Question

You are doing an EMSA experiment. The DNA sequence you study is about 1000bp long and contains the first two exons of a protein coding gene. You run your DNA alone on the gel for 1 hour at 72 volts and you notice that the DNA fragment matches the 1000bp marker in the DNA ladder, which is to be expected. You then start adding different transcription factors to your DNA sample and run the EMSA experiment to see which one would bind to your DNA. After adding 10 different transcription factor proteins to your DNA sample and doing the EMSA experiment you see that none of them changes the mobility of you DNA fragment. Explain this observation.

Answer 1

After adding 10 different transcription factor proteins to DNA sample and EMSA experiment wr see that none of them changes the mobility of you DNA fragment.

This means none of the transcription factor binds to DNA . So in absence of binding of these transcription factor bands remains at stable location and there is no change in the mobility or shifting of the band .

Explanation-

EMSA is also known as gel mobility assay or gel shift assay used to detect protein DNA interactions.

Here shift in the band is seen if a transcription factor bind to DNA band . If protein or transcription factor do not bind to DNA , then DNA band will remain at the same position.

This phenomenon we can easily explained by attached image below

Here in the above question,

After adding 10 different transcription factor proteins to DNA sample and EMSA experiment wr see that none of them changes the mobility of you DNA fragment.

This means none of the transcription factor binds to DNA . So in absence of binding of these transcription factor bands remains at stable location and there is no change in the mobility or shifting of the band .