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Dynamic Self-Assembly: Growth and Breakage of Synthetic DNA Nano-Structures


Biological systems reconfigure their shape in response to external stimuli at the level of single cells, tissues, and organs, for a variety of purposes such as growth, development, and self-repair. Cell shape reconfiguration is accomplished by directing the spatial organization of molecular materials (for example, cytoskeletal proteins) through molecular circuits which sense, process, and transmit information. Embedding a similar architecture in a synthetic material may greatly advance our ability to build responsive materials which can grow, reconfigure, and self-repair. DNA and RNA are programmable biological polymers which have been used to rationally build sensors and circuits, and a variety of nanostructures. The integration of nucleic acid circuits and structures promises to yield a new class of complex, reconfigurable materials. We aim at directing assembly and disassembly of DNA nanostructures with dynamic DNA inputs and circuits, mimicking the organization of dynamic cellular materials.

We focus on DNA nanotubes, and design pathways to control growth and breakage of tubes assembled from double crossover tiles. Our tiles include a toehold domain enabling strand invasion at the sticky ends of tiles. Invasion rapidly weakens the self-assembled structure, causing the nanotubes to collapse into smaller fragments. Removal of DNA species used for invasion, through second layer of strand displacement (denoted as anti-invasion), allows the nanotubes to reassemble isothermally. Our design thus makes it possible to control growth reversibly. We demonstrate this directed assembly process through a variety of experimental assays including optical microscopy and time-lapse movies, atomic force microscopy, and gel electrophoresis. We also characterize the influence of experimental design parameters such as toehold orientation (inside vs. outside of tube) and length, buffer conditions, and temperature, showing the overall tunability of breakage and reassembly dynamics.

Here, we bridge dynamic and structural DNA nanotechnology and demonstrate the programmable, dynamic control of self-assembly of DNA nanotubes, a well-known class of micron-sized DNA nanostructures. Nanotube assembly and disassembly is controlled with nucleic acid inputs and with transcriptional systems including an autonomous molecular oscillator.

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