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. Author manuscript; available in PMC: 2013 Mar 1.
Published in final edited form as: Plasmid. 2012 Jan 9;67(2):102–110. doi: 10.1016/j.plasmid.2011.12.009

Fig. 3. The 29-mer, like the 39-mer, binds RctB in vitro.

Fig. 3

The sequences of the 39-mers in rctA and in the middle of incII, and of several deletion derivatives of the latter are shown in the top, along with the sequence of the 29-mer. The 29-mer carrying fragment was bigger than the other fragments used here, as it contained more natural sequences flanking the site, exactly as present in pAS1 and shown on Fig. 1A (bottom sequence). To determine binding proficiency of these sequences to RctB, they were amplified by PCR (i.e. they were unmethylated) from the following plasmids: pTVC191, -222, -331, -332, -329, -330 and -327. The binding was monitored by EMSA (middle panel) at two different RctB concentrations. Percent binding ([intensity of the retarded band/combined intensities of free and retarded bands] × 100) at 6 nM and 30 nM are shown by white and grey bars, respectively. The error bars are from three independent measurements of band intensities from the same gel, which reflect the reproducibility of our measurements.