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. 2008 Jun 20;190(17):5890–5897. doi: 10.1128/JB.00459-08

FIG. 2.

FIG. 2.

Identification of the NemR box sequence. (A) DNase I footprinting of the NemR-binding site and the recognition sequences of NemR. The fluorescence-labeled SELEX segment (1.0 pmol) of the ydhL-nemR spacer region was incubated in the absence (lane 1) or presence of increasing concentrations of purified NemR (lane 2, 1.25 pmol; lane 3, 2.5 pmol; lane 4, 5.0 pmol; lane 5, 10 pmol) and then subjected to DNase I footprinting assays. Lanes A, T, G, and C represent the respective sequence ladders. (B) From the DNase I footprinting assay, a 22-bp-long sequence was found to be protected by NemR. (C) A total of 69 independent SELEX clones containing parts of the ydhL-nemR spacer sequence were aligned along the E. coli genome. The 22-bp sequence was present among all these 69 clones. The number of each SELEX clone is given in parentheses. (D) After alignment of four SELEX fragments, the consensus recognition sequence by NemR, designated the NemR box as shown on top of panel B, was predicted to be a palindromic sequence consisting of TAGACCnnnnGGTCTA.