DNA sequence motifs for structure-specific recognition and separation of carbon nanotubes


Single-walled carbon nanotubes (SWNTs) are a family of molecules that have the same cylindrical shape but different chiralities1. Many fundamental studies and technological applications2 of SWNTs require a population of tubes with identical chirality that current syntheses cannot provide. The SWNT sorting problem—that is, separation of a synthetic mixture of tubes into individual single-chirality components—has attracted considerable attention in recent years. Intense efforts so far have focused largely on, and resulted in solutions for, a weaker version of the sorting problem: metal/semiconductor separation3,4. A systematic and general method to purify each and every single-chirality species of the same electronic type from the synthetic mixture of SWNTs is highly desirable, but the task has proven to be insurmountable to date. Here we report such a method, which allows purification of all 12 major single-chirality semiconducting species from a synthetic mixture, with sufficient yield for both fundamental studies and application development. We have designed an effective search of a DNA library of 1060 in size, and have identified more than 20 short DNA sequences, each of which recognizes and enables chromatographic purification of a particular nanotube species from the synthetic mixture. Recognition sequences exhibit a periodic purine–pyrimidines pattern, which can undergo hydrogen-bonding to form a two-dimensional sheet, and fold selectively on nanotubes into a well-ordered three-dimensional barrel. We propose that the ordered two-dimensional sheet and three-dimensional barrel provide the structural basis for the observed DNA recognition of SWNTs.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1: Optical absorption spectra and atomic structures.
Figure 2: DNA structures.


  1. 1

    Saito, R., Dresselhaus, G. & Dresselhaus, M. S. Physical Properties of Carbon Nanotubes (Imperial College Press, 1999)

    Google Scholar 

  2. 2

    Baughman, R. H., Zakhidov, A. A. & de Heer, W. A. Carbon nanotubes-the route toward applications. Science 297, 787–792 (2002)

    ADS  CAS  Article  Google Scholar 

  3. 3

    Tu, X. & Zheng, M. A DNA-based approach to the carbon nanotube sorting problem. Nano Res. 1, 185–194 (2008)

    CAS  Article  Google Scholar 

  4. 4

    Hersam, M. C. Progress towards monodisperse single-walled carbon nanotubes. Nature Nanotechnol. 3, 387–394 (2008)

    ADS  CAS  Article  Google Scholar 

  5. 5

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

    ADS  CAS  Article  Google Scholar 

  6. 6

    Zheng, M. & Semke, E. D. Enrichment of single chirality carbon nanotubes. J. Am. Chem. Soc. 129, 6084–6085 (2007)

    CAS  Article  Google Scholar 

  7. 7

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

    ADS  CAS  Article  Google Scholar 

  8. 8

    Manohar, S. et al. Peeling single-stranded DNA from graphite surface to determine oligonucleotide binding energy by force spectroscopy. Nano Lett. 8, 4365–4372 (2008)

    ADS  CAS  Article  Google Scholar 

  9. 9

    Meng, S., Maregakis, P., Papaloukas, C. & Kaxiras, E. DNA nucleoside interaction and identification with carbon nanotubes. Nano Lett. 7, 45–50 (2007)

    ADS  CAS  Article  Google Scholar 

  10. 10

    Frischknecht, A. L. & Martin, M. G. Simulation of the adsorption of nucleotide monophosphates on carbon nanotubes in aqueous solution. J. Phys. Chem. C 112, 6271–6278 (2008)

    CAS  Article  Google Scholar 

  11. 11

    Gowtham, S., Scheicher, R. H., Pandey, R., Karna, S. P. & Ahuja, R. First-principles study of physisorption of nucleic acid bases on small-diameter carbon nanotubes. Nanotechnology 19, 125701 (2008)

    ADS  CAS  Article  Google Scholar 

  12. 12

    Johnson, R. R., Johnson, A. T. C. & Klein, M. L. Probing the structure of DNA-carbon nanotube hybrids with molecular dynamics. Nano Lett. 8, 69–75 (2008)

    ADS  CAS  Article  Google Scholar 

  13. 13

    Manohar, S., Tang, T. & Jagota, A. Structure of homopolymer DNA-CNT hybrids. J. Phys. Chem. C 111, 17835–17845 (2007)

    CAS  Article  Google Scholar 

  14. 14

    Martin, W., Zhu, W. & Krilov, G. Simulation study of noncovalent hybridization of carbon nanotubes by single-stranded DNA in water. J. Phys. Chem. B 112, 16076–16089 (2008)

    CAS  Article  Google Scholar 

  15. 15

    Johnson, R. R., Kohlmeyer, A., Johnson, A. T. C. & Klein, M. L. Free energy landscape of a DNA-carbon nanotube hybrid using replica exchange molecular dynamics. Nano Lett. 9, 537–541 (2009)

    ADS  CAS  Article  Google Scholar 

  16. 16

    Lustig, S. R., Jagota, A., Khripin, C. & Zheng, M. Theory of structure-based carbon nanotube separations by ion-exchange chromatography of DNA/CNT hybrids. J. Phys. Chem. B 109, 2559–2566 (2005)

    CAS  Article  Google Scholar 

  17. 17

    Bachilo, S. M. et al. Structure-assigned optical spectra of single-walled carbon nanotubes. Science 298, 2361–2366 (2002)

    ADS  CAS  Article  Google Scholar 

  18. 18

    Haroz, E. H., Bachilo, S. M., Weisman, R. B. & Doorn, S. K. Curvature effects on the E33 and E44 exciton transitions in semiconducting single-walled carbon nanotubes. Phys. Rev. B 77, 125405 (2008)

    ADS  Article  Google Scholar 

  19. 19

    Kim, W.-J. et al. Connecting single molecule electrical measurements to ensemble spectroscopic properties for quantification of single-walled carbon nanotube separation. J. Am. Chem. Soc. 131, 3128–3129 (2009)

    CAS  Article  Google Scholar 

  20. 20

    Zhang, L. et al. Optical characterizations and electronic devices of nearly pure (10,5) single-walled carbon nanotubes. J. Am. Chem. Soc. 131, 2454–2455 (2009)

    CAS  Article  Google Scholar 

  21. 21

    Bachilo, S. M. et al. Narrow (n,m)-distribution of single-walled carbon nanotubes grown using a solid supported catalyst. J. Am. Chem. Soc. 125, 11186–11187 (2003)

    CAS  Article  Google Scholar 

  22. 22

    Yao, Y., Feng, C., Zhang, J. & Liu, Z. “Cloning” of single-walled carbon nanotubes via open-end growth mechanism. Nano Lett. 9, 1673–1677 (2009)

    ADS  CAS  Article  Google Scholar 

  23. 23

    Stryer, L. Biochemistry (Freeman and Co., 1995)

    Google Scholar 

  24. 24

    Nish, A., Hwang, J., Doig, J. & Nicholas, R. J. Highly selective dispersion of single-walled carbon nanotubes using aromatic polymers. Nature Nanotechnology 2, 640–646 (2007)

    ADS  CAS  Article  Google Scholar 

  25. 25

    Chen, F., Wang, B., Chen, Y. & Li, L.-J. Toward the extraction of single species of single-walled carbon nanotubes using fluorene-based polymers. Nano Lett. 7, 3013–3017 (2007)

    ADS  CAS  Article  Google Scholar 

  26. 26

    Ju, S., Doll, J., Sharma, I. & Papadimitrakopoulos, F. Selection of carbon nanotubes with specific chiralities using helical assemblies of flavin mononucleotide. Nature Nanotechnol. 3, 356–362 (2008)

    ADS  CAS  Article  Google Scholar 

  27. 27

    Marquis, R. et al. Supramolecular discrimination of carbon nanotubes according to their helicity. Nano Lett. 8, 1830–1835 (2008)

    ADS  CAS  Article  Google Scholar 

  28. 28

    Zheng, M. & Diner, B. A. Solution redox chemistry of carbon nanotubes. J. Am. Chem. Soc. 126, 15490–15494 (2004)

    CAS  Article  Google Scholar 

Download references


This work was supported in part by the US National Science Foundation (grant CMS-060950). We thank T. Devine for technical assistance.

Author Contributions X.T. conducted all the separation experiments and participated in their design with M.Z.; S.M. and A.J. conducted DNA–SWNT structure analysis under direction from A.J.; all authors contributed to the manuscript writing; and M.Z. guided all aspects of the work.

Author information



Corresponding author

Correspondence to Ming Zheng.

Supplementary information

Supplementary Information

This file contains Supplementary Notes and Data, Supplementary Figures S1-S8 with Legends, Supplementary Tables S1-S2 and Supplementary References. (PDF 2639 kb)

PowerPoint slides

Rights and permissions

Reprints and Permissions

About this article

Cite this article

Tu, X., Manohar, S., Jagota, A. et al. DNA sequence motifs for structure-specific recognition and separation of carbon nanotubes. Nature 460, 250–253 (2009). https://doi.org/10.1038/nature08116

Download citation

Further reading


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.