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Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel

Nature Biotechnology volume 19, pages 248–252 (2001)Cite this article

A Corrigendum to this article was published on 01 July 2001

Abstract

RNA and DNA strands produce ionic current signatures when driven through an α-hemolysin channel by an applied voltage. Here we combine this nanopore detector with a support vector machine (SVM) to analyze DNA hairpin molecules on the millisecond time scale. Measurable properties include duplex stem length, base pair mismatches, and loop length. This nanopore instrument can discriminate between individual DNA hairpins that differ by one base pair or by one nucleotide.

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Figure 1: Blockade of the α-hemolysin nanopore by a DNA hairpin.
Figure 2: Standard free energy of hairpin formation versus shoulder blockade duration.
Figure 3: Discrimination between DNA hairpins at single-base pair resolution.
Figure 4: Detection of single-nucleotide differences between DNA hairpins.
Figure 5: Typical current blockade signatures caused by 7, 8, and 9 bp hairpins obtained using a voltage pulse routine.

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References

  1. Rief, M. Clausen-Schaumann, H. & Gaub, H.E. Sequence-dependent mechanics of single DNA molecules. Nat. Struct. Biol. 6, 346–349 (1999).

    Article  CAS  Google Scholar 

  2. Perkins, T.T., Quake, S.R., Smith, D.E. & Chu, S. Relaxation of a single DNA molecule observed by optical microscopy. Science 264, 822–826 (1994).

    Article  CAS  Google Scholar 

  3. Smith, S.B., Cui, Y. & Bustamante, C. Overstretching B-DNA: the elastic response of individual double- stranded and single-stranded DNA molecules. Science 271, 795–799 (1996).

    Article  CAS  Google Scholar 

  4. Voss, D. Gene express. New Sci. 164, 40–43 (1999).

    CAS  Google Scholar 

  5. Akeson, M., Branton, D., Kasianowicz, J.J., Brandin, E. & Deamer, D.W. Microsecond time-scale discrimination among polycytidylic acid, polyadenylic acid, and polyuridylic acid as homopolymers or as segments within single RNA molecules. Biophys. J. 77, 3227–3233 (1999).

    Article  CAS  Google Scholar 

  6. Meller, A., Nivon, L., Brandin, E., Golovchenko, J. & Branton, D. Rapid nanopore discrimination between single polynucleotide molecules. Proc. Natl. Acad. Sci. USA 97, 1079–1084 (2000).

    Article  CAS  Google Scholar 

  7. Kasianowicz, J.J., Brandin, E., Branton, D. & Deamer, D.W. Characterization of individual polynucleotide molecules using a membrane channel. Proc. Natl. Acad. Sci. USA 93, 13770–13773 (1996).

    Article  CAS  Google Scholar 

  8. Bayley, H., Braha, O. & Gu, L.Q. Stochastic sensing with protein pores. Advan. Mater. 12, 139–142 (2000).

    Article  CAS  Google Scholar 

  9. Song, L. et al. Structure of staphylococcal alpha-hemolysin, a heptameric transmembrane pore [see comments]. Science 274, 1859–1866 (1996).

    Article  CAS  Google Scholar 

  10. Senior, M.M., Jones, R.A. & Breslauer, K.J. Influence of loop residues on the relative stabilities of DNA hairpin structures. Proc. Natl. Acad. Sci. USA 85, 6242–6246 (1988).

    Article  CAS  Google Scholar 

  11. Michael, D. Chem-Site 3.01. (Pyramid Learning LLC, Hudson, OH; 1999).

    Google Scholar 

  12. Vapnik, V. The nature of statistical learning theory, Edn. 2. (Springer-Verlag, New York; 1999).

    Google Scholar 

  13. Burges, C.J.C. A tutorial on Support Vector Machines for pattern recognition. Data Mining and Knowledge Discovery 2, 121–167 (1998).

    Article  Google Scholar 

  14. Cormen, T.H., Leiserson, C.E. & Rivest, R.L. Introduction to algorithms. (McGraw-Hill, New York; 1989).

    Google Scholar 

  15. Nievergelt, Y. Wavelets made easy. (Birkhauser, Boston; 1999).

    Book  Google Scholar 

  16. Jaakkola, T.S. & Haussler, D. Exploiting generative models in discriminative classifiers. In Advances in neural information processing systems 11. (eds Kearnes, M.S., Solla, S.A. & Cohn, D.A.) (MIT Press, Cambridge, MA; 1999).

    Google Scholar 

  17. SantaLucia, J. Jr., A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl. Acad. Sci. USA 95, 1460–1465 (1998).

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by NRHGI grant HG01826-01. We wish to thank Laura Steinmann for thoughtful comments on the manuscript.

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Authors and Affiliations

  1. Department of Chemistry and Biochemistry, University of California, Santa Cruz, 95064, CA

    Wenonah Vercoutere, Hugh Olsen, David Deamer & Mark Akeson

  2. Center for Biomolecular Science and Engineering, University of California, Santa Cruz, 95064, CA

    Stephen Winters-Hilt, David Haussler & Mark Akeson

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  1. Wenonah Vercoutere
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Correspondence to Mark Akeson.

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Vercoutere, W., Winters-Hilt, S., Olsen, H. et al. Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel. Nat Biotechnol 19, 248–252 (2001). https://doi.org/10.1038/85696

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