a DNA-binding protein, which changes the effective tether length by looping and/or bending the DNA. For example, Lac repressor protein (LacR) has two binding sites, which recognize and bind to two specific sequences (“operators”) on DNA. ](calibrationfigPN/lac.eps "fig:"){width="4.4truein"}\
![\[fig:TPM\] Idea of the tethered particle motion method. Cartoons showing the tethered bead in the (a) absence and (b) presence of a DNA-binding protein, which changes the effective tether length by looping and/or bending the DNA. For example, Lac repressor protein (LacR) has two binding sites, which recognize and bind to two specific sequences (“operators”) on DNA. ](bitmaps/lac.eps "fig:"){width="4.4truein"}\

Results and Discussion
======================

Using differential interference contrast (DIC) microscopy, the projected position of several beads in a field of view are recorded using a CCD camera. position traces for each bead in the image is determined using a cross-correlation method [@Gelles1988]. Standard microscopy systems such as ours are limited to two spatial dimensions; tracking of three dimensions has been accomplished using evanescent fields or diffraction rings [@Blumberg2005], but this involves additional calibration and technical challenges. Two-dimensional tracking is sufficient for the applications we have in mind, such as DNA-looping studies. The tracked position of the bead is subject to slow drift, due 