XOR Gate Design Toward a Practical Complete Set for DNA Computing
XOR Gate Design Toward a Practical Complete Set for DNA Computing
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DOI：
10.1007/s00354-020-00090-3
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发表时间：
2020-03
影响因子：
2.6
通讯作者：
Katsuhiro Nishijima;T. Nakakuki
中科院分区：
文献类型：
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作者：
Katsuhiro Nishijima;T. Nakakuki
异或门的实际设计是DNA计算领域的一个重要里程碑。在这项研究中，我们的目标是开发一种无酶的异或门，这种异或门由一种具有真正检测特性的支点介导的链位移机制驱动。我们设计的优点是：不需要双轨逻辑，避免了非门的显式使用，电路结构简单，并且与四个NAND门组合设计的DNA链相比，可以实现更少的设计。进行了合理的电路设计，并通过计算机模拟确定了生化反应的动态行为和DNA链的二级结构。特别地，我们成功地实现了G-T错配碱基对的域级设计技术和碱基序列级微调技术，以减轻电路中存在的意外反应和漏反应引起的性能下降。实验研究证实了异或门设计的有效性。
Practical design of the XOR gate is an important milestone in the field of DNA computing. In this study, we aim to develop an enzyme-free XOR gate driven by a toehold-mediated strand displacement mechanism possessing the true detection property. The advantages of our design are as follows: dual-rail logic is not required, the explicit use of the NOT gate is avoided, the circuit structure is simple, and the design is achievable with fewer DNA strands than that designed by the combination of four NAND gates. A rational circuit design is performed and the dynamic behaviors of the biochemical reaction and the secondary structures of DNA strands are confirmed by computer simulation. In particular, both the domain-level design technique with G-T mismatched base pairs and base sequence-level fine-tuning are successfully achieved to alleviate the performance degradation arising from unintended and leaky reactions present in the circuit. The validity of the XOR gate design is confirmed by experimental studies.