Direct imaging of single molecules: from dynamics of a single DNA chain to the study of complex DNA-protein interactions

Laboratoire de Physico-Chimie Curie (UMR CNRS/IC 168), Institut Curie, Section de Recherche, 26 rue d'Ulm, F-75248 Paris, France.
Science Progress 02/2001; 84(Pt 4):267-90. DOI: 10.3184/003685001783238961
Source: PubMed

ABSTRACT Recent years have seen significant advances in the characterization and manipulation of individual molecules. The combination of single-molecule fluorescence and micromanipulation enables one to study physical and biological systems at new length scales, to unravel qualitative mechanisms, and to measure kinetic parameters that cannot be addressed by traditional biochemistry. DNA is one of the most studied biomolecules. Imaging single DNA molecules eliminates important limitations of classical techniques and provides a new method for testing polymer dynamics and DNA-protein interactions. Here we review some applications of this new approach to physical and biological problems, focusing on videomicroscopy observations of individual DNA chains extended in a shear flow. We will first describe data obtained on the stretching, relaxation and dynamics of a single tethered polymer in a shear flow, to demonstrate that the deformation of sheared tethered chains is partially governed by the thermally driven fluctuations of the chain transverse to the flow direction. Next, we will show how single-molecule videomicroscopy can be used to study in real time DNA folding into chromatin, a complex association of DNA and proteins responsible for the packaging of DNA in the nucleus of an eukaryotic cell.

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Available from: Benoit Ladoux, Sep 26, 2015
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    • "The characterization of polymer dynamics at the level of a single molecule is a first step towards the understanding of mechanical interactions between biomolecules (see e.g. [10] [11] [12] [13] [14] [15] [16] [17]), of the fundamental rheology of polymer solutions, and of the viscoelastic properties of more complex flows (see for example [18] and references therein for elastic turbulence). "
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    ABSTRACT: We investigate numerically the dynamics of a single polymer in a linear shear flow. The effects of thermal fluctuations and randomly fluctuating velocity gradients are both analyzed. Angular, elongation and tumbling time statistics are measured numerically. We perform analytical calculations and numerical simulations for a linear single-dumbbell polymer model comparing the results with previous theoretical and experimental studies. For thermally driven polymers the balance between relaxation and thermal fluctuations plays a fundamental role, whereas for random velocity gradients the ratio between the intensity of the random part and the mean shear is the most relevant quantity. In the low-noise limit, many universal aspects of the motion of a polymer in a shear flow can be understood in this simplified framework.
    Physica D Nonlinear Phenomena 11/2005; 211(1-2-211):9-22. DOI:10.1016/j.physd.2005.07.016 · 1.64 Impact Factor
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