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.

  • Letter
  • Published:

A proximity-based programmable DNA nanoscale assembly line



Our ability to synthesize nanometre-scale chemical species, such as nanoparticles with desired shapes and compositions, offers the exciting prospect of generating new functional materials and devices by combining them in a controlled fashion into larger structures. Self-assembly can achieve this task efficiently, but may be subject to thermodynamic and kinetic limitations: reactants, intermediates and products may collide with each other throughout the assembly time course to produce non-target species instead of target species. An alternative approach to nanoscale assembly uses information-containing molecules such as DNA1 to control interactions and thereby minimize unwanted cross-talk between different components. In principle, this method should allow the stepwise and programmed construction of target products by linking individually selected nanoscale components—much as an automobile is built on an assembly line. Here we demonstrate that a nanoscale assembly line can be realized by the judicious combination of three known DNA-based modules: a DNA origami2 tile that provides a framework and track for the assembly process, cassettes containing three independently controlled two-state DNA machines that serve as programmable cargo-donating devices3,4 and are attached4,5 in series to the tile, and a DNA walker that can move on the track from device to device and collect cargo. As the walker traverses the pathway prescribed by the origami tile track, it sequentially encounters the three DNA devices, each of which can be independently switched between an ‘ON’ state, allowing its cargo to be transferred to the walker, and an ‘OFF’ state, in which no transfer occurs. We use three different types of gold nanoparticle species as cargo and show that the experimental system does indeed allow the controlled fabrication of the eight different products that can be obtained with three two-state devices.

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

Access options

Buy this article

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

Figure 1: The molecular assembly line and its operation.
Figure 2: Details of the walker, movement and cargo transfer.
Figure 3: The eight products of the assembly line.

Similar content being viewed by others


  1. Seeman, N. C. & Lukeman, P. S. Nucleic acid nanostructures. Rep. Prog. Phys. 68, 237–270 (2005)

    Article  ADS  CAS  Google Scholar 

  2. Rothemund, P. W. K. Scaffolded DNA origami for nanoscale shapes and patterns. Nature 440, 297–302 (2006)

    Article  ADS  CAS  Google Scholar 

  3. Yan, H., Zhang, X., Shen, Z. & Seeman, N. C. A robust DNA mechanical device controlled by hybridization topology. Nature 415, 62–65 (2002)

    Article  ADS  CAS  Google Scholar 

  4. Ding, B. & Seeman, N. C. Operation of a DNA robot arm inserted into a 2D DNA crystalline substrate. Science 314, 1583–1585 (2006)

    Article  ADS  CAS  Google Scholar 

  5. Gu, H., Chao, J., Xiao, S. J. & Seeman, N. C. Dynamic patterning programmed by DNA tiles captured on a DNA origami substrate. Nature Nanotechnol. 4, 245–249 (2009)

    Article  ADS  CAS  Google Scholar 

  6. Ding, B., Sha, R. & Seeman, N. C. Pseudohexagonal 2D DNA crystals from double crossover cohesion. J. Am. Chem. Soc. 126, 10230–10231 (2004)

    Article  CAS  Google Scholar 

  7. Constantinou, P. E. et al. Double cohesion in structural DNA nanotechnology. Org. Biomol. Chem. 4, 3414–3419 (2006)

    Article  CAS  Google Scholar 

  8. Sherman, W. B. & Seeman, N. C. A precisely controlled DNA bipedal walking device. Nano Lett. 4, 1203–1207 (2004)

    Article  ADS  CAS  Google Scholar 

  9. Shin, J. S. & Pierce, N. A. A synthetic DNA walker for molecular transport. J. Am. Chem. Soc. 126, 10834–10835 (2004)

    Article  CAS  Google Scholar 

  10. Bath, J., Green, S. J., Allen, K. E. & Turberfield, A. J. Mechanism for a directional, processive and reversible DNA walker. Small 5, 1513–1516 (2009)

    Article  CAS  Google Scholar 

  11. Omabegho, T., Sha, R. & Seeman, N. C. A bipedal DNA Brownian motor with coordinated legs. Science 324, 67–71 (2009)

    Article  ADS  CAS  Google Scholar 

  12. Liu, D., Wang, W., Deng, Z., Walulu, R. & Mao, C. Tensegrity: construction of rigid DNA triangles with flexible four-arm junctions. J. Am. Chem. Soc. 126, 2324–2325 (2004)

    Article  CAS  Google Scholar 

  13. Yurke, B., Turberfield, A. J., Mills, A. P. Jr, Simmel, F. C. & Newmann, J. L. A DNA-fuelled molecular machine made of DNA. Nature 406, 605–608 (2000)

    Article  ADS  CAS  Google Scholar 

  14. Drexler, K. E. Machine-phase nanotechnology. Sci. Am. 285, 74–75 (2001)

    Article  CAS  Google Scholar 

  15. Smalley, R. E. Of chemistry, love and nanobots. Sci. Am. 285, 76–77 (2001)

    Article  CAS  Google Scholar 

  16. Gartner, Z. J., Kanan, M. W. & Liu, D. R. Multi-step small molecule synthesis programmed by DNA templates. J. Am. Chem. Soc. 124, 10304–10306 (2002)

    Article  CAS  Google Scholar 

  17. Seeman, N. C. De novo design of sequences for nucleic acid structure engineering. J. Biomol. Struct. Dyn. 8, 573–581 (1990)

    Article  CAS  Google Scholar 

  18. Caruthers, M. H. Gene synthesis machines: DNA chemistry and its uses. Science 230, 281–285 (1985)

    Article  ADS  CAS  Google Scholar 

  19. Ke, Y., Lindsay, S., Chang, Y., Liu, Y. & Yan, H. Self-assembled water-soluble nucleic acid probe tiles for label-free RNA hybridization assays. Science 319, 180–183 (2008)

    Article  ADS  CAS  Google Scholar 

  20. Zheng, J. et al. Two-dimensional nanoparticle arrays show the organizational power of robust DNA motifs. Nano Lett. 6, 1502–1504 (2006)

    Article  ADS  CAS  Google Scholar 

  21. Alivisatos, A. P. et al. Organization of ‘nanocrystal molecules’ using DNA. Nature 382, 609–611 (1996)

    Article  ADS  CAS  Google Scholar 

Download references


We are grateful to J. Canary, H. Yan, C. Mao and R. Sha for comments on this manuscript. This research has been supported by the following grants: GM-29544 from the US National Institute of General Medical Sciences, CTS-0608889 and CCF-0726378 from the US National Science Foundation, 48681-EL and W911NF-07-1-0439 from the US Army Research Office, N000140910181 and N000140911118 from the US Office of Naval Research and a grant from the W. M. Keck Foundation (to N.C.S.); and 2007CB925101 from the National Basic Research Program of China and 20721002 from the National Natural Science Foundation of China (to S.-J.X.). H.G. thanks New York University for a Dissertation Fellowship and J.C. thanks the Chinese Scholarship Council for a research fellowship.

Author information

Authors and Affiliations



H.G. and J.C. did the research, analysed data and wrote the paper. S.-J.X. analysed data and wrote the paper. N.C.S. designed the project, analysed data and wrote the paper.

Corresponding author

Correspondence to Nadrian C. Seeman.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Supplementary Information

This file comprises Supplementary Figures S1- S12 with legends and Supplementary Table S1 as follows: origami design (figure S1) and sequence; cassette design and sequence (figures S2-S4); walker locomotion and sequence design (figure S5); nondenaturing gels of the cassettes and walker (S6); agarose gels of the DNA-nanoparticle conjugates (figure S7), AFM images of the movement of the walker on the origami (figure S8); AFM images of the dynamic switching of each cassette on the origami (figure S9); zoomed TEM images for statistical analysis (figures S10 and S11); the distance distribution between particles on the walker (figure S12), and the statistical analysis for the different additions (table S1). (PDF 4267 kb)

PowerPoint slides

Rights and permissions

Reprints and permissions

About this article

Cite this article

Gu, H., Chao, J., Xiao, SJ. et al. A proximity-based programmable DNA nanoscale assembly line. Nature 465, 202–205 (2010).

Download citation

  • Received:

  • Accepted:

  • Issue Date:

  • DOI:


By submitting a comment you agree to abide by our Terms and Community Guidelines. If you find something abusive or that does not comply with our terms or guidelines please flag it as inappropriate.


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing