A tool for the design of DNA base sequences for molecular circuits

Designing a set of DNA base sequences for a large-scale molecular circuit is a difficult problem in the field of DNA computing. A DNA circuit frequently suffers from unintended DNA strand displacements among strands; this problem can ruin the desired function of a DNA circuit. In this study, our aim was to develop a computational tool for the design of DNA base sequences by means of an original algorithm based on mismatches in a DNA base sequence. Validity of the proposed algorithm is confirmed by practical redesign examples.