Kinetics of heterochiral strand displacement from PNA-DNA heteroduplexes.
Kinetics of heterochiral strand displacement from PNA-DNA heteroduplexes.
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DOI：
10.1093/nar/gkab499
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发表时间：
2021-06-21
影响因子：
14.9
通讯作者：
Sczepanski JT
中科院分区：
文献类型：
--
作者：
Kundu N;Young BE;Sczepanski JT
动态DNA纳米器件是审讯和操纵生物系统的有力工具。然而，由于核酸酶降解和其他细胞因素，实施仍然具有挑战性。天然d-DNA的核酸酶抗性对映体l-DNA的使用提供了有希望的解决方案。在此基础上，我们最近开发了一种链置换方法，称为“异手性”链置换，使强大的l-DNA纳米器件与内源性d-核酸序列特异性接口。然而，潜在的反应-从PNA-DNA异源双链链置换-仍然很难表征，限制了设计能力。在此，我们表征了PNA-DNA异源双链体链置换的动力学，并表明反应速率可以根据几个常见的设计参数（包括立足点长度和错配）进行可预测的调整。此外，我们研究了核酸立体化学对反应动力学和热力学的影响，揭示了异手性链置换的生物物理机制的重要见解。重要的是，我们表明，链置换从PNA-DNA异源双链体是兼容的RNA输入，最常见的核酸靶细胞内应用。总的来说，这项工作大大提高了对异手性链置换反应的理解，并将有助于在与生物学的界面处操作的l-DNA纳米器件的合理设计和优化。
Dynamic DNA nanodevices represent powerful tools for the interrogation and manipulation of biological systems. Yet, implementation remains challenging due to nuclease degradation and other cellular factors. Use of l-DNA, the nuclease resistant enantiomer of native d-DNA, provides a promising solution. On this basis, we recently developed a strand displacement methodology, referred to as ‘heterochiral’ strand displacement, that enables robust l-DNA nanodevices to be sequence-specifically interfaced with endogenous d-nucleic acids. However, the underlying reaction – strand displacement from PNA–DNA heteroduplexes – remains poorly characterized, limiting design capabilities. Herein, we characterize the kinetics of strand displacement from PNA–DNA heteroduplexes and show that reaction rates can be predictably tuned based on several common design parameters, including toehold length and mismatches. Moreover, we investigate the impact of nucleic acid stereochemistry on reaction kinetics and thermodynamics, revealing important insights into the biophysical mechanisms of heterochiral strand displacement. Importantly, we show that strand displacement from PNA–DNA heteroduplexes is compatible with RNA inputs, the most common nucleic acid target for intracellular applications. Overall, this work greatly improves the understanding of heterochiral strand displacement reactions and will be useful in the rational design and optimization of l-DNA nanodevices that operate at the interface with biology.
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DOI：
10.1073/pnas.0407024101
发表时间：
2004-10-26
影响因子：
11.1
作者：
Dirks, RM;Pierce, NA
通讯作者：
Pierce, NA
影响因子：
14.9
作者：
Amarzguioui, M;Holen, T;Prydz, H
通讯作者：
Prydz, H
影响因子：
38.3
作者：
Groves B;Chen YJ;Zurla C;Pochekailov S;Kirschman JL;Santangelo PJ;Seelig G
通讯作者：
Seelig G
影响因子：
16.6
作者：
Haley, Natalie E. C.;Ouldridge, Thomas E.;Turberfield, Andrew J.
通讯作者：
Turberfield, Andrew J.
影响因子：
14.9
作者：
Giesen, U;Kleider, W;Nielsen, PE
通讯作者：
Nielsen, PE