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.
|Number of pages||13|
|State||Published - 25 Oct 2022|
Bibliographical noteFunding Information:
This project was supported in its entirety by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Award No. DE-SC-0010595. We thank Rebecca Schulman, Misha Rubanov, Yi Li, Francesco Ricci, and Kuan-Lin “Charlie” Chen for support and advice in the development of this project.
© 2022 American Chemical Society. All rights reserved.
- DNA nanotechnology
- DNA nanotubes
- DNA tiles
- UV irradiation