Department of Mechanical and Aerospace Engineering, University of California at Los Angeles, Los Angeles90095, United States.
Department of Bioengineering, University of California at Los Angeles, Los Angeles90095, United States.
ACS Nano. 2022 Oct 25;16(10):16372-16384. doi: 10.1021/acsnano.2c05595. Epub 2022 Oct 14.
The development of responsive, multicomponent molecular materials requires means to physically separate yet easily couple distinct processes. Here we demonstrate methods to use molecules and reactions loaded into microliter-sized polyacrylamide hydrogels (mini-gels) to control the dynamic self-assembly of DNA nanotubes. We first characterize the UV-mediated release of DNA molecules from mini-gels, changing diffusion rates and minimizing spontaneous leakage of DNA. We then demonstrate that mini-gels can be used as compartments for storage and release of DNA that mediates the assembly or disassembly of DNA nanotubes in a one-pot process and that the speed of DNA release is controlled by the mini-gel porosity. With this approach, we achieve control of assembly and disassembly of nanotubes with distinct kinetics, including a finite delay that is obtained by loading distinct DNA regulators into distinct mini-gels. We finally show that mini-gels can also host and localize enzymatic reactions, by transcribing RNA regulators from synthetic genes loaded in the mini-gels, with diffusion of RNA to the aqueous phase resulting in the activation of self-assembly. Our experimental data are recapitulated by a mathematical model that describes the diffusion of DNA molecules from the gel phase to the aqueous phase in which they control self-assembly of nanotubes. Looking forward, DNA-loaded mini-gels may be further miniaturized and patterned to build more sophisticated storage compartments for use within multicomponent, complex biomolecular materials relevant for biomedical applications and artificial life.
响应性、多组分分子材料的发展需要物理分离但又易于耦联的不同方法。在这里，我们展示了使用加载到微升尺寸聚丙烯酰胺水凝胶（微型凝胶）中的分子和反应来控制 DNA 纳米管的动态自组装的方法。我们首先对 DNA 分子从微型凝胶中的紫外介导释放进行了表征，改变了扩散速率并最小化了 DNA 的自发泄漏。然后，我们证明微型凝胶可用作 DNA 的存储和释放的隔室，该 DNA 介导 DNA 纳米管的组装或解组装在一锅过程中进行，并且 DNA 释放的速度由微型凝胶的孔隙率控制。通过这种方法，我们实现了具有不同动力学特性的纳米管组装和拆卸的控制，包括通过将不同的 DNA 调节剂加载到不同的微型凝胶中来获得的有限延迟。我们最后表明，微型凝胶还可以容纳和定位酶反应，通过从加载在微型凝胶中的合成基因转录 RNA 调节剂，将 RNA 扩散到水相导致自组装的激活。我们的实验数据通过一个数学模型得到了概括，该模型描述了 DNA 分子从凝胶相扩散到水相的过程，在该过程中它们控制着纳米管的自组装。展望未来，加载 DNA 的微型凝胶可以进一步微型化和图案化，以构建更复杂的存储隔室，用于与生物医学应用和人工生命相关的多组分复杂生物分子材料。
