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Plénat T, Tardin C, Rousseau P, Salomé L. High-throughput single-molecule analysis of DNA-protein interactions by tethered particle motion. Nucleic Acids Res 2012; 40:e89. [PMID: 22422843 PMCID: PMC3384352 DOI: 10.1093/nar/gks250] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2012] [Revised: 02/21/2012] [Accepted: 03/05/2012] [Indexed: 11/19/2022] Open
Abstract
Tethered particle motion (TPM) monitors the variations in the effective length of a single DNA molecule by tracking the Brownian motion of a bead tethered to a support by the DNA molecule. Providing information about DNA conformations in real time, this technique enables a refined characterization of DNA-protein interactions. To increase the output of this powerful but time-consuming single-molecule assay, we have developed a biochip for the simultaneous acquisition of data from more than 500 single DNA molecules. The controlled positioning of individual DNA molecules is achieved by self-assembly on nanoscale arrays fabricated through a standard microcontact printing method. We demonstrate the capacity of our biochip to study biological processes by applying our method to explore the enzymatic activity of the T7 bacteriophage exonuclease. Our single molecule observations shed new light on its behaviour that had only been examined in bulk assays previously and, more specifically, on its processivity.
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Affiliation(s)
- Thomas Plénat
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, 205 route de Narbonne, Toulouse, F-31077, Université de Toulouse, UPS, Institut de Pharmacologie et de Biologie Structurale, Toulouse, F-31077, Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000 and Centre National de la Recherche Scientifique, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000, France
| | - Catherine Tardin
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, 205 route de Narbonne, Toulouse, F-31077, Université de Toulouse, UPS, Institut de Pharmacologie et de Biologie Structurale, Toulouse, F-31077, Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000 and Centre National de la Recherche Scientifique, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000, France
| | - Philippe Rousseau
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, 205 route de Narbonne, Toulouse, F-31077, Université de Toulouse, UPS, Institut de Pharmacologie et de Biologie Structurale, Toulouse, F-31077, Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000 and Centre National de la Recherche Scientifique, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000, France
| | - Laurence Salomé
- Centre National de la Recherche Scientifique, Institut de Pharmacologie et de Biologie Structurale, 205 route de Narbonne, Toulouse, F-31077, Université de Toulouse, UPS, Institut de Pharmacologie et de Biologie Structurale, Toulouse, F-31077, Université de Toulouse, UPS, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000 and Centre National de la Recherche Scientifique, Laboratoire de Microbiologie et Génétique Moléculaires, Toulouse, F-31000, France
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