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DNA nanoswitches: a quantitative platform for gel-based biomolecular interaction analysis

Nature Methods volume 12, pages 123126 (2015) | Download Citation

Abstract

We introduce a nanoscale experimental platform that enables kinetic and equilibrium measurements of a wide range of molecular interactions using a gel electrophoresis readout. Programmable, self-assembled DNA nanoswitches serve both as templates for positioning molecules and as sensitive, quantitative reporters of molecular association and dissociation. We demonstrated this low-cost, versatile, 'lab-on-a-molecule' system by characterizing ten different interactions, including a complex four-body interaction with five discernible states.

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References

  1. 1.

    Virology 29, 234–239 (1966).

  2. 2.

    , & J. Mol. Biol. 26, 373–387 (1967).

  3. 3.

    Biochem. J. 61, 629–641 (1955).

  4. 4.

    & Nat. Protoc. 2, 1849–1861 (2007).

  5. 5.

    , & Nanotechnology 22, 494005 (2011).

  6. 6.

    & Angew. Chem. Int. Ed. Engl. 51, 58–66 (2012).

  7. 7.

    Annu. Rev. Biochem. 79, 65–87 (2010).

  8. 8.

    & Biochim. Biophys. Acta 269, 192–200 (1972).

  9. 9.

    & Chem. Biol. 15, 979–989 (2008).

  10. 10.

    & Annu. Rev. Phys. Chem. 56, 521–548 (2005).

  11. 11.

    , , & J. Biol. Chem. 276, 46422–46428 (2001).

  12. 12.

    , & Biochemistry 37, 7657–7663 (1998).

  13. 13.

    et al. Nat. Methods 7, 391–393 (2010).

  14. 14.

    , & Science 264, 415–417 (1994).

  15. 15.

    , & Proc. Natl. Acad. Sci. USA 108, 11399–11404 (2011).

  16. 16.

    , & Methods 67, 134–141 (2014).

  17. 17.

    , , & Proc. Natl. Acad. Sci. USA 96, 11277–11282 (1999).

Download references

Acknowledgements

The authors gratefully acknowledge D. Corey, G. Yellen, R. Wilson, J. Holt, H. Ploegh, G. Wong, A. Badran, Z. Tsun, A. Golden and members of the Wong and Corey Labs for critical discussions and T. Kao for her early work on the project. Funding for this project was provided by US National Institutes of Health R01 DC02281 to D. Corey; M.A.K. was supported by National Science Foundation USA GRFP 2012147612; W.P.W. was supported by Boston Children's Hospital startup funds and Takeda New Frontier Science.

Author information

Author notes

    • Mounir A Koussa
    •  & Ken Halvorsen

    These authors contributed equally to this work.

Affiliations

  1. Program in Neuroscience, Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA.

    • Mounir A Koussa
  2. The RNA Institute, University at Albany, Albany, New York, USA.

    • Ken Halvorsen
  3. Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts, USA.

    • Ken Halvorsen
    • , Andrew Ward
    •  & Wesley P Wong
  4. Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts, USA.

    • Wesley P Wong
  5. Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA.

    • Wesley P Wong

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Contributions

The initial idea was conceived by K.H. and W.P.W. Experiments were designed by all authors. The method was expanded by M.A.K. and A.W., and experiments were carried out by K.H., M.A.K. and A.W. All authors participated in data analysis, critical discussion and writing of the manuscript.

Competing interests

Patent applications have been filed for various aspects of this work by K.H., M.A.K. and W.P.W.

Corresponding authors

Correspondence to Ken Halvorsen or Wesley P Wong.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–7, Supplementary Tables 1–4, 7 and 8, Supplementary Notes 1 and 2 and Supplementary Protocol.

Zip files

  1. 1.

    Supplementary Data

    Annotated M13 Scaffold This file is a SnapGene .DNA file that indicates the sequence and positions of all of the backbone and variable oligonucleotides

Excel files

  1. 1.

    Supplementary Table 5

    Backbone Oligonucleotide sequences This file contains all of the sequences for the 109 backbone oligonucleotides, and can be sent to IDT to place an order for a mixture of the backbone oligonucleotides.

  2. 2.

    Supplementary Table 6

    Variable Oligonucleotide Regions This file contains all of the sequences for the 12 variable oligonucleotides, and can be sent to IDT to place an order for the individual variable oligonucleotides.

About this article

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DOI

https://doi.org/10.1038/nmeth.3209

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