title: Algorithm for thermodynamically based prediction of DNA/DNA cross-hybridisation.
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.
authors.affiliation: Department of Computer Engineering, Hamburg University of Technology, 21071 Hamburg, Germany. torgasin@tuhh.de
authors.forename: Svetlana
authors.initials: S
authors.lastname: Torgasin
authors.forename: Karl-Heinz
authors.initials: KH
authors.lastname: Zimmermann
mesh_terms: D000465:Algorithms; D020029:Base Pairing; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D013816:Thermodynamics
chemical_list: D004247:DNA