Calibration of Tethered Particle Motion Experiments

Details Calibration of Tethered Particle Motion Experiments Calibration of Tethered Particle Motion Experiments

2008-10-13

arxiv.org/abs/0810.2284v1

Biology

Quantitative Biology

Quantitative Methods

To appear in Mathematics of DNA Structure, Function and Interactions eds. C.J. Benham et al. (Springer, 2008)

Scientific paper

The Tethered Particle Motion (TPM) method has been used to observe and characterize a variety of protein-DNA interactions including DNA looping and transcription. TPM experiments exploit the Brownian motion of a DNA-tethered bead to probe biologically relevant conformational changes of the tether. In these experiments, a change in the extent of the bead's random motion is used as a reporter of the underlying macromolecular dynamics and is often deemed sufficient for TPM analysis. However, a complete understanding of how the motion depends on the physical properties of the tethered particle complex would permit more quantitative and accurate evaluation of TPM data. For instance, such understanding can help extract details about a looped complex geometry (or multiple coexisting geometries) from TPM data. To better characterize the measurement capabilities of TPM experiments involving DNA tethers, we have carried out a detailed calibration of TPM magnitude as a function of DNA length and particle size. We also explore how experimental parameters such as acquisition time and exposure time affect the apparent motion of the tethered particle. We vary the DNA length from 200bp to 2.6kbp and consider particle diameters of 200, 490 and 970nm. We also present a systematic comparison between measured particle excursions and theoretical expectations, which helps clarify both the experiments and models of DNA conformation.

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