Institute for Cellular and Molecular Biology , University of Texas at Austin , Austin , Texas 78712 , United States.
Chem Rev. 2019 May 22;119(10):6370-6383. doi: 10.1021/acs.chemrev.8b00625. Epub 2019 Mar 13.
Biological and biochemical systems are manifestations of chemical reaction networks (CRNs). The ability to design and engineer such networks may allow the construction of artificial systems that are as complex as those seen in biology, opening the way to translational possibilities including adaptive materials. One venue for progress is the design of autonomous systems capable of pattern generation; however many synthetic CRNs, such as the Belousov-Zhabotinsky reaction, cannot be rewired to encode more complex interactions and thus lack the capacity for more detailed engineering algorithms. In contrast, DNA is an information-rich molecule with predictable and reliable base-pairing interactions and well-studied kinetics, and the use of DNA has greatly enabled the rational design of much more complex synthetic CRNs. Recent advances in the DNA computing field include circuits for pattern transformation, an example of self-organization. An arsenal of tools for designing DNA circuits to implement various CRNs has been developed by DNA nanotechnologists, including software to reliably program strand-displacement nucleic acid circuits. In addition, DNA walkers can be used to create CRNs with controlled diffusivity, while DNA gels similarly represent a new medium for implementing CRNs that may ultimately lead to the development of smart materials. As we will argue, future endeavors in nucleic acid-based pattern generation will be most greatly advanced by harnessing well-known enzymatic processes to serve as generators and amplifiers. Once nucleic acid computing tools are further developed to expedite the design process of pattern generation, we anticipate a transition from proof-of-concept curiosities to application-driven inquiries.
生物和生化系统是化学反应网络 (CRN) 的表现形式。设计和工程此类网络的能力可能允许构建与生物学中所见一样复杂的人工系统，为适应性材料等转化可能性开辟道路。一个取得进展的途径是设计能够生成模式的自主系统；然而，许多合成的 CRN，如 Belousov-Zhabotinsky 反应，不能被重新布线以编码更复杂的相互作用，因此缺乏更详细的工程算法的能力。相比之下，DNA 是一种信息丰富的分子，具有可预测和可靠的碱基配对相互作用以及经过充分研究的动力学，并且 DNA 的使用极大地促进了更复杂的合成 CRN 的合理设计。DNA 计算领域的最新进展包括用于模式转换的电路，这是自组织的一个例子。DNA 纳米技术人员已经开发出用于设计实现各种 CRN 的 DNA 电路的工具套件，包括用于可靠编程链置换核酸电路的软件。此外，DNA 步行者可用于创建具有受控扩散率的 CRN，而 DNA 凝胶同样代表用于实现 CRN 的新介质，这可能最终导致智能材料的发展。正如我们将论证的那样，通过利用众所周知的酶促过程作为发生器和放大器，核酸基模式生成的未来工作将得到最大程度的推进。一旦核酸计算工具进一步开发以加快模式生成的设计过程，我们预计将从概念验证的好奇心过渡到应用驱动的探究。
