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

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

1,* email, 1,2email, 1email, 1,3email and 1,2,4,5email
Received: 15 December 2012; in revised form: 13 January 2013 / Accepted: 4 February 2013 / Published: 18 February 2013
(This article belongs to the Special Issue Advances in Single Molecule Spectroscopy)
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
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.
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
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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.

AMA Style

Monico C, Capitanio M, Belcastro G, Vanzi F, Pavone FS. Optical Methods to Study Protein-DNA Interactions in Vitro and in Living Cells at the Single-Molecule Level. International Journal of Molecular Sciences. 2013; 14(2):3961-3992.

Chicago/Turabian Style

Monico, Carina; Capitanio, Marco; Belcastro, Gionata; Vanzi, Francesco; Pavone, Francesco S. 2013. "Optical Methods to Study Protein-DNA Interactions in Vitro and in Living Cells at the Single-Molecule Level." Int. J. Mol. Sci. 14, no. 2: 3961-3992.

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