Jahnke Kevin, Grubmüller Helmut, Igaev Maxim, Göpfrich Kerstin
Max Planck Institute for Medical Research, Biophysical Engineering Group, Jahnstraße 29, 69120 Heidelberg, Germany.
Department of Physics and Astronomy, Heidelberg University, 69120 Heidelberg, Germany.
Nucleic Acids Res. 2021 Apr 19;49(7):4186-4195. doi: 10.1093/nar/gkab201.
The ability to dynamically remodel DNA origami structures or functional nanodevices is highly desired in the field of DNA nanotechnology. Concomitantly, the use of fluorophores to track and validate the dynamics of such DNA-based architectures is commonplace and often unavoidable. It is therefore crucial to be aware of the side effects of popular fluorophores, which are often exchanged without considering the potential impact on the system. Here, we show that the choice of fluorophore can strongly affect the reconfiguration of DNA nanostructures. To this end, we encapsulate a triple-stranded DNA (tsDNA) into water-in-oil compartments and functionalize their periphery with a single-stranded DNA handle (ssDNA). Thus, the tsDNA can bind and unbind from the periphery by reversible opening of the triplex and subsequent strand displacement. Using a combination of experiments, molecular dynamics (MD) simulations, and reaction-diffusion modelling, we demonstrate for 12 different fluorophore combinations that it is possible to alter or even inhibit the DNA nanostructure formation-without changing the DNA sequence. Besides its immediate importance for the design of pH-responsive switches and fluorophore labelling, our work presents a strategy to precisely tune the energy landscape of dynamic DNA nanodevices.
在DNA纳米技术领域，人们非常渴望能够动态重塑DNA折纸结构或功能性纳米器件。与此同时，使用荧光团来追踪和验证此类基于DNA的结构的动态变化是很常见且往往不可避免的。因此，了解常用荧光团的副作用至关重要，因为这些荧光团在交换时常常没有考虑到对系统的潜在影响。在这里，我们表明荧光团的选择会强烈影响DNA纳米结构的重新配置。为此，我们将三链DNA（tsDNA）封装到油包水隔室中，并用单链DNA手柄（ssDNA）对其外围进行功能化。这样，tsDNA可以通过三链体的可逆打开和随后的链置换从外围结合和解离。通过结合实验、分子动力学（MD）模拟和反应扩散建模，我们针对12种不同的荧光团组合证明，有可能改变甚至抑制DNA纳米结构的形成——而无需改变DNA序列。除了对pH响应开关和荧光团标记设计具有直接重要性外，我们的工作还提出了一种精确调节动态DNA纳米器件能量景观的策略。
