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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.

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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.

References

  1. Mann, S. Life as a nanoscale phenomenon. Angew. Chem. Int. Ed. 47, 5306–5320 (2008).

    Article  CAS  Google Scholar 

  2. Li, R. & Gundersen, G. G. Beyond polymer polarity: how the cytoskeleton builds a polarized cell. Nat. Rev. Mol. Cell Biol. 9, 860–873 (2008).

    Article  CAS  Google Scholar 

  3. Desai, A. & Mitchison, T. J. Microtubule polymerization dynamics. Annu. Rev. Cell Dev. Biol. 13, 83–117 (1997).

    Article  CAS  Google Scholar 

  4. Conde, C. & Cáceres, A. Microtubule assembly, organization and dynamics in axons and dendrites. Nat. Rev. Neurosci. 10, 319–332 (2009).

    Article  CAS  Google Scholar 

  5. Mattila, P. K. & Lappalainen, P. Filopodia: molecular architecture and cellular functions. Nat. Rev. Mol. Cell Biol. 9, 446–454 (2008).

    Article  CAS  Google Scholar 

  6. Carlson, E. D., Gan, R., Hodgman, C. E. & Jewett, M. C. Cell-free protein synthesis: applications come of age. Biotechnol. Adv. 30, 1185–1194 (2012).

    Article  CAS  Google Scholar 

  7. Zhang, F., Nangreave, J., Liu, Y. & Yan, H. Structural DNA nanotechnology: state of the art and future perspective. J. Am. Chem. Soc. 136, 11198–11211 (2014).

    Article  CAS  Google Scholar 

  8. Blind, M. & Blank, M. Aptamer selection technology and recent advances. Mol. Ther. Nucleic Acids 4, e223 (2015).

    Article  Google Scholar 

  9. Zhang, D. Y. & Seelig, G. Dynamic DNA nanotechnology using strand-displacement reactions. Nat. Chem. 3, 103–113 (2011).

    Article  CAS  Google Scholar 

  10. Douglas, S. M. et al. Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res. 37, 5001–5006 (2009).

    Article  CAS  Google Scholar 

  11. Zadeh, J. N. et al. Nupack: analysis and design of nucleic acid systems. J. Comput. Chem. 32, 170–173 (2011).

    Article  CAS  Google Scholar 

  12. Fu, T. & Seeman, N. DNA double-crossover molecules. Biochemistry 32, 3211–3220 (1993).

    Article  CAS  Google Scholar 

  13. Winfree, E., Liu, F., Wenzler, L. A. & Seeman, N. C. Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539–544 (1998).

    Article  CAS  Google Scholar 

  14. Rothemund, P. W. K. et al. Design and characterization of programmable DNA nanotubes. J. Am. Chem. Soc. 126, 16344–16352 (2004).

    Article  CAS  Google Scholar 

  15. Rothemund, P. W. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).

    Article  CAS  Google Scholar 

  16. Douglas, S. M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414–418 (2009).

    Article  CAS  Google Scholar 

  17. Ke, Y., Ong, L. L., Shih, W. M. & Yin, P. Three-dimensional structures self-assembled from DNA bricks. Science 338, 1177–1183 (2012).

    Article  CAS  Google Scholar 

  18. Zhang, F. et al. Complex wireframe DNA origami nanostructures with multi-arm junction vertices. Nat. Nanotechnol. 10, 779–784 (2015).

    Article  CAS  Google Scholar 

  19. Benson, E. et al. DNA rendering of polyhedral meshes at the nanoscale. Nature 523, 441–444 (2015).

    Article  CAS  Google Scholar 

  20. Zheng, J. et al. From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature 461, 74–77 (2009).

    Article  CAS  Google Scholar 

  21. Jones, M. R., Seeman, N. C. & Mirkin, C. A. Programmable materials and the nature of the DNA bond. Science 347, 1260901 (2015).

    Article  Google Scholar 

  22. Yurke, B. & Mills, A. P. Using DNA to power nanostructures. Genet. Program. Evol. M. 4, 111–122 (2003).

    Article  Google Scholar 

  23. Seelig, G., Soloveichik, D., Zhang, D. Y. & Winfree, E. Enzyme-free nucleic acid logic circuits. Science 314, 1585–1588 (2006).

    Article  CAS  Google Scholar 

  24. Qian, L. & Winfree, E. Scaling up digital circuit computation with DNA strand displacement cascades. Science 3, 1196–1201 (2011).

    Article  Google Scholar 

  25. Chen, Y.-J. et al. Programmable chemical controllers made from DNA. Nat. Nanotechnol. 8, 755–762 (2013).

    Article  CAS  Google Scholar 

  26. Li, B., Ellington, A. D. & Chen, X. Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods. Nucleic Acids Res. 39, e110 (2011).

    Article  CAS  Google Scholar 

  27. Kim, J., White, K. S. & Winfree, E. Construction of an in vitro bistable circuit from synthetic transcriptional switches. Mol. Syst. Biol. 2, 68 (2006).

    Article  Google Scholar 

  28. Kim, J. & Winfree, E. Synthetic in vitro transcriptional oscillators. Mol. Syst. Biol. 7, 465 (2011).

    Article  Google Scholar 

  29. Montagne, K., Plasson, R., Sakai, Y., Fujii, T. & Rondelez, Y. Programming an in vitro DNA oscillator using a molecular networking strategy. Mol. Syst. Biol. 7, 466 (2011).

    Article  Google Scholar 

  30. Padirac, A., Fujii, T. & Rondelez, Y. Bottom-up construction of in vitro switchable memories. Proc. Natl Acad. Sci. USA 109, E3212–E3220 (2012).

    Article  CAS  Google Scholar 

  31. Ekani-Nkodo, A., Kumar, A. & Fygenson, D. K. Joining and scission in the self-assembly of nanotubes from DNA tiles. Phys. Rev. Lett. 93, 268301 (2004).

    Article  Google Scholar 

  32. Zhang, D. Y., Hariadi, R. F., Choi, H. M. T. & Winfree, E. Integrating DNA strand-displacement circuitry with DNA tile self-assembly. Nat. Commun. 4, 1965 (2013).

    Article  Google Scholar 

  33. Amodio, A., Adedeji, A. F., Castronovo, M., Franco, E. & Ricci, F. pH-controlled assembly of DNA tiles. J. Am. Chem. Soc. 138, 12735–12738 (2016).

    Article  CAS  Google Scholar 

  34. Green, L. N., Amodio, A., Subramanian, H. K. K. S., Ricci, F. & Franco, E. pH-driven reversible self-assembly of micron-scale DNA scaffolds. Nano Lett. 17, 7283–7288 (2017).

    Article  CAS  Google Scholar 

  35. Jeong, B. & Gutowska, A. Lessons from nature: stimuli-responsive polymers and their biomedical applications. Trends Biotechnol. 20, 305–311 (2002).

    Article  CAS  Google Scholar 

  36. Szostak, J. W., Bartel, D. P. & Luisi, P. L. Synthesizing life. Nature 409, 387–390 (2001).

    Article  CAS  Google Scholar 

  37. Phillips, J. A. et al. Using azobenzene incorporated DNA aptamers to probe molecular binding interactions. Bioconjug. Chem. 22, 282–288 (2011).

    Article  CAS  Google Scholar 

  38. He, X. et al. Synthetic homeostatic materials with chemo-mechano-chemical self-regulation. Nature 487, 214–218 (2012).

    Article  CAS  Google Scholar 

  39. Chr'etien, D. & Wade, R. H. New data on the microtubule surface lattice. Biol. Cell 71, 161–174 (1991).

    Article  CAS  Google Scholar 

  40. Wade, R. H., Chr´etien, D. & Job, D. Characterization of microtubule protofilament numbers: how does the surface lattice accommodate? J. Mol. Biol. 212, 775–786 (1990).

    Article  CAS  Google Scholar 

  41. Gittes, F., Mickey, B., Nettleton, J. & Howard, J. Flexural rigidity of microtubules and actin filaments measured from thermal fluctuations in shape. J. Cell Biol. 120, 923–934 (1993).

    Article  CAS  Google Scholar 

  42. Mohammed, A. M. & Schulman, R. Directing self-assembly of DNA nanotubes using programmable seeds. Nano Lett. 13, 4006–4013 (2013).

    Article  CAS  Google Scholar 

  43. Oosawa, F. et al. Thermodynamics of the Polymerization of Protein (Academic Press, Cambridge, 1975).

  44. Hariadi, R. F., Yurke, B. & Winfree, E. Thermodynamics and kinetics of DNA nanotube polymerization from single-filament measurements. Chem. Sci. 6, 2252–2267 (2015).

    Article  CAS  Google Scholar 

  45. Evans, C. G., Hariadi, R. F. & Winfree, E. Direct atomic force microscopy observation of DNA tile crystal growth at the single-molecule level. J. Am. Chem. Soc. 134, 10485–10492 (2012).

    Article  CAS  Google Scholar 

  46. Zhang, D. Y. & Winfree, E. Robustness and modularity properties of a non-covalent DNA catalytic reaction. Nucleic Acids Res. 38, 4182–4197 (2010).

    Article  CAS  Google Scholar 

  47. Evangelista, M., Zigmond, S. & Boone, C. Formins: signaling effectors for assembly and polarization of actin filaments. J. Cell Sci. 116, 2603–2611 (2003).

    Article  CAS  Google Scholar 

  48. Kim, J. In Vitro Synthetic Transcriptional Networks. PhD thesis, California Institute of Technology (2007).

  49. Schaffter, S. et al. T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures. Nucleic Acids Res. 46, 5332–5343 (2018).

    Article  CAS  Google Scholar 

  50. Franco, E. et al. Timing molecular motion and production with a synthetic transcriptional clock. Proc. Natl Acad. Sci. USA 108, E784–E793 (2011).

    Article  CAS  Google Scholar 

  51. Rahi, S. J., Pecani, K., Ondracka, A., Oikonomou, C. & Cross, F. R. The CFK-APC/C oscillator predominantly entrains periodic cell-cycle transcription. Cell 165, 475–487 (2016).

    Article  CAS  Google Scholar 

  52. Huang, C.-H., Tang, M., Shi, C., Iglesias, P. A. & Devreotes, P. N. An excitable signal integrator couples to an idling cytoskeletal oscillator to drive cell migration. Nat. Cell Biol. 15, 1307–1316 (2013).

    Article  CAS  Google Scholar 

  53. Weitz, M. et al. Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator. Nat. Chem. 6, 295–302 (2014).

    Article  CAS  Google Scholar 

  54. Cuba Samaniego, C., Giordano, G., Kim, J., Blanchini, F. & Franco, E. Molecular titration promotes oscillations and bistability in minimal network models with monomeric regulators. ACS Synth. Biol 5, 321–333 (2016).

    Article  CAS  Google Scholar 

  55. Del Vecchio, D., Ninfa, A. J. & Sontag, E. D. Modular cell biology: retroactivity and insulation. Mol. Syst. Biol. 4, 161 (2008).

    PubMed  PubMed Central  Google Scholar 

  56. Israelachvili, J. N. Intermolecular and Surface Forces revised 3rd edn (Academic Press, Cambridge, 2011).

  57. Mardanlou, V. et al. A coarse-grained model of DNA nanotube population growth in International Conference on DNA-Based Computers, 135–147 (Springer, 2016).

  58. Mardanlou, V. et al. A coarse-grained model captures the temporal evolution of DNA nanotube length distributions. Nat. Comput. 17, 183–199 (2018).

    Article  CAS  Google Scholar 

  59. Hariadi, R. F., Winfree, E. & Yurke, B. Determining hydrodynamic forces in bursting bubbles using DNA nanotube mechanics. Proc. Natl Acad. Sci. USA 112, E6086–E6095 (2015).

    Article  CAS  Google Scholar 

  60. Schulman, R. & Winfree, E. Synthesis of crystals with a programmable kinetic barrier to nucleation. Proc. Natl Acad. Sci. USA 104, 15236–15241 (2007).

    Article  CAS  Google Scholar 

  61. Qian, L. & Winfree, E. A simple DNA gate motif for synthesizing large-scale circuits. J. R. Soc. Interface 8, 1281–1297 (2011).

    Article  CAS  Google Scholar 

  62. Soloveichik, D., Seelig, G. & Winfree, E. DNA as a universal substrate for chemical kinetics. Proc. Natl Acad. Sci. USA 107, 5393–5398 (2010).

    Article  CAS  Google Scholar 

  63. Kim, J., Hopfield, J. & Winfree, E. Neural network computation by in vitro transcriptional circuits in Advances in Neural Information Processing Systems 681–688 (NIPS Foundation, 2004).

  64. Feng, L., Park, S. H., Reif, J. H. & Yan, H. A two-state DNA lattice switched by DNA nanoactuator. Angew. Chem. Int. Ed. 115, 4342–4346 (2003).

    Article  Google Scholar 

  65. Aldaye, F. A. & Sleiman, H. F. Dynamic DNA templates for discrete gold nanoparticle assemblies: control of geometry, modularity, write/erase and structural switching. J. Am. Chem. Soc. 129, 4130–4131 (2007).

    Article  CAS  Google Scholar 

  66. Gerling, T., Wagenbauer, K. F., Neuner, A. M. & Dietz, H. Dynamic DNA devices and assemblies formed by shape-complementary, non–base pairing 3D components. Science 347, 1446–1452 (2015).

    Article  CAS  Google Scholar 

  67. Mishra, D., Rivera, P. M., Lin, A., Del Vecchio, D. & Weiss, R. A load driver device for engineering modularity in biological networks. Nat. Biotechnol. 32, 1268–1275 (2014).

    Article  CAS  Google Scholar 

  68. Rondelez, Y. Competition for catalytic resources alters biological network dynamics. Phys. Rev. Lett. 108, 018102 (2012).

    Article  Google Scholar 

  69. Srinivas, N., Parkin, J., Seelig, G., Winfree, E. & Soloveichik, D. Enzyme-free nucleic acid dynamical systems. Science 358, eaal2052 (2017).

    Article  Google Scholar 

  70. Yan, H., Park, S. H., Finkelstein, G., Reif, J. H. & LaBean, T. H. DNA-templated self-assembly of protein arrays and highly conductive nanowires. Science 301, 1882–1884 (2003).

    Article  CAS  Google Scholar 

  71. LaBean, T. H. et al. Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes. J. Am. Chem. Soc. 122, 1848–1860 (2000).

    Article  CAS  Google Scholar 

  72. Zhao, Z., Liu, Y. & Yan, H. Organizing DNA origami tiles into larger structures using preformed scaffold frames. Nano Lett. 11, 2997–3002 (2011).

    Article  CAS  Google Scholar 

  73. Woo, S. & Rothemund, P. W. K. Programmable molecular recognition based on the geometry of DNA nanostructures. Nat. Chem 3, 620–627 (2011).

    Article  CAS  Google Scholar 

  74. Cho, E. J., Lee, J.-W. & Ellington, A. D. Applications of aptamers as sensors. Annu. Rev. Anal. Chem. 2, 241–264 (2009).

    Article  CAS  Google Scholar 

  75. Sharma, J. et al. Control of self-assembly of DNA tubules through integration of gold nanoparticles. Science 323, 112–116 (2009).

    Article  CAS  Google Scholar 

  76. Liu, D., Park, S. H., Reif, J. H. & LaBean, T. H. DNA nanotubes self-assembled from triple-crossover tiles as templates for conductive nanowires. Proc. Natl Acad. Sci. USA 101, 717–722 (2004).

    Article  CAS  Google Scholar 

  77. O’ Brien, M. N., Jones, M. R., Lee, B. & Mirkin, C. A. Anisotropic nanoparticle complementarity in DNA-mediated co-crystallization. Nat. Mater. 14, 833–839 (2015).

    Article  Google Scholar 

  78. Hadorn, M. et al. Specific and reversible DNA-directed self-assembly of oil-in-water emulsion droplets. Proc. Natl Acad. Sci. USA 109, 20320–20325 (2012).

    Article  CAS  Google Scholar 

  79. Hariadi, R. F., Appukutty, A. J. & Sivaramakrishnan, S. Engineering circular gliding of actin filaments along myosin-patterned DNA nanotube rings to study long-term actin–myosin behaviors. ACS Nano 10, 8281–8288 (2016).

    Article  CAS  Google Scholar 

  80. Delebecque, C. J., Lindner, A. B., Silver, P. A. & Aldaye, F. A. Organization of intracellular reactions with rationally designed RNA assemblies. Science 333, 470–474 (2011).

    Article  CAS  Google Scholar 

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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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Authors and Affiliations

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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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