I am new to EMSAs, basically I want to do an EMSA-western to determine if my protein of interest binds DNA. I plan to IP my protein and a known TF say myc. Since i dont know if my protein binds DNA, I am going double digest genomic DNA with a combination of different restriction enzymes. I will incubate my IPed proteins with the DNA and run it on a native gel and then transfer to nitrocellulose paper and probe with specific ab for western blotting.
I plan to run IPed proteins without DNA as my baseline to detect the protein bands. I hope to see single bands in my IP alone lanes and several bands in my IP+ DNA fragments lane which would represent my protein binding to DNA.
I wanted to know if this protocol was feasible, basically I am looking for yes/no answer to base my future expts (chip-chip etc) on. I would appreciate any input or comments on this!