Autonomous dynamic control of DNA nanostructure self-assembly

Abstract

Biological cells routinely reconfigure their shape using dynamic signalling and regulatory networks that direct self-assembly processes in time and space, through molecular components that sense, process and transmit information from the environment. A similar strategy could be used to enable life-like behaviours in synthetic materials. Nucleic acid nanotechnology offers a promising route towards this goal through a variety of sensors, logic and dynamic components and self-assembling structures. Here, by harnessing both dynamic and structural DNA nanotechnology, we demonstrate dynamic control of the self-assembly of DNA nanotubes—a well-known class of programmable DNA nanostructures. Nanotube assembly and disassembly is controlled with minimal synthetic gene systems, including an autonomous molecular oscillator. We use a coarse-grained computational model to capture nanotube length distribution dynamics in response to inputs from nucleic acid circuits. We hope that these results may find use for the development of responsive nucleic acid materials, with potential applications in biomaterials science, nanofabrication and drug delivery.

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Fig. 1: Schematics of DNA nanotube self-assembly and proposed control mechanisms.
Fig. 2: Control of DNA nanotube length distribution via strand invasion and displacement reactions.
Fig. 3: Transcriptional control of nanotube self-assembly.
Fig. 4: Schematic of a system in which nanotube assembly is directed by a synthetic molecular oscillator.
Fig. 5: Controlling nanotube self-assembly with a molecular oscillator.
Fig. 6: Modelling dynamic control of DNA nanotube mean length.

Data availability

All the data sets generated and/or analysed during this study and supporting the findings described are available within the Article and its Supplementary Information and/or from the corresponding author upon reasonable request.

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Acknowledgements

The authors thank M. Weitz for initial assistance with experiments and P.W.K. Rothemund, E. Winfree, R. Schulman, B. Yurke, G. Seelig, F. Ricci and L. Mangolini for helpful advice and discussions. This research was primarily supported by the US Department of Energy under grant SC0010595, which paid for reagents and salary for H.K.K.S., L.N.G., V.M. and E.F. The authors also acknowledge funding by the Bourns College of Engineering at U.C. Riverside and by the US National Science Foundation through grant CMMI-1266402, which supported V.M. and the experimental and modelling work on the molecular oscillator.

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Contributions

E.F., J.K. and R.F.H. conceived and designed research and analysed the data. L.N.G. and H.K.K.S. designed and performed the experiments and analysed the data. V.M. and J.K. performed numerical simulations. E.F., L.N.G. and H.K.K.S. co-wrote the paper.

Corresponding author

Correspondence to Elisa Franco.

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Supplementary information

Supplementary Information

Detailed descriptions of the methods; additional data; derivation and discussion of mathematical models and numerical simulations.

Supplementary Movie 1

Example view of a control sample of annealed nanotubes with external toehold (prior to invasion and anti-invasion). This movie shows that over the imaging period the nanotubes are stable in the absence of invader and that the Cy3 fluorophore does not bleach within the relevant time-frame. Nanotubes were imaged for 11 minutes at a rate of 1 frame every 15 seconds; video is accelerated to last 9 seconds. Exposure time at every frame: 200 ms.

Supplementary Movie 2

Time-lapse video of invasion reaction on nanotubes with external toehold. The video clearly shows the nanotubes breaking at many positions along their axis (instead of breaking from the extrema as in the case of internal-toeholded nanotubes).The video starts at around 120 seconds after addition of invader to nanotubes. The video ends at 431 seconds after invader addition. The video was captured at the rate of one frame every 30 seconds, with 200 ms exposure time at every frame.

Supplementary Movie 3

Time-lapse video of invasion reaction on nanotubes with internal toehold. Some of the nanotubes shrink from the ends upon invasion while others sometimes break along the axis (presumably due to defects on nanotube surface). The video starts at around 120 seconds after addition of invader to the sample, and it ends at 810 seconds after invader addition. The video was captured at the rate of one frame every 30 seconds. Exposure time at every frame: 200 ms.

Supplementary Movie 4

This time-lapse video zooms on a specific area of SI Movie 3, and shows example internal-toeholded nanotubes shrinking from the ends upon invasion.

Supplementary Movie 5

Time-lapse video showing the regrowth of broken down (invaded) nanotubes after addition of anti-invader. The invader was added to the sample at 0 mins, and the anti-invader was added at 6 minutes. The video was recorded from 20 minutes and ends at 50 minutes. The video was originally captured at the rate of one frame every 15 seconds, in the current form it has been accelerated to have a total runtime of 18 seconds. Exposure time at every frame: 200 ms.

Supplementary Movie 6

This time-lapse video zooms on a specific area of SI Movie 5 to show examples of nanotubes joining. Video starts at 20 minutes and ends at 35 minutes.

Supplementary Movie 7

This time-lapse video zooms on a specific area of SI Movie 5 to show additional examples of nanotubes joining. Video starts at 20 minutes and ends at 50 minutes.

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Green, L.N., Subramanian, H.K.K., Mardanlou, V. et al. Autonomous dynamic control of DNA nanostructure self-assembly. Nat. Chem. 11, 510–520 (2019). https://doi.org/10.1038/s41557-019-0251-8

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