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.

中文翻译：

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用三联体碱基不配对限制DNA序列。

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，具有许多应用前景。DNA计算的准确性取决于可靠的DNA序列，其质量会影响杂交反应的准确性。通过评估从NUPACK中先前组合约束获得的序列以进行模拟实验，我们发现进入溶液后的序列浓度明显低于进入溶液前的浓度，这将影响DNA杂交反应的准确性。因此，在这项研究中，我们提出了一个新的约束条件，即基于三重态的不成对约束条件，可以将其与其他约束条件组合起来以形成新的组合约束条件。此外，我们将“和谐搜索”算法与“鲸鱼优化算法”（WOA）相结合，提出了一种称为HSWOA的新算法，该算法用于设计满足新组合约束的DNA序列。最后，与以前的发现相比，我们的结果表明我们的算法不仅提高了杂交反应的效率，而且产生了更好的适应性值。