Published online 19 July 2006
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Structural parameters affecting the kinetics of RNA hairpin formation
Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University 2300 RA Leiden, The Netherlands 1 Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien A-1090 Vienna, Austria 2 IBA NAPS GmbH Rudolf-Wissell-Strasse 28 D-37079 Göttingen Germany
*To whom correspondence should be addressed. Tel: +31-71-5274769; Fax: +31-71-5274340; Email: c.pley{at}chem.leidenuniv.nl
Received January 28, 2005. Revised June 7, 2006. Accepted June 7, 2006.
There is little experimental knowledge on the sequence dependent rate of hairpin formation in RNA. We have therefore designed RNA sequences that can fold into either of two mutually exclusive hairpins and have determined the ratio of folding of the two conformations, using structure probing. This folding ratio reflects their respective folding rates. Changing one of the two loop sequences from a purine- to a pyrimidine-rich loop did increase its folding rate, which corresponds well with similar observations in DNA hairpins. However, neither changing one of the loops from a regular non-GNRA tetra-loop into a stable GNRA tetra-loop, nor increasing the loop size from 4 to 6 nt did affect the folding rate. The folding kinetics of these RNAs have also been simulated with the program ‘Kinfold’. These simulations were in agreement with the experimental results if the additional stabilization energies for stable tetra-loops were not taken into account. Despite the high stability of the stable tetra-loops, they apparently do not affect folding kinetics of these RNA hairpins. These results show that it is possible to experimentally determine relative folding rates of hairpins and to use these data to improve the computer-assisted simulation of the folding kinetics of stem–loop structures.
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