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Combining DNA scaffolds and acoustic force spectroscopy to characterize individual protein bonds

Yong Jian Wang, Claire Valotteau, Adrien Aimard, Lorenzo Villanueva, Dorota Kostrz, Maryne Follenfant, Terence Strick, Patrick Chames, Felix Rico, Charlie Gosse, Laurent Limozin
doi: https://doi.org/10.1101/2022.08.14.503897
Yong Jian Wang
1Aix-Marseille Université, CNRS, INSERM, Laboratoire Adhesion et Inflammation, Turing Centre for Living systems, Marseille, France
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  • For correspondence: laurent.limozin@inserm.fr yong-jian.wang@inserm.fr claire.valotteau@inserm.fr
Claire Valotteau
1Aix-Marseille Université, CNRS, INSERM, Laboratoire Adhesion et Inflammation, Turing Centre for Living systems, Marseille, France
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  • For correspondence: laurent.limozin@inserm.fr yong-jian.wang@inserm.fr claire.valotteau@inserm.fr
Adrien Aimard
2Aix-Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, Centre de Recherche en Cancerologie de Marseille, Marseille, France
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Lorenzo Villanueva
1Aix-Marseille Université, CNRS, INSERM, Laboratoire Adhesion et Inflammation, Turing Centre for Living systems, Marseille, France
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Dorota Kostrz
3Institut de Biologie de l’Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
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Maryne Follenfant
3Institut de Biologie de l’Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
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Terence Strick
3Institut de Biologie de l’Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
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Patrick Chames
2Aix-Marseille Université, CNRS, INSERM, Institut Paoli-Calmettes, Centre de Recherche en Cancerologie de Marseille, Marseille, France
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Felix Rico
1Aix-Marseille Université, CNRS, INSERM, Laboratoire Adhesion et Inflammation, Turing Centre for Living systems, Marseille, France
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Charlie Gosse
3Institut de Biologie de l’Ecole Normale Supérieure, ENS, CNRS, INSERM, PSL Research University, Paris, France
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Laurent Limozin
1Aix-Marseille Université, CNRS, INSERM, Laboratoire Adhesion et Inflammation, Turing Centre for Living systems, Marseille, France
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  • For correspondence: laurent.limozin@inserm.fr yong-jian.wang@inserm.fr claire.valotteau@inserm.fr
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Abstract

Single-molecule data are of great significance in biology, chemistry, and medicine. However, experimental tools to characterize, in a multiplexed manner, protein bond rupture under force are needed. Acoustic force spectroscopy (AFS) is an emerging manipulation technique which generates acoustic waves to apply force in parallel on a large population of microbeads tethered to a surface. We have exploited this configuration on a recently developed modular Junctured-DNA (J-DNA) scaffold designed to study protein-protein interactions at the single-molecule level. By applying repetitive constant force steps on the FKBP12-rapamycin-FRB complex, we measured its unbinding kinetics under force at the single-bond level. Special effort was made in analyzing the data in order to identify potential pitfalls. We established a calibration method allowing in situ force determination during the course of the unbinding measurement. We compare our results with well established techniques, such as magnetic tweezers, to ensure their accuracy. We also apply our strategy for measuring the force dependent rupture of a single domain antibody with its antigen. We get a good agreement with standard measurement at zero force. Our technique offers single molecule precision for multiplexed measurements of interactions of biotechnological and medical interest.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted August 15, 2022.
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Combining DNA scaffolds and acoustic force spectroscopy to characterize individual protein bonds
Yong Jian Wang, Claire Valotteau, Adrien Aimard, Lorenzo Villanueva, Dorota Kostrz, Maryne Follenfant, Terence Strick, Patrick Chames, Felix Rico, Charlie Gosse, Laurent Limozin
bioRxiv 2022.08.14.503897; doi: https://doi.org/10.1101/2022.08.14.503897
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Combining DNA scaffolds and acoustic force spectroscopy to characterize individual protein bonds
Yong Jian Wang, Claire Valotteau, Adrien Aimard, Lorenzo Villanueva, Dorota Kostrz, Maryne Follenfant, Terence Strick, Patrick Chames, Felix Rico, Charlie Gosse, Laurent Limozin
bioRxiv 2022.08.14.503897; doi: https://doi.org/10.1101/2022.08.14.503897

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