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EMSA/ band shift enquiries


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#1 cdoc100

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Posted 14 October 2004 - 01:43 PM

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!!!!

#2 indevus

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Posted 20 October 2004 - 11:40 AM

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.




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