Autonomous dynamic control of DNA nanostructure self-assemblyMay 15, 2019 | 0 | Autonomous , dynamic
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.
Access optionsAccess options
Subscribe to Journal
Get full journal access for 1 year
only $13.33 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
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.
Publisher’s note: Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Mann, S. Life as a nanoscale phenomenon. Angew. Chem. Int. Ed. 47, 5306–5320 (2008).
Li, R. & Gundersen, G. G. Beyond polymer polarity: how the cytoskeleton builds a polarized cell. Nat. Rev. Mol. Cell Biol. 9, 860–873 (2008).
Desai, A. & Mitchison, T. J. Microtubule polymerization dynamics. Annu. Rev. Cell Dev. Biol. 13, 83–117 (1997).
Conde, C. & Cáceres, A. Microtubule assembly, organization and dynamics in axons and dendrites. Nat. Rev. Neurosci. 10, 319–332 (2009).
Mattila, P. K. & Lappalainen, P. Filopodia: molecular architecture and cellular functions. Nat. Rev. Mol. Cell Biol. 9, 446–454 (2008).
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).
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).
Blind, M. & Blank, M. Aptamer selection technology and recent advances. Mol. Ther. Nucleic Acids 4, e223 (2015).
Zhang, D. Y. & Seelig, G. Dynamic DNA nanotechnology using strand-displacement reactions. Nat. Chem. 3, 103–113 (2011).
Douglas, S. M. et al. Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res. 37, 5001–5006 (2009).
Zadeh, J. N. et al. Nupack: analysis and design of nucleic acid systems. J. Comput. Chem. 32, 170–173 (2011).
Fu, T. & Seeman, N. DNA double-crossover molecules. Biochemistry 32, 3211–3220 (1993).
Winfree, E., Liu, F., Wenzler, L. A. & Seeman, N. C. Design and self-assembly of two-dimensional DNA crystals. Nature 394, 539–544 (1998).
Rothemund, P. W. K. et al. Design and characterization of programmable DNA nanotubes. J. Am. Chem. Soc. 126, 16344–16352 (2004).
Rothemund, P. W. Folding DNA to create nanoscale shapes and patterns. Nature 440, 297–302 (2006).
Douglas, S. M. et al. Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459, 414–418 (2009).
Ke, Y., Ong, L. L., Shih, W. M. & Yin, P. Three-dimensional structures self-assembled from DNA bricks. Science 338, 1177–1183 (2012).
Zhang, F. et al. Complex wireframe DNA origami nanostructures with multi-arm junction vertices. Nat. Nanotechnol. 10, 779–784 (2015).
Benson, E. et al. DNA rendering of polyhedral meshes at the nanoscale. Nature 523, 441–444 (2015).
Zheng, J. et al. From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal. Nature 461, 74–77 (2009).
Jones, M. R., Seeman, N. C. & Mirkin, C. A. Programmable materials and the nature of the DNA bond. Science 347, 1260901 (2015).
Yurke, B. & Mills, A. P. Using DNA to power nanostructures. Genet. Program. Evol. M. 4, 111–122 (2003).
Seelig, G., Soloveichik, D., Zhang, D. Y. & Winfree, E. Enzyme-free nucleic acid logic circuits. Science 314, 1585–1588 (2006).
Qian, L. & Winfree, E. Scaling up digital circuit computation with DNA strand displacement cascades. Science 3, 1196–1201 (2011).
Chen, Y.-J. et al. Programmable chemical controllers made from DNA. Nat. Nanotechnol. 8, 755–762 (2013).
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).
Kim, J., White, K. S. & Winfree, E. Construction of an in vitro bistable circuit from synthetic transcriptional switches. Mol. Syst. Biol. 2, 68 (2006).
Kim, J. & Winfree, E. Synthetic in vitro transcriptional oscillators. Mol. Syst. Biol. 7, 465 (2011).
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).
Padirac, A., Fujii, T. & Rondelez, Y. Bottom-up construction of in vitro switchable memories. Proc. Natl Acad. Sci. USA 109, E3212–E3220 (2012).
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).
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).
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).
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).
Jeong, B. & Gutowska, A. Lessons from nature: stimuli-responsive polymers and their biomedical applications. Trends Biotechnol. 20, 305–311 (2002).
Szostak, J. W., Bartel, D. P. & Luisi, P. L. Synthesizing life. Nature 409, 387–390 (2001).
Phillips, J. A. et al. Using azobenzene incorporated DNA aptamers to probe molecular binding interactions. Bioconjug. Chem. 22, 282–288 (2011).
He, X. et al. Synthetic homeostatic materials with chemo-mechano-chemical self-regulation. Nature 487, 214–218 (2012).
Chr’etien, D. & Wade, R. H. New data on the microtubule surface lattice. Biol. Cell 71, 161–174 (1991).
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).
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).
Mohammed, A. M. & Schulman, R. Directing self-assembly of DNA nanotubes using programmable seeds. Nano Lett. 13, 4006–4013 (2013).
Oosawa, F. et al. Thermodynamics of the Polymerization of Protein (Academic Press, Cambridge, 1975).
Hariadi, R. F., Yurke, B. & Winfree, E. Thermodynamics and kinetics of DNA nanotube polymerization from single-filament measurements. Chem. Sci. 6, 2252–2267 (2015).
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).
Zhang, D. Y. & Winfree, E. Robustness and modularity properties of a non-covalent DNA catalytic reaction. Nucleic Acids Res. 38, 4182–4197 (2010).
Evangelista, M., Zigmond, S. & Boone, C. Formins: signaling effectors for assembly and polarization of actin filaments. J. Cell Sci. 116, 2603–2611 (2003).
Kim, J. In Vitro Synthetic Transcriptional Networks. PhD thesis, California Institute of Technology (2007).
Schaffter, S. et al. T7 RNA polymerase non-specifically transcribes and induces disassembly of DNA nanostructures. Nucleic Acids Res. 46, 5332–5343 (2018).
Franco, E. et al. Timing molecular motion and production with a synthetic transcriptional clock. Proc. Natl Acad. Sci. USA 108, E784–E793 (2011).
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).
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).
Weitz, M. et al. Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator. Nat. Chem. 6, 295–302 (2014).
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).
Del Vecchio, D., Ninfa, A. J. & Sontag, E. D. Modular cell biology: retroactivity and insulation. Mol. Syst. Biol. 4, 161 (2008).
Israelachvili, J. N. Intermolecular and Surface Forces revised 3rd edn (Academic Press, Cambridge, 2011).
Mardanlou, V. et al. A coarse-grained model of DNA nanotube population growth in International Conference on DNA-Based Computers, 135–147 (Springer, 2016).
Mardanlou, V. et al. A coarse-grained model captures the temporal evolution of DNA nanotube length distributions. Nat. Comput. 17, 183–199 (2018).
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).
Schulman, R. & Winfree, E. Synthesis of crystals with a programmable kinetic barrier to nucleation. Proc. Natl Acad. Sci. USA 104, 15236–15241 (2007).
Qian, L. & Winfree, E. A simple DNA gate motif for synthesizing large-scale circuits. J. R. Soc. Interface 8, 1281–1297 (2011).
Soloveichik, D., Seelig, G. & Winfree, E. DNA as a universal substrate for chemical kinetics. Proc. Natl Acad. Sci. USA 107, 5393–5398 (2010).
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).
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).
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).
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).
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).
Rondelez, Y. Competition for catalytic resources alters biological network dynamics. Phys. Rev. Lett. 108, 018102 (2012).
Srinivas, N., Parkin, J., Seelig, G., Winfree, E. & Soloveichik, D. Enzyme-free nucleic acid dynamical systems. Science 358, eaal2052 (2017).
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).
LaBean, T. H. et al. Construction, analysis, ligation, and self-assembly of DNA triple crossover complexes. J. Am. Chem. Soc. 122, 1848–1860 (2000).
Zhao, Z., Liu, Y. & Yan, H. Organizing DNA origami tiles into larger structures using preformed scaffold frames. Nano Lett. 11, 2997–3002 (2011).
Woo, S. & Rothemund, P. W. K. Programmable molecular recognition based on the geometry of DNA nanostructures. Nat. Chem 3, 620–627 (2011).
Cho, E. J., Lee, J.-W. & Ellington, A. D. Applications of aptamers as sensors. Annu. Rev. Anal. Chem. 2, 241–264 (2009).
Sharma, J. et al. Control of self-assembly of DNA tubules through integration of gold nanoparticles. Science 323, 112–116 (2009).
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).
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).
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).
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).
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).
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.
Detailed descriptions of the methods; additional data; derivation and discussion of mathematical models and numerical simulations.
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.
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.
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.
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.
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.
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.
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.