nearly pure fraction of DNA binding protein (around 6.6 kda) is contaminated with the Nucleic acid size of around 100 - 150 bp , How can we separate them and collect protein fraction intact?
Addition of DNase I and MgCl₂ to the cell lysate before purification helps remove most or all DNA contamination. If the presence of the 100 - 150 bp fragment has been a repeatable result, it could suggest this fragment is a natural binding partner of your protein and not necessarily a contamination.
I have tried DNase I , The DNA contamination is gone, Agarose gel , 12 % DNA PAGE didnot show any band but A260 (and A260/280 appr 2) of nanodrop reading is high, indicating DNTP contamination ? Dialysis could not remove the DNTP contamination? can DNTP' s bind to DNA binding proteins? If so how can we remove them ?