Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montreal , Quebec H3A 0B8 , Canada.
ACS Nano. 2018 Dec 26;12(12):12836-12846. doi: 10.1021/acsnano.8b08016. Epub 2018 Dec 3.
Dynamic wireframe DNA structures have gained significant attention in recent years, with research aimed toward using these architectures for sensing and encapsulation applications. For these assemblies to reach their full potential, however, knowledge of the rates of strand displacement and hybridization on these constructs is required. Herein, we report the use of single-molecule fluorescence methodologies to observe the reversible switching between double- and single-stranded forms of triangular wireframe DNA nanotubes. Specifically, by using fluorescently labeled DNA strands, we were able to monitor changes in intensity over time as we introduced different sequences. This allowed us to extract detailed kinetic information on the strand displacement and hybridization processes. Due to the polymeric nanotube structure, the ability to individually address each of the three sides, and the inherent polydispersity of our samples as a result of the step polymerization by which they are formed, a library of compounds could be studied independently yet simultaneously. Kinetic models relying on mono-exponential decays, multi-exponential decays, or sigmoidal behavior were adjusted to the different constructs to retrieve erasing and refilling kinetics. Correlations were made between the kinetic behavior observed, the site accessibility, the nanotube length, and the structural robustness of wireframe DNA nanostructures, including fully single-stranded analogs. Overall, our results reveal how the length, morphology, and rigidity of the DNA framework modulate the kinetics of strand displacement and hybridization as well as the overall addressability and structural stability of the structures under study.
近年来，动态线状 DNA 结构引起了广泛关注，研究旨在将这些结构应用于传感和封装应用。然而，为了使这些组装物充分发挥其潜力，需要了解这些构建体上链置换和杂交的速率。在此，我们报告了使用单分子荧光方法学来观察三角形线状 DNA 纳米管的双链和单链形式之间的可逆切换。具体而言，通过使用荧光标记的 DNA 链，我们能够在引入不同序列时随时间监测强度变化。这使我们能够提取关于链置换和杂交过程的详细动力学信息。由于聚合物纳米管结构、能够单独寻址三个侧面中的每一个以及由于它们形成的逐步聚合而导致的样品固有多分散性，可以独立但同时研究化合物库。依赖于单指数衰减、多指数衰减或 S 形行为的动力学模型被调整为不同的构建体，以获取擦除和填充动力学。将观察到的动力学行为、位点可及性、纳米管长度以及线状 DNA 纳米结构的结构稳健性（包括完全单链类似物）之间进行了相关性分析。总体而言，我们的结果揭示了 DNA 框架的长度、形态和刚性如何调节链置换和杂交的动力学以及所研究结构的整体可寻址性和结构稳定性。
