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. Author manuscript; available in PMC: 2015 Dec 12.
Published in final edited form as: J Mol Biol. 2014 Oct 13;426(24):3973–3984. doi: 10.1016/j.jmb.2014.10.005

Figure 5. The effect of DksA/ppGpp on binding of upstream and downstream fork junction probes to RNAP.

Figure 5

(A) curve 1, titration of RNAP beacon with upstream fork junction (probe 34). Curve 2, same as curve 1, but RNAP beacon was preincubated with 2 μM DksA and 100 μM ppGpp for 2 min prior to the addition of downstream fork junction. The Kd values were determined by fitting the dependence of relative fluorescence signal amplitude (F/Fo) on probe concentration to a chemical equilibrium equation (5).

(B) RNAP occupancy by downstream fork junction 36 was measured in samples containing 1 nM RNAP beacon or RNAP beacon preincubated with 2 μM DksA and 100 μM and 2nM of downstream fork junction probe.