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.

Beneficial and Detrimental Effects of Nonspecific Binding During DNA Hybridization

“…While there are numerous tools to predict the thermodynamic stability of DNA duplexes 5,[23][24][25][26][27][28][29] , the kinetics of hybridization are less well understood. This is a major limitation because kinetic limitations can prevent DNA molecules from finding the most stable state.…”