Mapping Single-Molecule Protein Complexes in 3D with DNA Nanoswitch Calipers

Prakash Shrestha; Darren Yang; Andrew Ward; William M. Shih; Wesley P. Wong

doi:10.1021/jacs.3c10262

Mapping Single-Molecule Protein Complexes in 3D with DNA Nanoswitch Calipers

Prakash Shrestha
, Darren Yang
, Andrew Ward
, William M. Shih
, Wesley P. Wong

Chemistry

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

Abstract

The ability to accurately map the 3D geometry of single-molecule complexes in trace samples is a challenging goal that would lead to new insights into molecular mechanics and provide an approach for single-molecule structural proteomics. To enable this, we have developed a high-resolution force spectroscopy method capable of measuring multiple distances between labeled sites in natively folded protein complexes. Our approach combines reconfigurable nanoscale devices, we call DNA nanoswitch calipers, with a force-based barcoding system to distinguish each measurement location. We demonstrate our approach by reconstructing the tetrahedral geometry of biotin-binding sites in natively folded streptavidin, with 1.5-2.5 Å agreement with previously reported structures.

Original language	English
Pages (from-to)	27916-27921
Number of pages	6
Journal	Journal of the American Chemical Society
Volume	145
Issue number	51
DOIs	https://doi.org/10.1021/jacs.3c10262
State	Published - Dec 27 2023

Bibliographical note

Publisher Copyright:
© 2023 The Authors. Published by American Chemical Society

Funding

This work was funded by support from ONR Award N000141510073, NIH NIGMS R35 GM119537 (W.P.W.), Alfred P. Sloan Foundation Award G-2021-169145, and the Wyss Institute at Harvard. The authors acknowledge that some figures were prepared using BioRender.

Funders	Funder number
Wyss Institute at Harvard
Office of Naval Research Naval Academy	N000141510073
National Institute of General Medical Sciences DP2GM119177 Sophie Dumont National Institute of General Medical Sciences	R35 GM119537
Alfred P Sloan Foundation	G-2021-169145

ASJC Scopus subject areas

Catalysis
Biochemistry
General Chemistry
Colloid and Surface Chemistry

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10.1021/jacs.3c10262

Cite this

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abstract = "The ability to accurately map the 3D geometry of single-molecule complexes in trace samples is a challenging goal that would lead to new insights into molecular mechanics and provide an approach for single-molecule structural proteomics. To enable this, we have developed a high-resolution force spectroscopy method capable of measuring multiple distances between labeled sites in natively folded protein complexes. Our approach combines reconfigurable nanoscale devices, we call DNA nanoswitch calipers, with a force-based barcoding system to distinguish each measurement location. We demonstrate our approach by reconstructing the tetrahedral geometry of biotin-binding sites in natively folded streptavidin, with 1.5-2.5 {\AA} agreement with previously reported structures.",

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AU - Shih, William M.

AU - Wong, Wesley P.

PY - 2023/12/27

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AB - The ability to accurately map the 3D geometry of single-molecule complexes in trace samples is a challenging goal that would lead to new insights into molecular mechanics and provide an approach for single-molecule structural proteomics. To enable this, we have developed a high-resolution force spectroscopy method capable of measuring multiple distances between labeled sites in natively folded protein complexes. Our approach combines reconfigurable nanoscale devices, we call DNA nanoswitch calipers, with a force-based barcoding system to distinguish each measurement location. We demonstrate our approach by reconstructing the tetrahedral geometry of biotin-binding sites in natively folded streptavidin, with 1.5-2.5 Å agreement with previously reported structures.

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Mapping Single-Molecule Protein Complexes in 3D with DNA Nanoswitch Calipers

Abstract

Bibliographical note

Funding

ASJC Scopus subject areas

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