intervening DNA (). The TPM technique has been used to explore these problems. The calibration analysis performed here can serve as the basis of a more careful evaluation of DNA looping and bending by DNA-binding proteins, and a guide to optimize the design of subsequent DNA looping experiments. For example, one may ask, what is the optimal total DNA length and bead size needed to reliably detect a particular type of loop? To answer such questions, first note that quantifies how smaller beads and shorter tethers both allow us to work with small window size $t$, while still giving the narrow peak widths necessary to resolve substructure in the distribution of $\Jrmst$. reinforces this point and also quantifies how smaller beads also optimize the resolution of TPM by maintaining a high slope to the calibration curve over a wide range of $L$. There are limits to what can be achieved in this way, of course: Small beads are hard to observe, and short DNA tethers tend to collapse (due to surface absorption). Our work helps the experimenter to make appropriate tradeoffs when designing experiments.

Another benefit derived from the calibration curve is a better understanding of the geometry of the 