How Were GadE and GadX Demonstrated to Be Transcription Factors

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The Answer is Footprint analysis can be used to find out what nucleotides in a DNA fragment directly interact with DNA-binding proteins. The principle is that the DNA region bound by protein is protected from endonuclease activity (e.g., DNase I). After disruption of the protein-DNA interactions, protected DNA fragments are electrophoretically separated in a gel along with protein-free DNA that had been treated with DNase I under the same conditions. A set of sequencing reactions help in localizing the transcriptional start site and nucleotides that directly bind the protein, as only one of the DNA strands is labeled and migrates to a position that matches one base of the sequencing reactions. Both GadE and GadX protect several regions upstream of the transcriptional start of gadA.

How Were GadE and GadX Demonstrated to Be Transcription Factors

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