Optical Methods to Study Protein-DNA Interactions in Vitro and in Living Cells at the Single-Molecule Level
Year: 2013
Authors: Monico C., Capitanio M., Belcastro G., Vanzi F., Pavone F.S.
Autors Affiliation: European Lab Nonlinear Spect, I-50019 Sesto Fiorentino, FI, Italy; Univ Florence, Dept Phys & Astron, I-50019 Sesto Fiorentino, FI, Italy; Univ Florence, Dept Evolutionary Biol Leo Pardi, I-50125 Florence, Italy; CNR, Natl Inst Opt, I-50125 Florence, Italy; Int Ctr Computat Neurophoton, I-50019 Sesto Fiorentino, FI, Italy.
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.
Journal/Review: INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
Volume: 14 (2) Pages from: 3961 to: 3992
More Information: We are grateful to Blaine Bisel and Lucia Gardini for discussion on the manuscript. This work was funded by the European Union Seventh Framework Programme (FP7/2007-2013) under grant agreements no211383, no228334, no241526, and no284464. This work was also supported by the Italian Ministry of University and Research (PRIN 2006, 2006051323_003, FIRB 2011 RBAP11X42L006 and Flagship Project NANOMAX) and by the Ente Cassa di Risparmio di Firenze.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 dynamicsDOI: 10.3390/ijms14023961Citations: 51data from “WEB OF SCIENCE” (of Thomson Reuters) are update at: 2025-01-12References taken from IsiWeb of Knowledge: (subscribers only)