EMSA/ band shift enquiries - EMSA/ band shift enquiries (Oct/14/2004 )

Hi there,

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!!!!

You may try DNA binding sites selection assays, which is also known as SELEX. It will give you an answer in 16 weeks with all the required experiements done properly.