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Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

Dynamic Self-Assembly of DNA Nanotubes

Cells reconfigure their shape in response to external stimuli for a variety of purposes such as growth, development, and self-repair. Shape control is accomplished by directing the spatial organization of molecular materials (for example, cytoskeletal proteins) through molecular circuits that 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. However, cellular pathways are still too complex to be directly used in a synthetic material, because they involve hundreds of tightly connected components. An alternative route is offered by nucleic acid nanotechnology: DNA and RNA are programmable biological polymers that have been used to rationally build sensors and circuits (Franco et al., 2011), and a variety of nanostructures (Pinheiro et al., 2011). These devices can be engineered to operate together. We aim at directing assembly and disassembly of DNA nanostructures with dynamic DNA inputs and circuits, mimicking the organization of dynamic cellular materials.

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We focus on DNA nanotubes, and design pathways to control growth and breakage of tubes assembled from double crossover tiles (Rothemund et al., 2004). Our tilesinclude 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 the DNA species used for invasion, through another layer of strand displacement, allows the nanotubes to reassemble isothermally. Thus, unlike previously proposed approaches (Zhang et al., 2013), we are able 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 and length, buffer conditions, and temperature, showing the overall tunability of breakage and reassembly dynamics.

The integration of nucleic acid circuits and structures promises to yield a new class of complex, reconfigurable biomaterials. This research is supported by grant DE-SC0010595.

References
Franco, E., Friedrichs, E., Kim, J., Jungmann, R., Murray, R., Winfree, E., & Simmel, F. C. (2011). Timing molecular motion and production with a synthetic transcriptional clock. Proceedings of the National Academy of Sciences, 108(40), E784-E793.

Pinheiro, A. V., Han, D., Shih, W. M., & Yan, H. (2011). Challenges and opportunities for structural DNA nanotechnology. Nature nanotechnology, 6(12), 763-772.

Rothemund, P. W., Ekani-Nkodo, A., Papadakis, N., Kumar, A., Fygenson, D. K., & Winfree, E. (2004). Design and characterization of programmable DNA nanotubes. Journal of the American Chemical Society, 126(50), 16344-16352.

Zhang, D. Y., Hariadi, R. F., Choi, H. M., & Winfree, E. (2013). Integrating DNA strand-displacement circuitry with DNA tile self-assembly. Nature communications, 4.

Leopold N. Green1
Hari K. K. Subramanian 2
Vahid Mardanlou 3
Jongmin Kim 4
Rizal F. Hariadi 5
Elisa Franco 2*

1Department of Bioengineering
University of California
Riverside, CA 92521, USA
2Department of Mechanical Engineering, University of California
Riverside, CA 92521, USA
3 Department of Electrical Engineering, University of California
Riverside, CA 92521, USA
4Wyss Institute for Biologically Inspired Engineering
Harvard University
Cambridge MA 02115, USA
5Department of Cell and Developmental Biology
University of Michigan
Ann Arbor, MI 48109

Ph: +1 (626) 215-0543
Fx: (951) 827-3188
efranco@ucr.edu