Specificity of hybridization between DNA sequences based on free energy

Abstract

We investigated the specificity of hybridization based on a minimum free energy (ΔGmin) 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 ΔG min ≤ -14.0, but cannot be separated using the number of base pairs (BP) in the range from 9 to 18. This demonstrates that the ΔG min 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 ΔGmin 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. © Springer-Verlag Berlin Heidelberg 2006.