Hi Neeraj, An absorption spectra between 220 and 400 nm (for example) should show you if there is DNA coming along with your protein. In theory A280 is about 1.7 times A260 for a pure protein sample. This is a rough estimate. If your peak is shifted towards 260 instead of 280 then you can suspect the presence of contaminating DNA or RNA.
As to get rid of the DNA, I can suggest several ways to do it. 1-An heparin affinity column could out-compete your contaminating DNA while binding your protein. They work really well. 2-Ion exchange is worth trying. It has worked for me with an extremely basic archeal RNA binding protein purified in E.coli and bringing along some endogenous RNA/DNA. An ion exchange ( Mono-S type) got rid of the contaminating nucleic acid, however with some loss of protein. 3-DNAse treatment may be worth trying but the presence of traces of DNase may be a problem with subsequent crystallization trials in presence of the bona-fide target DNA sequence. 4-Precipitation of the DNA with streptomycine sulfate. You could also loss some protein. 1 and 2 are in my opinion the less invasive soutions. Hope this helps. Best regards Pascal Egea
