Talbot Hannah, Chandrasekaran Arun Richard
The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States.
Department of Biological Sciences, University at Albany, State University of New York, Albany, New York 12222, United States.
ACS Synth Biol. 2025 Jun 20;14(6):1931-1935. doi: 10.1021/acssynbio.5c00107. Epub 2025 May 28.
Dynamic DNA structures are controlled through toehold-based strand displacement, a method in which a DNA or RNA strand can bind to a single-stranded extension, cause branch migration, and result in the displacement of previously bound DNA. Here, we developed a toehold-free strand displacement method utilizing mismatched base pairs and stability differences between DNA complexes to control the reconfiguration of DNA nanostructures. We demonstrate this method using simple DNA duplexes and apply the strategy to reconfigure a paranemic crossover (PX) DNA based nanodevice into its topoisomer juxtaposed (JX) DNA. While the mismatch-induced toehold-free strand displacement was efficient in a simple double-stranded DNA model, the efficiency of strand displacement was lower in complex nanostructures. Increasing the number of mismatches increased the efficiency of the PX-JX conversion, and the process could be further controlled by tuning the number of mismatches. This device can be useful in stimuli-responsive mechanisms that have applications in biosensing, drug delivery, and molecular computation.
动态DNA结构是通过基于引发链的链置换来控制的，在这种方法中，一条DNA或RNA链可以与单链延伸部分结合，引发分支迁移，并导致先前结合的DNA被置换。在此，我们开发了一种无引发链的链置换方法，利用错配碱基对和DNA复合物之间的稳定性差异来控制DNA纳米结构的重新配置。我们使用简单的DNA双链体演示了这种方法，并将该策略应用于将平行交叉（PX）DNA基纳米器件重新配置为其拓扑异构体并列（JX）DNA。虽然在简单的双链DNA模型中，错配诱导的无引发链置换是有效的，但在复杂的纳米结构中，链置换的效率较低。增加错配的数量提高了PX-JX转换的效率，并且可以通过调整错配的数量进一步控制该过程。该器件可用于具有生物传感、药物递送和分子计算应用的刺激响应机制。
