Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Self-assembling DNA nanotubes to connect molecular landmarks


Within cells, nanostructures are often organized using local assembly rules that produce long-range order1,2. Because these rules can take into account the cell's current structure and state, they can enable complexes, organelles or cytoskeletal structures to assemble around existing cellular components to form architectures3,4,5,6. Although many methods for self-assembling biomolecular nanostructures have been developed7,8,9,10,11, few can be programmed to assemble structures whose form depends on the identity and organization of structures already present in the environment. Here, we demonstrate that DNA nanotubes can grow to connect pairs of molecular landmarks with different separation distances and relative orientations. DNA tile nanotubes nucleate at these landmarks and grow while their free ends diffuse. The nanotubes can then join end to end to form stable connections, with unconnected nanotubes selectively melted away. Connections form between landmark pairs separated by 1–10 µm in more than 75% of cases and can span a surface or three dimensions. This point-to-point assembly process illustrates how self-assembly kinetics can be designed to produce structures with a desired physical property rather than a specific shape.

This is a preview of subscription content, access via your institution

Relevant articles

Open Access articles citing this article.

Access options

Rent or buy this article

Get just this article for as long as you need it


Prices may be subject to local taxes which are calculated during checkout

Figure 1: Scheme for assembling interconnects between fixed molecular landmarks and the DNA nanostructures used within the assembly process.
Figure 2: DNA nanotubes connecting molecular landmarks.
Figure 3: Model calibrated using measured nanotube growth rates, and rotational and translational diffusion constants that reproduces the connection yields from experiment.
Figure 4: Assembly of DNA nanotube interconnects in three dimensions and selective melting of unconnected nanotubes.


  1. Fletcher, D. A. & Mullins, D. Cell mechanics and the cytoskeleton. Nature 463, 485–492 (2010).

    Article  CAS  Google Scholar 

  2. Misteli, T. The concept of self-organization in cellular architecture. J. Cell Biol. 155, 181–185 (2001).

    Article  CAS  Google Scholar 

  3. Vignaud, T., Blanchoin, L. & Thery, M. Directed cytoskeleton self-organization. Trends Cell Biol. 22, 671–682 (2012).

    Article  CAS  Google Scholar 

  4. Wang, N., Tytell, J. D. & Ingber, D. E. Mechanotransduction at a distance: mechanically coupling the extracellular matrix with the nucleus. Nat. Rev. Mol. Cell Biol. 10, 75–82 (2009).

    Article  CAS  Google Scholar 

  5. Greenfield, D. et al. Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy. PLoS Biol. 7, e1000137 (2009).

    Article  Google Scholar 

  6. Alberts, B. et al. Molecular Biology of the Cell 4th edn (Garland Science, 2002).

  7. Hartgerink, J. D., Beniash, E. & Stupp, S. I. Self-assembly and mineralization of peptide-amphiphile nanofibers. Science 294, 1684–1688 (2001).

    Article  CAS  Google Scholar 

  8. Percec, V. et al. Self-assembly of janus dendrimers into uniform dendrimersomes and other complex architectures. Science 328, 1009–1014 (2010).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  10. Barish, R. D., Schulman, R., Rothemund, P. W. K. & Winfree, E. An information-bearing seed for nucleating algorithmic self-assembly. Proc. Natl Acad. Sci. USA 106, 6054–6059 (2009).

    Article  CAS  Google Scholar 

  11. Wei, B., Dai, M. J. & Yin, P. Complex shapes self-assembled from single-stranded DNA tiles. Nature 485, 623–626 (2012).

    Article  CAS  Google Scholar 

  12. Dinarina, A. et al. Chromatin shapes the mitotic spindle. Cell 138, 502–513 (2009).

    Article  CAS  Google Scholar 

  13. Gadde, S. & Heald, R. Mechanisms and molecules of the mitotic spindle. Curr. Biol. 14, R797–R805 (2004).

    Article  CAS  Google Scholar 

  14. Helmke, K. J., Heald, R. & Wilbur, J. D. Interplay between spindle architecture and function. Int. Rev. Cell Mol. Biol. 306, 83–125 (2013).

    Article  CAS  Google Scholar 

  15. 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 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  18. Rothwell, S. W., Grasser, W. A. & Murphy, D. B. End-to-end annealing of microtubules in vitro. J. Cell Biol. 102, 619–627 (1986).

    Article  CAS  Google Scholar 

  19. 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 

  20. Doi, M. & Edwards, S. F. The Theory of Polymer Dynamics (Clarendon, 1988).

  21. 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 

  22. Mardanlou, V. et al. A coarse-grained model of DNA nanotube population growth. in DNA Computing and Molecular Programming (eds Rondelez, Y. & Woods, D.) 135–147 (2016).

  23. Brackley, C. A., Morozov, A. N. & Marenduzzo, D. Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS. J. Chem. Phys. 140, 135103 (2014).

    Article  CAS  Google Scholar 

  24. Schiffels, D., Liedl, T. & Fygenson, D. K. Nanoscale structure and microscale stiffness of DNA nanotubes. ACS Nano 7, 6700–6710 (2013).

    Article  CAS  Google Scholar 

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

    Article  Google Scholar 

  26. 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 

  27. Tan, S., Campolongo, M., Luo, D. & Cheng, W. Building plasmonic nanostructures with DNA. Nat. Nanotech. 6, 268–276 (2011).

    Article  CAS  Google Scholar 

  28. Knudsen, J. B. et al. Routing of individual polymers in designed patterns. Nat. Nanotech. 10, 892–898 (2015).

    Article  CAS  Google Scholar 

  29. Wilner, O. I. & Willner, I. Functionalized DNA nanostructures. Chem. Rev. 112, 2528–2556 (2012).

    Article  CAS  Google Scholar 

Download references


The authors thank D. Fygenson, M. Bevan, D. Gracias, E. Winfree, D. Agrawal, S. Schaffter and E. Franco for discussions and advice on the manuscript, J. Liphardt for the use of equipment and advice, and J. Fern, E. Pryce, R. Zuckermann and C. Ajo-Franklin for technical advice. This research has been supported by DOE grant DE-SC0010595, which provided money for materials, supplies and computing time, NSF CAREER award 125387, and the Miller Institute for Basic Science. P.Š. is supported by a grant from the Simons Foundation. Preliminary work related to this project at the Molecular Foundry was supported by the Office of Science, Office of Basic Energy Sciences, of the US Department of Energy, under contract no. DE-AC02-05CH11231.

Author information

Authors and Affiliations



A.M.M. and R.S. designed the experiments and carried out the experimental analysis. A.M.M. conducted the experiments. P.Š. and R.S. designed the simulations. P.Š. and J.Z. developed simulations and analysed simulation results. All the authors discussed the results and wrote the manuscript.

Corresponding author

Correspondence to Rebecca Schulman.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary information

Supplementary information (PDF 14042 kb)

Supplementary Movie 1

Supplementary Movie 1 (MOV 65 kb)

Supplementary Movie 2

Supplementary Movie 2 (MOV 2871 kb)

Supplementary Movie 3

Supplementary Movie 3 (MOV 27 kb)

Supplementary Movie 4

Supplementary Movie 4 (MOV 118 kb)

Supplementary Movie 5

Supplementary Movie 5 (MOV 515 kb)

Rights and permissions

Reprints and Permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Mohammed, A., Šulc, P., Zenk, J. et al. Self-assembling DNA nanotubes to connect molecular landmarks. Nature Nanotech 12, 312–316 (2017).

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI:

This article is cited by


Quick links

Find nanotechnology articles, nanomaterial data and patents all in one place. Visit Nano by Nature Research