Biology Department, University of Rome Tor Vergata, Rome 00133, Italy.
Chemistry Department, University of Rome Tor Vergata, Rome 00133, Italy.
Nucleic Acids Res. 2018 Nov 2;46(19):9951-9959. doi: 10.1093/nar/gky857.
We propose an experimental and simulative approach to study the effect of integrating a DNA functional device into a large-sized DNA nanostructure. We selected, as a test bed, a well-known and characterized pH-dependent clamp-switch, based on a parallel DNA triple helix, to be integrated into a truncated octahedral scaffold. We designed, simulated and experimentally characterized two different functionalized DNA nanostructures, with and without the presence of a spacer between the scaffold and the functional elements. The experimental and simulative data agree in validating the need of a spacer for the occurrence of the pH dependent switching mechanism. The system is fully reversible and the switching can be monitored several times without any perturbation, maintaining the same properties of the isolated clamp switch in solution.
我们提出了一种实验和模拟的方法来研究将 DNA 功能器件集成到大尺寸 DNA 纳米结构中的效果。我们选择了一个基于平行 DNA 三螺旋的著名且经过表征的 pH 依赖性夹合开关作为测试平台，将其集成到截角八面体支架中。我们设计、模拟并实验表征了两种不同的功能化 DNA 纳米结构，一种在支架和功能元件之间有间隔物，另一种没有。实验和模拟数据一致，验证了在发生 pH 依赖性开关机制时需要间隔物。该系统是完全可逆的，并且可以在不产生任何干扰的情况下多次监测开关，同时保持在溶液中隔离夹合开关的相同性能。
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