TBI-Preprint 00-05-027

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Design of Multi-Stable RNA Molecules

Christoph Flamm, Ivo L. Hofacker, Sebastian Maurer-Stroh, Peter F. Stadler, Martin Zehl

Appeared in:
RNA, 7, 254-265 (2001)

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.

RNA switches, sequence design, RNA folding, RNA secondary structure prediction

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