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Quantitative analysis of tethered particle motion

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Idealization of the experimental geometry:
A large, optically visible bead reports on the state of a nanoscale DNA configuration, potentially including a looping-protein complex.

PIs: Philip Nelson, John Beausang, University of Pennsylvania. Chiara Zurla, David Dunlap, Laura Finzi, Emory University. Darren Segall, Rob Phillips, Caltech

Motivation:

One strategy used by cells for gene regulation involves DNA looping. The single-particle tracking method now allows us to study the kinetics of this intra-molecular reaction at the single-molecule level, in a way that does not perturb the reaction itself. But interpretation of the experimental results requires that we first solve a fundamental problem in the statistics of a semiflexible polymer: to find the tether length given the excursion of the center of an attached bead.

Conclusions:

The problem cuts across the fields of statistical mechanics, polymer science, and molecular biology. The success of our method for extracting the lengths of known tethers shows that it’s suitable for real-time of DNA loop formation. Here the tether length is not known a priori; changes in this length signal the formation and breakdown of loops. With this calibration, we are now proceeding to explore the effects of drugs and physical stresses on loop formation, and hence on bacterial gene regulation.

Reference:
D Segall, PC Nelson, and R Phillips. Phys. Rev. Lett. 96 art. number 088306 (2006).
PC Nelson, C Zurla, D Brogioli, L Finzi , and D Dunlap, submitted (2006).

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Colored dots: experimental distributions of bead position for tethers of three different lengths. Each color is a different bead/tether system, showing high reproducibility. Curves: our first-principles predictions of these three distributions.
 

 

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