DNA encoding for solving the NP problems

Most existing DNA computing methods follow the Adlemanpsilas coding scheme to solve NP-complete problems. Effective encoding can reduce the false hybridization. Helix twist angle distances describe quantitatively difference of helix twist angles. In this paper, by translating helix twist angle distance function into proper constraint term, the new evaluation formula of every DNA individual corresponding to the selected constraint term is proposed. Immune genetic algorithm is presented to solve the problem, and the better DNA sequences are found. By comparing experimental data with the previous data, we find that the sequences generated by helix twist angle distance function satisfy simultaneously the constraint terms of Hamming distance, reverse Hamming distance and reverse-complement Hamming distance. Accordingly, the complexity of encoding problem is reduced.