A programming language for composable DNA circuits
A programming language for composable DNA circuits
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DOI：
10.1098/rsif.2009.0072.focus
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发表时间：
2009-08-06
影响因子：
3.9
通讯作者：
Cardelli, Luca
中科院分区：
文献类型：
--
作者：
Phillips, Andrew;Cardelli, Luca
最近，一系列的信息处理电路已经在DNA中实现，通过使用链置换作为它们的主要计算机制。实例包括数字逻辑电路和催化信号放大电路，其用作有效的分子检测器。随着新的DNA计算范式的出现，开发相应的语言和工具，这些范式将有助于促进DNA电路的设计和自动编译为核苷酸序列。我们提出了一种编程语言，用于设计和模拟DNA电路，其中链置换是主要的计算机制。该语言包括序列结构域、立足点和分支迁移的基本元素，并假设链不具有任何二级结构。该语言用于建模和模拟各种电路，包括熵驱动的催化门，用于合成大规模电路的简单门基序和用于实现任意化学反应系统的方案。该语言是设计DNA链置换建模和仿真工具的第一步，它补充了DNA计算新实现策略的出现。
Recently, a range of information-processing circuits have been implemented in DNA by using strand displacement as their main computational mechanism. Examples include digital logic circuits and catalytic signal amplification circuits that function as efficient molecular detectors. As new paradigms for DNA computation emerge, the development of corresponding languages and tools for these paradigms will help to facilitate the design of DNA circuits and their automatic compilation to nucleotide sequences. We present a programming language for designing and simulating DNA circuits in which strand displacement is the main computational mechanism. The language includes basic elements of sequence domains, toeholds and branch migration, and assumes that strands do not possess any secondary structure. The language is used to model and simulate a variety of circuits, including an entropy-driven catalytic gate, a simple gate motif for synthesizing large-scale circuits and a scheme for implementing an arbitrary system of chemical reactions. The language is a first step towards the design of modelling and simulation tools for DNA strand displacement, which complements the emergence of novel implementation strategies for DNA computing.