Specificity of Hybridization between DNA Sequences Based on Free Energy

Abstract. We investigated the specificity of hybridization based on a minimum free energy (∆Gmin) through gel electrophoresis analysis. The analysis, using 94 pairs of sequences with length 20, showed that sequences that hybridize each other can be separated using the constraint ∆Gmin ≤ −14.0, but cannot be separated using the number of base pairs (BP) in the range from 9 to 18. This demonstrates that the ∆Gmin is superior to the BP in terms of the capability to separate specific from non-specific sequences. Furthermore, the comparison between sequence design based on ∆Gmin and that based on the BP, done through a computer simulation, showed that the former outperformed the latter in terms of the number of sequences designed successfully as well as the ratio of successfully designed sequences to the total number of sequences checked.