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An approximation of loop free energy values of RNA H-pseudoknots

Published online by Cambridge University Press:  01 May 1999

ALEXANDER P. GULTYAEV ,
F.H.D. VAN BATENBURG  and
CORNELIS W.A. PLEIJ
ALEXANDER P. GULTYAEV
Affiliation:
Section Theoretical Biology and Phylogenetics, Institute of Evolutionary and Ecological Sciences, Leiden University, 2311 GP Leiden, The Netherlands Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands
F.H.D. VAN BATENBURG
Affiliation:
Section Theoretical Biology and Phylogenetics, Institute of Evolutionary and Ecological Sciences, Leiden University, 2311 GP Leiden, The Netherlands
CORNELIS W.A. PLEIJ
Affiliation:
Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RA Leiden, The Netherlands

Abstract

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A set of free energy values is suggested for RNA H-pseudoknot loops. The parameters are adjusted to be consistent with the theory of polymer thermodynamics and known data on pseudoknots. The values can be used for estimates of pseudoknot stabilities and computer predictions of RNA structures.

Keywords

helix–coil transitionspseudoknot loopsRNA structureRNA thermodynamics
Type
LETTERS TO THE EDITOR
Information
RNA , Volume 5 , Issue 5 , May 1999 , pp. 609 - 617
Copyright
© 1999 RNA Society