society

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