Rapid Exchange of Stably Bound Protein and DNA Cargo on a DNA Origami Receptor

Biomolecular complexes can form stable assemblies yet can also rapidly exchange their subunits to adapt to environmental changes. Simultaneously allowing for both stability and rapid exchange expands the functional capacity of biomolecular machines and enables continuous function while navigating a complex molecular world. Inspired by biology, we design and synthesize a DNA origami receptor that exploits multivalent interactions to form stable complexes that are also capable of rapid subunit exchange. The system utilizes a mechanism first outlined in the context of the DNA replisome, known as multisite competitive exchange, and achieves a large separation of time scales between spontaneous subunit dissociation, which requires days, and rapid subunit exchange, which occurs in minutes. In addition, we use the DNA origami receptor to demonstrate stable interactions with rapid exchange of both DNA and protein subunits, thus highlighting the applicability of our approach to arbitrary molecular cargo, an important distinction with canonical toehold exchange between single-stranded DNA. We expect this study to benefit future studies that use DNA origami structures to exploit multivalent interactions for the design and synthesis of a wide range of possible kinetic behaviors.生物分子复合物既可形成稳定组装体，又可通过快速交换亚基以适应环境变化。同时兼顾稳定性与快速亚基交换能力，可拓展生物分子机器的功能潜能，并使其在复杂分子环境中维持持续运作。受生物学机制启发，我们设计并合成了一种DNA折纸（DNA origami）受体，该受体通过利用多价相互作用形成稳定复合物，同时具备快速亚基交换的能力。本系统采用了最初在DNA复制体（DNA replisome）研究中提出的多位点竞争性交换（multisite competitive exchange）机制，实现了自发亚基解离（耗时可达数日）与快速亚基交换（仅需数分钟）之间的大幅时间尺度分离。此外，我们利用该DNA折纸受体，证实其可在DNA与蛋白质亚基均发生快速交换的情况下维持稳定相互作用，从而凸显了本方法可适配任意分子载荷的优势，这与单链DNA间的经典锚定臂交换（toehold exchange）存在显著差异。我们期望本研究能够为未来利用DNA折纸结构、借助多价相互作用设计并合成具备多样动力学行为的相关研究提供助力。