Programmable and autonomous computing machine made of biomolecules
Programmable and autonomous computing machine made of biomolecules
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DOI：
10.1038/35106533
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发表时间：
2001-11-22
期刊：
影响因子：
64.8
通讯作者：
Shapiro, E
中科院分区：
文献类型：
--
作者：
Benenson, Y;Paz-Elizur, T;Shapiro, E
按照一定的程序把信息从一种形式转换成另一种形式的装置称为自动机。其中一个假想的装置就是通用图灵机(1)，它激发了导致现代计算机发展的工作。图灵机及其特殊情况(2)，包括有限自动机(3)，通过扫描数据带来运行，其与信息编码生物聚合物的惊人相似性启发了分子DNA计算机的几种设计（4-8）。使用DNA和人类辅助协议的实验室规模计算已经得到证实（9-15），但在分子尺度上自主操作的计算设备的实现仍然很少（16-20）。在这里，我们描述了一个由DNA和DNA操纵酶组成的可编程有限自动机，它可以自主地解决计算问题。自动机的硬件由限制性核酸酶和连接酶组成，软件和输入由双链DNA编码，编程相当于选择合适的软件分子。在混合含有这些成分的溶液后，自动机通过一系列限制、杂交和连接循环处理输入分子，产生可检测的输出分子，该输出分子编码自动机的最终状态，从而获得计算结果。在我们的实现中，共享相同软件的10（12）个自动机在室温下的120多溶液中以每秒10(9)次转换的组合速率独立并行运行（原则上可以不同），转换保真度大于99.8%，消耗小于10(-10)W。
Devices that convert information from one form into another according to a definite procedure are known as automata. One such hypothetical device is the universal Turing machine(1), which stimulated work leading to the development of modern computers. The Turing machine and its special cases(2), including finite automata(3), operate by scanning a data tape, whose striking analogy to information-encoding biopolymers inspired several designs for molecular DNA computers(4-8). Laboratory-scale computing using DNA and human-assisted protocols has been demonstrated(9-15), but the realization of computing devices operating autonomously on the molecular scale remains rare(16-20). Here we describe a programmable finite automaton comprising DNA and DNA-manipulating enzymes that solves computational problems autonomously. The automaton's hardware consists of a restriction nuclease and ligase, the software and input are encoded by double-stranded DNA, and programming amounts to choosing appropriate software molecules. Upon mixing solutions containing these components, the automaton processes the input molecule via a cascade of restriction, hybridization and ligation cycles, producing a detectable output molecule that encodes the automaton's final state, and thus the computational result. In our implementation 10(12) automata sharing the same software run independently and in parallel on inputs (which could, in principle, be distinct) in 120 mul solution at room temperature at a combined rate of 10(9) transitions per second with a transition fidelity greater than 99.8%, consuming less than 10(-10) W.