Certain DNA binding protein DBPs might not be removed and affect the downstream activity, any suggestions to eliminate all DBPs effectively?Any way to verify the removal?
You can use protease to hydrolysis the protein and then you must to use TCA/acetone precipitation to precipitate both DBP and protease.
Also there are some procedures that help you to purify genomic DNA with minimal contamination of proteins (Please go to the following article: J Biomol Tech. 2009 December; 20(5): 278–281).
If you need these procedure please don't hesitate to contact me.