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核酸链置换——从 DNA 纳米技术到翻译调控。

Nucleic acid strand displacement - from DNA nanotechnology to translational regulation.

机构信息

TU Munich, School of Natural Sciences, Department of Bioscience, Garching, Germany.

出版信息

RNA Biol. 2023 Jan;20(1):154-163. doi: 10.1080/15476286.2023.2204565.

Abstract

Nucleic acid strand displacement reactions involve the competition of two or more DNA or RNA strands of similar sequence for binding to a complementary strand, and facilitate the isothermal replacement of an incumbent strand by an invader. The process can be biased by augmenting the duplex comprising the incumbent with a single-stranded extension, which can act as a toehold for a complementary invader. The toehold gives the invader a thermodynamic advantage over the incumbent, and can be programmed as a unique label to activate a specific strand displacement process. Toehold-mediated strand displacement processes have been extensively utilized for the operation of DNA-based molecular machines and devices as well as for the design of DNA-based chemical reaction networks. More recently, principles developed initially in the context of DNA nanotechnology have been applied for the de novo design of gene regulatory switches that can operate inside living cells. The article specifically focuses on the design of RNA-based translational regulators termed toehold switches. Toehold switches utilize toehold-mediated strand invasion to either activate or repress translation of an mRNA in response to the binding of a trigger RNA molecule. The basic operation principles of toehold switches will be discussed as well as their applications in sensing and biocomputing. Finally, strategies for their optimization will be described as well as challenges for their operation in vivo.

摘要

核酸链置换反应涉及两条或更多具有相似序列的 DNA 或 RNA 链之间的竞争,以与互补链结合,并促进热等温和入侵链取代现有链。通过增加包含现有链的双链体中的单链延伸,可以使该过程偏向于入侵链,该单链延伸可以作为互补入侵链的结合点。结合点为入侵链提供了相对于现有链的热力学优势,并且可以作为独特的标签进行编程,以激活特定的链置换过程。已广泛利用结合点介导的链置换过程来操作基于 DNA 的分子机器和设备,以及设计基于 DNA 的化学反应网络。最近,最初在 DNA 纳米技术背景下开发的原理已被应用于从头设计可在活细胞内运行的基因调控开关。本文特别关注基于 RNA 的翻译调节剂(称为结合点开关)的设计。结合点开关利用结合点介导的链入侵,根据触发 RNA 分子的结合,激活或抑制 mRNA 的翻译。将讨论结合点开关的基本操作原理及其在传感和生物计算中的应用。最后,将描述它们的优化策略以及在体内操作的挑战。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/dd91/10132225/8334ffcb6366/KRNB_A_2204565_F0001_OC.jpg

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