Jung Cheulhee, Ellington Andrew D
Institute for Cellular and Molecular Biology, University of Texas at Austin , Austin, Texas 78712, United States.
Acc Chem Res. 2014 Jun 17;47(6):1825-35. doi: 10.1021/ar500059c. Epub 2014 May 14.
While the field of DNA computing and molecular programming was engendered in large measure as a curiosity-driven exercise, it has taken on increasing importance for analytical applications. This is in large measure because of the modularity of DNA circuitry, which can serve as a programmable intermediate between inputs and outputs. These qualities may make nucleic acid circuits useful for making decisions relevant to diagnostic applications. This is especially true given that nucleic acid circuits can potentially directly interact with and be triggered by diagnostic nucleic acids and other analytes. Chemists are, by and large, unaware of many of these advances, and this Account provides a means of touching on what might seem to be an arcane field. We begin by explaining nucleic acid amplification reactions that can lead to signal amplification, such as catalytic hairpin assembly (CHA) and the hybridization chain reaction (HCR). In these circuits, a single-stranded input acts on kinetically trapped substrates via exposed toeholds and strand exchange reactions, refolding the substrates and allowing them to interact with one another. As multiple duplexes (CHA) or concatemers of increasing length (HCR) are generated, there are opportunities to couple these outputs to different analytical modalities, including transduction to fluorescent, electrochemical, and colorimetric signals. Because both amplification and transduction are at their root dependent on the programmability of Waston-Crick base pairing, nucleic acid circuits can be much more readily tuned and adapted to new applications than can many other biomolecular amplifiers. As an example, robust methods for real-time monitoring of isothermal amplification reactions have been developed recently. Beyond amplification, nucleic acid circuits can include logic gates and thresholding components that allow them to be used for analysis and decision making. Scalable and complex DNA circuits (seesaw gates) capable of carrying out operations such as taking square roots or implementing neural networks capable of learning have now been constructed. Into the future, we can expect that molecular circuitry will be designed to make decisions on the fly that reconfigure diagnostic devices or lead to new treatment options.
虽然DNA计算和分子编程领域在很大程度上是由好奇心驱动的探索，但它在分析应用中变得越来越重要。这在很大程度上是因为DNA电路的模块化，它可以作为输入和输出之间的可编程中间体。这些特性可能使核酸电路在做出与诊断应用相关的决策方面很有用。鉴于核酸电路有可能直接与诊断核酸和其他分析物相互作用并被其触发，情况尤其如此。总的来说，化学家们并未意识到这些进展中的许多内容，本综述提供了一种方式来探讨这个看似神秘的领域。我们首先解释可以导致信号放大的核酸扩增反应，例如催化发夹组装（CHA）和杂交链式反应（HCR）。在这些电路中，单链输入通过暴露的链端和链交换反应作用于动力学捕获的底物，使底物重新折叠并允许它们相互作用。随着多个双链体（CHA）或长度不断增加的串联体（HCR）的产生，有机会将这些输出与不同的分析方式耦合，包括转换为荧光、电化学和比色信号。由于扩增和转换从根本上都依赖于沃森-克里克碱基配对的可编程性，核酸电路比许多其他生物分子放大器更容易调整和适应新应用。例如，最近已经开发出用于实时监测等温扩增反应的可靠方法。除了扩增，核酸电路还可以包括逻辑门和阈值组件，使其能够用于分析和决策。现在已经构建了能够执行诸如求平方根或实现能够学习的神经网络等操作的可扩展且复杂的DNA电路（跷跷板门）。展望未来，我们可以预期分子电路将被设计用于即时做出决策，从而重新配置诊断设备或带来新的治疗选择。
