The diffusion constant of a labeled protein sliding along DNA |
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Authors: | I Bonnet P Desbiolles |
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Institution: | (1) MicroInstruments and Systems Laboratory (MISL), University of Maine, Orono, ME, USA; |
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Abstract: | Long ago inferred by biochemists, the linear diffusion of proteins along DNA has recently been observed at a single-molecule
level using fluorescence microscopy. This imaging technique requires labeling the protein of interest with a fluorophore,
usually an organic nanosized dye that is not supposed to impact the dynamics of the protein. Yet individual proteins can also
be tracked using much larger labels, like quantum dots or beads. We investigate here the impact of such a large label on the
protein diffusion along DNA. Solving a Fokker-Planck equation, we estimate the diffusion constant of a protein-label complex
diffusing in a periodic potential that mimics the DNA-protein interaction, the link between the protein and the label being
modeled as a Hookean spring. Our results indicate that the diffusion constant can generally be calculated by considering that
the motion of the protein in the DNA potential is decoupled from the Brownian motion of the label. Our conclusions are in
good agreement with the experimental results we obtained with the restriction enzyme EcoRV, assuming a rotation-coupled diffusion
of the enzyme along DNA. |
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