Jiang Shuoxing, Pal Nibedita, Hong Fan, Fahmi Nour Eddine, Hu Huiyu, Vrbanac Matthew, Yan Hao, Walter Nils G, Liu Yan
Center for Molecular Design and Biomimetics at the Biodesign Institute, and School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States.
Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States.
ACS Nano. 2021 Mar 23;15(3):5384-5396. doi: 10.1021/acsnano.1c00027. Epub 2021 Mar 11.
Controlling the nucleation step of a self-assembly system is essential for engineering structural complexity and dynamic behaviors. Here, we design a "frame-filling" model system that comprises one type of self-complementary DNA tile and a hosting DNA origami frame to investigate the inherent dynamics of three general nucleation modes in nucleated self-assembly: unseeded, facet, and seeded nucleation. Guided by kinetic simulation, which suggested an optimal temperature range to differentiate the individual nucleation modes, and complemented by single-molecule observations, the transition of tiles from a metastable, monomeric state to a stable, polymerized state through the three nucleation pathways was monitored by Mg-triggered kinetic measurements. The temperature-dependent kinetics for all three nucleation modes were correlated by a "nucleation-growth" model, which quantified the tendency of nucleation using an empirical nucleation number. Moreover, taking advantage of the temperature dependence of nucleation, tile assembly can be regulated externally by the hosting frame. An ultraviolet (UV)-responsive trigger was integrated into the frame to simultaneously control "when" and "where" nucleation started. Our results reveal the dynamic mechanisms of the distinct nucleation modes in DNA tile-based self-assembly and provide a general strategy for controlling the self-assembly process.
控制自组装系统的成核步骤对于构建结构复杂性和动态行为至关重要。在此，我们设计了一种“框架填充”模型系统，其由一种自互补DNA瓦片和一个宿主DNA折纸框架组成，以研究成核自组装中三种一般成核模式的内在动力学：无种晶成核、晶面成核和种晶成核。在动力学模拟的指导下（该模拟提出了区分各个成核模式的最佳温度范围），并辅以单分子观察，通过镁触发的动力学测量监测了瓦片通过三种成核途径从亚稳态单体状态转变为稳定聚合状态的过程。所有三种成核模式的温度依赖性动力学通过“成核 - 生长”模型相关联，该模型使用经验成核数来量化成核趋势。此外，利用成核的温度依赖性，瓦片组装可由宿主框架进行外部调节。将紫外线（UV）响应触发器集成到框架中，以同时控制成核开始的“时间”和“位置”。我们的结果揭示了基于DNA瓦片的自组装中不同成核模式的动态机制，并提供了一种控制自组装过程的通用策略。
