Thermodynamic simulation of deoxyoligonucleotide hybridization for DNA computation

Nearly every model of DNA computation proposed to date depends upon sequence-specific hybridization operations. In order to better predict the binding specificity of arbitrary deoxyoligonucleotides, a simulator named bind is implemented. Bind operates on a single template DNA sequence and a number of shorter primer sequences. For each primer sequence, bind calculates a theoretical melting temperature at every position of the primer along the template, yielding a measure of binding specificity between each primer and the template. The simulator differs from previous melting temperature programs in that it is intended to be used with oligonucleotides, is designed to handle mismatched base pairs, makes use of the latest thermodynamic parameters, and provides features with DNA computation expressly in mind. This paper describes how bind is implemented, provides corroborating evidence as to its accuracy, and offers instances of its usefulness to a range of DNA computing applications.