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Int. J. Mol. Sci. 2013, 14(2), 3961-3992; doi:10.3390/ijms14023961

Optical Methods to Study Protein-DNA Interactions in Vitro and in Living Cells at the Single-Molecule Level

1
European Laboratory for Non-linear Spectroscopy, Via Nello Carrara 1, 50019 Sesto Fiorentino (FI), Italy
2
Department of Physics and Astronomy, University of Florence, Via Sansone 1, 50019 Sesto Fiorentino (FI), Italy
3
Department of Evolutionary Biology "Leo Pardi", University of Florence, Via Romana 17, 50125 Florence, Italy
4
National Institute of Optics—National Research Council, Largo Fermi 6, 50125 Florence, Italy
5
International Center of Computational Neurophotonics, Via Nello Carrara 1, 50019 Sesto Fiorentino (FI), Italy
*
Author to whom correspondence should be addressed.
Received: 15 December 2012 / Revised: 13 January 2013 / Accepted: 4 February 2013 / Published: 18 February 2013
(This article belongs to the Special Issue Advances in Single Molecule Spectroscopy)
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Abstract

The maintenance of intact genetic information, as well as the deployment of transcription for specific sets of genes, critically rely on a family of proteins interacting with DNA and recognizing specific sequences or features. The mechanisms by which these proteins search for target DNA are the subject of intense investigations employing a variety of methods in biology. A large interest in these processes stems from the faster-than-diffusion association rates, explained in current models by a combination of 3D and 1D diffusion. Here, we present a review of the single-molecule approaches at the forefront of the study of protein-DNA interaction dynamics and target search in vitro and in vivo. Flow stretch, optical and magnetic manipulation, single fluorophore detection and localization as well as combinations of different methods are described and the results obtained with these techniques are discussed in the framework of the current facilitated diffusion model. View Full-Text
Keywords: single-molecule techniques; protein-DNA interactions; facilitated diffusion; tethered particle motion; optical tweezers; magnetic tweezers; DNA curtains; single-molecule imaging; combining single-molecule fluorescence and optical trapping; in vivo transcription factors dynamics single-molecule techniques; protein-DNA interactions; facilitated diffusion; tethered particle motion; optical tweezers; magnetic tweezers; DNA curtains; single-molecule imaging; combining single-molecule fluorescence and optical trapping; in vivo transcription factors dynamics
This is an open access article distributed under the Creative Commons Attribution License (CC BY 3.0).

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MDPI and ACS Style

Monico, C.; Capitanio, M.; Belcastro, G.; Vanzi, F.; Pavone, F.S. Optical Methods to Study Protein-DNA Interactions in Vitro and in Living Cells at the Single-Molecule Level. Int. J. Mol. Sci. 2013, 14, 3961-3992.

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