Title: Algorithm for thermodynamically based prediction of DNA/DNA cross-hybridisation

Authors: Svetlana Torgasin, Karl-Heinz Zimmermann

Addresses: Department of Computer Engineering, Hamburg University of Technology, 21071 Hamburg, Germany. ' Department of Computer Engineering, Hamburg University of Technology, 21071 Hamburg, Germany

Abstract: A careful design of DNA strands is crucial for several biological applications such as microarray techniques, Polymerase Chain Reaction (PCR), and DNA computing. For this, the important criterion under laboratory conditions is the hybridisation energy of two DNA strands. During the last decade, a thermodynamic model was developed that allows for the calculation of the DNA/DNA hybridisation energy and recently also the cross-hybridisation energy of structural motifs. Employing this model a new algorithm for the secondary structure prediction of DNA/DNA cross-hybridisation complexes called HYBGRAPH is introduced. The method is based on Gibbs free energy minimisation and the paradigm of dynamic programming.

Keywords: DNA hybridisation; dynamic programming; Gibbs free energy; nearest neighbour model; DNA structural motifs; bioinformatics; thermodynamic modelling; secondary structure prediction.

DOI: 10.1504/IJBRA.2010.031294

International Journal of Bioinformatics Research and Applications, 2010 Vol.6 No.1, pp.82 - 97

Published online: 27 Jan 2010 *

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