Why do sliding length measurements vary widely?
A critical parameter in this analysis is sliding length, s. Our analysis may help to understand the wide range in the measurements of sliding lengths for different proteins (Table 3). Some of these differences are certainly due to differences in the proteins and experimental conditions. In particular, since the non-specific binding of a protein to DNA is driven almost entirely by electrostatics, a protein’s non-specific affinity depends strongly on ion concentration (19–21). We also propose that, in some experiments, it is likely that hops are included in the sliding measurement. In the first two experiments listed in Table 3, the experimental designs allow for the unambiguous identification of hops and slides, and the measured slide lengths are on the low end of the scale (14,15).
