I'm new to DNA-protein interactions and was hoping to do an EMSA (either 32P or biotin-chemiluminescent) with my protein of interest. However, I do not yet know for sure if it binds DNA, but I was hoping EMSA would tell me.
However, what DNA sequence should I use for this, as the protein's specificity (if any) is thus unknown at present. Maybe Poly[I].Poly[C] alone or alternating copolymer DNA, or even any old duplex small PCR product perhaps? Or should I just use a labelled random oligo library?
Also, can EMSA be used to assess RNA binding potential, or would a North-Western blot be more suitable? What RNA probes are recommened if so?
Thanks for your help and I hope these are not daft questions!!!!
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