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Rapid exchange of stably bound protein and DNA cargo on a DNA origami receptor

James W.P. Brown, Rokiah G. Alford, James C. Walsh, Richard E. Spinney, Stephanie Y. Xu, Sophie Hertel, Jonathan F. Berengut, Lisanne M. Spenkelink, Antoine M. van Oijen, View ORCID ProfileTill Böcking, Richard G. Morris, View ORCID ProfileLawrence K. Lee
doi: https://doi.org/10.1101/2022.01.16.476526
James W.P. Brown
1EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, 2052, Australia
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Rokiah G. Alford
1EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, 2052, Australia
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James C. Walsh
1EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, 2052, Australia
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Richard E. Spinney
1EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, 2052, Australia
2School of Physics, University of New South Wales, Sydney 2052, Australia
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Stephanie Y. Xu
1EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, 2052, Australia
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Sophie Hertel
1EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, 2052, Australia
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Jonathan F. Berengut
1EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, 2052, Australia
3School of Chemistry, University of Sydney, Sydney, 2006, Australia
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Lisanne M. Spenkelink
4Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
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Antoine M. van Oijen
4Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, NSW 2522, Australia
5Illawarra Health & Medical Research Institute, Wollongong, NSW 2522, Australia
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Till Böcking
1EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, 2052, Australia
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  • ORCID record for Till Böcking
Richard G. Morris
1EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, 2052, Australia
2School of Physics, University of New South Wales, Sydney 2052, Australia
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Lawrence K. Lee
1EMBL Australia Node for Single Molecule Science, School of Medical Sciences, UNSW Sydney, 2052, Australia
6ARC Centre of Excellence in Synthetic Biology, University of New South Wales, Sydney, Australia
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  • ORCID record for Lawrence K. Lee
  • For correspondence: lawrence.lee@unsw.edu.au
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ABSTRACT

Biomolecular complexes can form stable assemblies yet can also rapidly exchange their subunits to adapt to environmental changes. Simultaneously allowing for both stability and rapid exchange expands the functional capacity of biomolecular machines and enables continuous function while navigating a complex molecular world. Inspired by biology, we design and synthesize a DNA origami receptor that exploits multi-valent interactions to form stable complexes that are simultaneously capable of rapid subunit exchange. The system utilizes a mechanism first outlined in the context of the DNA replisome, known as multi-site competitive exchange, and achieves a large separation of time scales between spontaneous subunit dissociation, which requires days, and rapid subunit exchange, which occurs in minutes. In addition, we use the DNA origami receptor to demonstrate stable interactions with rapid exchange of both DNA and protein subunits, thus highlighting the applicability of our approach to arbitrary molecular cargo; an important distinction with canonical toehold exchange between single-stranded DNA. We expect this study to be the first of many that use DNA origami structures to exploit multi-valent interactions for the design and synthesis of a wide range of possible kinetic behaviors.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted January 17, 2022.
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Rapid exchange of stably bound protein and DNA cargo on a DNA origami receptor
James W.P. Brown, Rokiah G. Alford, James C. Walsh, Richard E. Spinney, Stephanie Y. Xu, Sophie Hertel, Jonathan F. Berengut, Lisanne M. Spenkelink, Antoine M. van Oijen, Till Böcking, Richard G. Morris, Lawrence K. Lee
bioRxiv 2022.01.16.476526; doi: https://doi.org/10.1101/2022.01.16.476526
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Rapid exchange of stably bound protein and DNA cargo on a DNA origami receptor
James W.P. Brown, Rokiah G. Alford, James C. Walsh, Richard E. Spinney, Stephanie Y. Xu, Sophie Hertel, Jonathan F. Berengut, Lisanne M. Spenkelink, Antoine M. van Oijen, Till Böcking, Richard G. Morris, Lawrence K. Lee
bioRxiv 2022.01.16.476526; doi: https://doi.org/10.1101/2022.01.16.476526

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