Figure 6.

Interrogation of binding of IHF to full-length cos274 and ns274 duplex substrates using sedimentation velocity analytical ultracentrifugation (SV-AUC). Increasing concentrations of IHF were added to each duplex, and their sedimentation behavior was monitored by SV-AUC as described in Experimental Procedures. The c(s) distribution for each binding experiment were calculated using Sedfit. (A) Normalized c(s) profiles for the specific cos274 duplex. (B) Normalized c(s) profiles for the nonspecific ns274 duplex. (C) Weight-average sedimentation coefficients for each of the c(s) distributions shown in panel A (red circles, cos274) and panel B (black circles, ns274) were calculated using Sedfit and are plotted as a function of IHF concentration. The solid lines represent the best fits of simultaneous (global) analysis of the ensemble of binding data to the DNA unbending model (Scheme 1) as described in Supporting Information. The binding parameters derived from global analysis are presented in Table S2 of the Supporting Information.