Diagnostic applications of nucleic acid circuits.
Diagnostic applications of nucleic acid circuits.
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DOI：
10.1021/ar500059c
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发表时间：
2014-06-17
影响因子：
18.3
通讯作者：
Ellington, Andrew D.
中科院分区：
文献类型：
--
作者：
Jung, Cheulhee;Ellington, Andrew D.
虽然DNA计算和分子编程领域在很大程度上是作为好奇心驱动的练习而产生的，但它对分析应用的重要性越来越大。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。这些品质可以使核酸电路用于做出与诊断应用相关的决策。考虑到核酸电路可以潜在地直接与诊断核酸和其他分析物相互作用并由其触发，这尤其正确。总的来说，化学家们并不知道其中的许多进展，而本书提供了一种触及这一似乎是《双城之战》领域的方法。我们开始通过解释核酸扩增反应，可以导致信号放大，如催化发夹组装（CHA）和杂交链反应（HCR）。在这些回路中，单链输入通过暴露的支点和链交换反应作用于动力学捕获的底物，使底物重新折叠并使它们彼此相互作用。随着多个双链体（CHA）或长度增加的多联体（HCR）的产生，有机会将这些输出耦合到不同的分析模式，包括转导到荧光、电化学和比色信号。因为扩增和转导都在其根源上依赖于Waston-Crick碱基配对的可编程性，所以核酸电路可以比许多其他生物分子放大器更容易地调整和适应新的应用。例如，最近已经开发了用于实时监测等温扩增反应的稳健方法。除了扩增之外，核酸电路还可以包括逻辑门和阈值组件，以允许它们用于分析和决策。现在已经构建了能够执行诸如平方根或实现能够学习的神经网络的操作的可扩展和复杂的DNA电路（跷跷板门）。在未来，我们可以预期分子电路将被设计成在飞行中做出决定，重新配置诊断设备或导致新的治疗方案。
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.
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