Skip to main content

Thank you for visiting nature.com. 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.

  • Article
  • Published:

Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates

Nature Nanotechnology volume 5, pages 61–66 (2010)Cite this article

Abstract

A central challenge in nanotechnology is the parallel fabrication of complex geometries for nanodevices. Here we report a general method for arranging single-walled carbon nanotubes in two dimensions using DNA origami—a technique in which a long single strand of DNA is folded into a predetermined shape. We synthesize rectangular origami templates (∼75 nm × 95 nm) that display two lines of single-stranded DNA ‘hooks’ in a cross pattern with ∼6 nm resolution. The perpendicular lines of hooks serve as sequence-specific binding sites for two types of nanotubes, each functionalized non-covalently with a distinct DNA linker molecule. The hook-binding domain of each linker is protected to ensure efficient hybridization. When origami templates and DNA-functionalized nanotubes are mixed, strand displacement-mediated deprotection and binding aligns the nanotubes into cross-junctions. Of several cross-junctions synthesized by this method, one demonstrated stable field-effect transistor-like behaviour. In such organizations of electronic components, DNA origami serves as a programmable nanobreadboard; thus, DNA origami may allow the rapid prototyping of complex nanotube-based structures.

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

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

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

Figure 1: Overview of cross-junction assembly.
Figure 2: Distributions showing sequence-specific attachment of NL-SWNTs to DNA templates and angular control over orientation.
Figure 3: Electrical characterization of a self-assembled SWNT cross-junction.

Similar content being viewed by others

References

  1. Hata, K. et al. Water-assisted highly efficient synthesis of impurity-free single-walled carbon nanotubes. Science 306, 1362–1364 (2004).

    Article  CAS  Google Scholar 

  2. Zheng, M. et al. DNA-assisted dispersion and separation of carbon nanotubes. Nature Mater. 2, 338–342 (2003).

    Article  CAS  Google Scholar 

  3. Zheng, M. et al. Structure-based carbon nanotube sorting by sequence-dependent DNA assembly. Science 302, 1545–1548 (2003).

    Article  CAS  Google Scholar 

  4. Huang, X., McLean, R. S. & Zheng, M. High-resolution length sorting and purification of DNA-wrapped carbon nanotubes by size-exclusion chromatography. Anal. Chem. 77, 6225–6228 (2005).

    Article  CAS  Google Scholar 

  5. Deng, W.-Q., Matsuda, Y. & Goddard, W. A. Bifunctional anchors connecting carbon nanotubes to metal electrodes for improved nanoelectronics. J. Am. Chem. Soc. 129, 9834–9835 (2007).

    Article  CAS  Google Scholar 

  6. Cao, Q. & Rogers, J. A. Ultrathin films of single-walled carbon nanotubes for electronics and sensors: a review of fundamental and applied aspects. Adv. Mater. 21, 29–53 (2009).

    Article  CAS  Google Scholar 

  7. Piner, R. D., Zhu, J., Xu, F., Hong, S. & Mirkin, C. A. ‘Dip-pen’ nanolithography. Science 283, 661–663 (1999).

    CAS  Google Scholar 

  8. Vieu, C. et al. Electron beam lithography: resolution limits and applications. Appl. Surf. Sci. 164, 111–117 (2000).

    Article  CAS  Google Scholar 

  9. Chou, S. Y., Krauss, P. R. & Renstrom, P. J. Imprint lithography with 25-nanometer resolution. Science 272, 85–87 (1996).

    Article  CAS  Google Scholar 

  10. Wu, W. et al. Sub-10 nm nanoimprint lithography by wafer bowing. J. Am. Chem. Soc. 8, 3865–3869 (2008).

    CAS  Google Scholar 

  11. Wang, Y., Maspoch, D., Zou, S. & Schatz, G. C. Controlling the shape, orientation, and linkage of carbon nanotube features with nano affinity templates. Proc. Natl Acad. Sci. USA 103, 2026–2031 (2006).

    Article  CAS  Google Scholar 

  12. Diehl, M. R., Yaliraki, S. N., Beckman, R. A., Barahona, M. & Heath, J. R. Self-assembled, deterministic carbon nanotube wiring networks. Angew. Chem. Int. Ed. 41, 353–356 (2002).

    Article  CAS  Google Scholar 

  13. Williams, K. A., Veenhuizen, P. T. M., de la Torre, B. G., Eritja, R. & Dekker, C. Nanotechnology: carbon nanotubes with DNA recognition. Nature 420, 761 (2002).

    Article  CAS  Google Scholar 

  14. Lyonnais, S. et al. A three-branched DNA template for carbon nanotube self-assembly into nanodevice configuration. Chem. Commun. 683–685 (2009).

  15. Keren, K., Berman, R. S., Buchstab, E., Sivan, U. & Braun, E. DNA-templated carbon-nanotube field effect transistor. Science 302, 1380–1382 (2003).

    Article  CAS  Google Scholar 

  16. Hazani, M. et al. DNA-mediated self-assembly of carbon nanotube-based electronic devices. Chem. Phys. Lett. 391, 389–392 (2004).

    Article  CAS  Google Scholar 

  17. Bourgoin, J. P. et al. Directed assembly for carbon nanotube device fabrication. Int. Electron Devices Meet. (IEDM '06) 1–4 (2006).

  18. Seeman, N. C. Nucleic-acid junctions and lattices. J. Theor. Biol. 99, 237–247 (1982).

    Article  CAS  Google Scholar 

  19. Seeman, N. C. An overview of structural DNA nanotechnology. Mol. Biotechnol. 37, 246–257 (2007).

    Article  CAS  Google Scholar 

  20. Robinson, B. H. & Seeman, N. C. The design of a biochip: a self-assembling molecular-scale memory device. Protein Eng. 1, 295–300 (1987).

    Article  CAS  Google Scholar 

  21. Pinto, Y. Y. et al. Sequence-encoded self-assembly of multiple-nanocomponent arrays by 2D DNA scaffolding. Nano Lett. 5, 2399–2402 (2005).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  23. DeHon, A. Array-based architecture for FET-based, nanoscale electronics. IEEE Trans. Nanotechnol. 2, 23–32 (2003).

    Article  Google Scholar 

  24. Dwyer, C. et al. Design tools for a DNA-guided self-assembling carbon nanotube technology. Nanotechnology 15, 1240–1245 (2004).

    Article  CAS  Google Scholar 

  25. Avouris, Ph., Chen, J., Freitag, M., Perebeinos, V. & Tsang, J. C. Carbon nanotube optoelectronics. Phys. Status Solidi B. 243, 3197–3203 (2006).

    Article  CAS  Google Scholar 

  26. 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  CAS  Google Scholar 

  27. Lu, Y. et al. DNA functionalization of carbon nanotubes for ultrathin atomic layer deposition of high κ dielectrics for nanotube transistors with 60 mv/decade switching. J. Am. Chem. Soc. 128, 3518–3519 (2006).

    Article  CAS  Google Scholar 

  28. Jeng, E. S., Barone, P. W., Nelson, J. D. & Strano, M. S. Hybridization kinetics and thermodynamics of DNA adsorbed to individually dispersed single-walled carbon nanotubes. Small 3, 1602–1609 (2007).

    Article  CAS  Google Scholar 

  29. Chen, Y., Liu, H., Ye, T., Kim, J. & Mao, C. DNA-directed assembly of single-wall carbon nanotubes. J. Am. Chem. Soc. 129, 8696–8697 (2007).

    Article  CAS  Google Scholar 

  30. Li, Y., Han, X. & Deng, Z. Grafting single-walled carbon nanotubes with highly hybridizable DNA sequences: Potential building blocks for DNA-programmed material assembly. Angew. Chem. Int. Ed. 46, 7481–7484 (2007).

    Article  CAS  Google Scholar 

  31. Hwang, E.-S. et al. The DNA hybridization assay using single-walled carbon nanotubes as ultrasensitive, long-term optical labels. Nanotechnology 17, 3442–3445 (2006).

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  34. Vogel, S. R., Kappes, M. M., Hennrich, F. & Richert, C. An unexpected new optimum in the structure space of DNA solubilizing single-walled carbon nanotubes. Chem. Eur. J. 13, 1815–1820 (2007).

    Article  CAS  Google Scholar 

  35. Yurke, B. & Mills, A. P. Jr . Using DNA to power nanostructures. Genet. Progr. Evol. Mach. 4, 111–122 (2003).

    Article  Google Scholar 

  36. Panyutin, I. G. & Hsieh, P. Kinetics of spontaneous DNA branch migration. Proc. Natl Acad. Sci. USA 91, 2021–2025 (1994).

    Article  CAS  Google Scholar 

  37. Christensen, U., Jacobsen, N., Rajwanshi, V. K., Wengel, J. & Koch, T. Stopped-flow kinetics of locked nucleic acid (LNA)–oligonucleotide duplex formation: studies of LNA–DNA and DNA–DNA interactions. Biochem. J. 354, 481–484 (2001).

    CAS  Google Scholar 

  38. 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 

  39. 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 

  40. Gao, B., Komnik, A., Egger, R., Glattli, D. C. & Bachtold, A. Evidence for Luttinger-liquid behavior in crossed metallic single-wall nanotubes. Phys. Rev. Lett. 92, 216804 (2004).

    Article  CAS  Google Scholar 

  41. Fuhrer, M. S. et al. Crossed nanotubes junctions. Science 288, 494–497 (2000).

    Article  CAS  Google Scholar 

  42. Bachtold, A. et al. Scanned probe microscopy of electronic transport in carbon nanotubes. Phys. Rev. Lett. 84, 6082–6085 (2000).

    Article  CAS  Google Scholar 

  43. Postma, H. W. Ch., de Jonge, M., Yao, Z. & Dekker, C. Electrical transport through carbon nanotube junctions created by mechanical manipulation. Phys. Rev. B 62, R10653–R10656 (2000).

    Article  CAS  Google Scholar 

  44. Ahlskog, M., Tarkiainen, R., Roschier, L. & Hakonen, P. Single-electron transistor made of two crossing multiwalled carbon nanotubes and its noise properties. J. Appl. Phys. 77, 4037–4039 (2000).

    CAS  Google Scholar 

  45. Park, J. W., Kim, J. & Yoo, K.-H. Electrical transport through crossed carbon nanotube junctions. J. Appl. Phys. 93, 4191–4193 (2003).

    Article  CAS  Google Scholar 

  46. Lee, D. S., Svensson, J., Lee, S. W., Park, Y. W. & Campbell, E. E. B. Fabrication of crossed junctions of semiconducting and metallic carbon nanotubes: a CNT-gated CNT–FET. J. Nanosci. Nanotechnol. 6, 1325–1330 (2006).

    Article  CAS  Google Scholar 

  47. Kershner, R. J. et al. Placement and orientation of individual DNA shapes on lithographically patterned surfaces. Nature Nanotech. 4, 557–561 (2009).

    Article  CAS  Google Scholar 

  48. Rueckes, T. et al. Carbon nanotube-based non-volatile random access memory for molecular computing. Science 289, 94–97 (2000).

    Article  CAS  Google Scholar 

  49. Bachtold, A., Hadley, P., Nakanishi, T. & Dekker, C. Logic circuits with carbon nanotube transistors. Science 294, 1317–1320 (2001).

    Article  CAS  Google Scholar 

  50. O'Neill, P., Rothemund, P.W. K., Kumar, A. & Fygenson, D. K. Sturdier DNA nanotubes via ligation. Nano Lett. 6, 1379–1383 (2006).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the National Science Foundation (CBET/NIRT 0608889; CCF/NANO/EMT 0622254 and 0829951), the Office of Naval Research (N00014-05-1-0562) and the Center on Functional Engineered Nano Architectures (FENA, Theme 2 and Theme 3). P.W.K.R. thanks Microsoft Corporation for support. S.H. thanks Julie Norville for helpful discussions.

Author information

Author notes

  1. Hareem T. Maune, Si-ping Han and Robert D. Barish: These authors contributed equally to this work

Authors and Affiliations

  1. California Institute of Technology, Pasadena, California, 91125, USA

    Hareem T. Maune, Si-ping Han, Robert D. Barish, Marc Bockrath, William A. Goddard III, Paul W. K. Rothemund & Erik Winfree

Authors
  1. Hareem T. Maune
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Si-ping Han
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Robert D. Barish
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Marc Bockrath
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. William A. Goddard III
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Paul W. K. Rothemund
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Erik Winfree
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

H.T.M., S.H. and R.D.B. conceived of the project, designed the structures, conducted the experiments and took the measurements with advice and consultation from all authors. All authors contributed to writing the paper. M.B., W.A.G., P.W.K.R. and E.W. provided financial support.

Corresponding author

Correspondence to Si-ping Han.

Supplementary information

Supplementary information

Supplementary information (PDF 2001 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Maune, H., Han, Sp., Barish, R. et al. Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. Nature Nanotech 5, 61–66 (2010). https://doi.org/10.1038/nnano.2009.311

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nnano.2009.311

This article is cited by

Search

Advanced search

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