I tried to do some DNA protein assay for my project, but just found the method, EMSA I used, is not very repeatable. I wonder if other methods are repeatable. ChIP, DNase footpring, filter binding? Any advice is welcome. In addition, I hope we can discuss more on the topic of DNA protein interactions. Here are some protocols in the field of DNA (RNA) protein interaction assay. http://dnaandprotein.blogspot.com

Each of the methods you mentioned will have advantages and caveats. The specific experimental goals and situation will dictate which to use. If you want to post more particulars we can discuss possible areas of variability with the EMSA analysis.