I just googled this and found lots of info.

I think ChIP is more concerned with where the protein is bound(the DNA) whereas EMSA is more concerned about the protein complex. I’m not sure if you can release the protein from the antibody after it’s bound.

Here is a link with some tech info on EMSA

http://www.piercenet.com/Proteomics/bro … F#techtips

Here is some more info.
http://books.google.com/books?id=yOYpak … 1-PA124,M1

I think CHIP is used for In Vivo study protein-DNA interaction in whole genome setting whereas EMSA is used for in vitro protein-DNA interaction with in vitro synthesied oligo DNA and recomninant protein or nuclear extract. EMSA can be used to confirm specific DNA binding site for a transcription factor whereas CHIP resolution won’t be high in that CHIP can only show a protein associate with a genomic DNA (>200 bp). EMSA can be used to identify a novel transcription factor binding site. CHIP-on-chip can also be used to identify genome-wide transcription factor target genes. EMSA can be easily done in a couple of hours whereas old fasion CHIP requires 2 to 3 days work. Recent advance in fast Chromatin IP kit also proves CHIP can be done in 4 hours as I googled and found a fast Chromatin IP kit from AmericanGeneTech.com can do just as fast as EMSA.

EMSA – Naked DNA binding – Not very reliable
ChIP – Chromatin binding – If works well quite quite reliable.