IEEE Trans Nanobioscience. 2020 Apr;19(2):299-307. doi: 10.1109/TNB.2020.2971644. Epub 2020 Feb 4.
DNA computing, the combination of computer science and molecular biology, is a burgeoning research field that holds promise for many applications. The accuracy of DNA computing is determined by reliable DNA sequences, the quality of which affects the accuracy of hybridization reactions. Evaluating the sequences obtained from the previous combination constraints in NUPACK for simulation experiments, we find that the concentration of the sequences after entering solution was significantly lower than that before entering solution, which should affect the accuracy of DNA hybridization reactions. Therefore, in this study, we propose a new constraint, a triplet-bases unpaired constraint, which can be combined with other constraints to form a new combination constraint. In addition, we combine the Harmony Search algorithm with the Whale Optimization Algorithm (WOA) to present a new algorithm, termed HSWOA, which we used to design DNA sequences that meet the new combination constraint. Finally, compared with previous findings, our result shows that our algorithm not only improves the efficiency of hybridization reactions but also yields a better fitness value.
DNA 计算，是计算机科学和分子生物学的结合，是一个新兴的研究领域，在许多应用中具有广阔的前景。DNA 计算的准确性取决于可靠的 DNA 序列，其质量影响杂交反应的准确性。通过对 NUPACK 中之前的组合约束进行模拟实验得到的序列进行评估，我们发现序列进入溶液后的浓度明显低于进入溶液前的浓度，这应该会影响 DNA 杂交反应的准确性。因此，在本研究中，我们提出了一个新的约束条件，即三联体碱基未配对约束条件，它可以与其他约束条件相结合，形成新的组合约束条件。此外，我们将 Harmony Search 算法与鲸鱼优化算法 (WOA) 相结合，提出了一种新的算法，称为 HSWOA，我们使用该算法来设计满足新组合约束条件的 DNA 序列。最后，与之前的研究结果相比，我们的结果表明，我们的算法不仅提高了杂交反应的效率，而且还获得了更好的适应度值。
