DNA polymerase programmed with a hairpin DNA incorporates a multiple-instruction architecture into molecular computing
DNA polymerase programmed with a hairpin DNA incorporates a multiple-instruction architecture into molecular computing
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DOI：
10.1016/j.biosystems.2005.07.005
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发表时间：
2006-01-01
期刊：
影响因子：
1.6
通讯作者：
Hagiya, M
中科院分区：
文献类型：
--
作者：
Komiya, K;Sakamoto, K;Hagiya, M
分子计算的主要优点之一是它的非线性。DNA分子中编码的大量数据可以通过分子生物学技术同时处理，尽管在解决方案中只实现了一组指令。我们已经开发出一种计算机，叫做“鞭击”机器，它是由DNA聚合酶和发夹DNA组成的。这台机器模拟了一个有限状态机，执行自己的指令编码在DNA部分，因此将适用于多指令操作的解决方案。在本研究中，我们探讨了这种新类型的并行性的可行性，通过应用鞭打机在有向哈密顿路径问题的计算。给定图中的可能路径用不同的指令集表示，然后由试管中的挥鞭机单独实现。在机器的自主操作之后，只有执行与哈密尔顿路径相对应的指令集的机器才能从管中恢复。根据实验确定的机器操作效率，可以在1 ml溶液中同时实现10（10）个不同的指令集。(C)2005爱思唯尔爱尔兰有限公司保留所有权利。
Parallelism is one of the major advantages of molecular computation. A large number of data encoded in DNA molecules can be processed simultaneously by molecular biology techniques, although only a single set of instructions has been implemented in a solution. We have developed a computing machine, called the "whiplash" machine, which is made of DNA polymerase and a hairpin DNA. This machine simulates a finite state machine, executing its own instructions encoded in the DNA moiety, and would thus be applicable to multiple-instruction operation in a solution. In the present study, we explored the feasibility of this novel type of parallelism by applying the whiplash machine in a computation of the directed Hamiltonian path problem. The possible paths in a given graph were represented with different instruction sets, which were then implemented separately by whiplash machines in a test tube. After an autonomous operation of the machines, only the machine that implemented the instruction set corresponding to the Hamiltonian path was recovered from the tube. On the basis of the efficiency of machine operation, which was experimentally determined, 10(10) different instruction sets could be implemented simultaneously in a 1-ml solution. (C) 2005 Elsevier Ireland Ltd. All rights reserved.