Dear Prafulla Katkar,

basically you are performing electrophoretic mobility shift assay (EMSA) or mobility shift electrophoresis. if your drug will bind with DNA the motility of the DNA is shifted It becomes heavier and moves slowly. But weather your drug binds to minor groove or major groove? the nature of binding? etc will remain unanswered. You may choose your experimental design as per your requirement.

but yes you can detect binding of your drug with DNA with EMSA.

Thanks vivek !!!

yeah i did EMSA, but cant conclude binding to any of the grooves. More i need to see binding at major or minor groove. Ethidium bromide generally binds to minor groove, so something i need to see its displacement or shift in presence of drug.

Ethidium Bromide do not bind to minor groove otherwise it would never dye single stranded DNA or mRNA. by EMSA you would only know the shift in DNA. the band would be shifted as compared to control.

I agree with Vivek. Ethidium bromide is an intercalator in dsDNA. Melting curves in the presence or absence of drug will tell you whether your drug binds to DNA or not, but will not tell you how. Diamidines such as the fluorescent probe DAPI are minor groove binders so you might be able to develop a displacement or competition assay.

How about methyl orange, ActD

methyl red