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Structural Transformation of Wireframe DNA Origami via DNA Polymerase Assisted Gap-Filling

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    Structural Transformation of Wireframe DNA Origami via DNA Polymerase Assisted Gap-Filling
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    • Nayan P. Agarwal
      Nayan P. Agarwal
      Center for Advancing Electronics Dresden (cfaed), Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, 01062, Germany
      More by Nayan P. Agarwal
    • Michael Matthies
      Michael Matthies
      Center for Advancing Electronics Dresden (cfaed), Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, 01062, Germany
      More by Michael Matthies
    • Bastian Joffroy
      Bastian Joffroy
      Center for Advancing Electronics Dresden (cfaed), Faculty of Chemistry and Food Chemistry, Technische Universität Dresden, Dresden, 01062, Germany
      More by Bastian Joffroy
    • Thorsten L. Schmidt*
      Thorsten L. Schmidt
      Center for Advancing Electronics Dresden (cfaed), Faculty of Chemistry and Food Chemistry  and  B CUBE—Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, 01062, Germany
      *E-mail: [email protected]
      More by Thorsten L. Schmidt
      Orcidhttp://orcid.org/0000-0002-6798-5241
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    ACS Nano

    Cite this: ACS Nano 2018, 12, 3, 2546–2553
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    https://doi.org/10.1021/acsnano.7b08345
    Published February 16, 2018
    Copyright © 2018 American Chemical Society
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    Abstract

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    The programmability of DNA enables constructing nanostructures with almost any arbitrary shape, which can be decorated with many functional materials. Moreover, dynamic structures can be realized such as molecular motors and walkers. In this work, we have explored the possibility to synthesize the complementary sequences to single-stranded gap regions in the DNA origami scaffold cost effectively by a DNA polymerase rather than by a DNA synthesizer. For this purpose, four different wireframe DNA origami structures were designed to have single-stranded gap regions. This reduced the number of staple strands needed to determine the shape and size of the final structure after gap filling. For this, several DNA polymerases and single-stranded binding (SSB) proteins were tested, with T4 DNA polymerase being the best fit. The structures could be folded in as little as 6 min, and the subsequent optimized gap-filling reaction was completed in less than 3 min. The introduction of flexible gap regions results in fully collapsed or partially bent structures due to entropic spring effects. Finally, we demonstrated structural transformations of such deformed wireframe DNA origami structures with DNA polymerases including the expansion of collapsed structures and the straightening of curved tubes. We anticipate that this approach will become a powerful tool to build DNA wireframe structures more material-efficiently, and to quickly prototype and test new wireframe designs that can be expanded, rigidified, or mechanically switched. Mechanical force generation and structural transitions will enable applications in structural DNA nanotechnology, plasmonics, or single-molecule biophysics.

    Copyright © 2018 American Chemical Society

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    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acsnano.7b08345.

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    • Schematics or DNA origami wireframe structures; AGE films; tSEM micrographs; efficiency comparisons; other figures as described in the text (PDF)

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    ACS Nano

    Cite this: ACS Nano 2018, 12, 3, 2546–2553
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acsnano.7b08345
    Published February 16, 2018
    Copyright © 2018 American Chemical Society
    Request reuse permissions

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