RNA



RNA folding at elementary step resolution


CHRISTOPH  FLAMM a1c1, WALTER  FONTANA a2p1, IVO L.  HOFACKER a1 and PETER  SCHUSTER a1
a1 Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, A-1090 Wien, Austria
a2 Santa Fe Institute, Santa Fe, New Mexico 87501 USA

Abstract

We study the stochastic folding kinetics of RNA sequences into secondary structures with a new algorithm based on the formation, dissociation, and the shifting of individual base pairs. We discuss folding mechanisms and the correlation between the barrier structure of the conformational landscape and the folding kinetics for a number of examples based on artificial and natural sequences, including the influence of base modification in tRNAs.

(Accepted November 23 1999)


Key Words: conformational spaces; foldability; RNA folding kinetics; RNA secondary structure.

Correspondence:
c1 Reprint requests to: Christoph Flamm, Institut für Theoretische Chemie und Molekulare Strukturbiologie, Währingerstrasse 17, A-1090 Wien, Austria; e-mail: xtof@tbi.univie.ac.at.
p1 Present address: Institute for Advanced Study, Program in Theoretical Biology, 310 Olden Lane, Princeton, New Jersey 08540, USA.