As the title describe, I wanna ask if anybody has known any method to eliminate the NTPs/dNTPs from the protein without nucleotiges that I use specific enzyme and ultraphonic method to broke them as possible as I can. Now I want to move the amounts of NTPs/dNTPs existing among the protein circumstance.
Sonication, extrusion, benzonase are all effective means of breaking down nucleic acids to nucleotides, which eventually can be removed from protein following your preferred protocol (diafiltration, IEX, SE, etc, depending how you are going to purify your protein). If using sonication you should make sure to use a gentle method not increasing solution temperature with the risk of denaturing your target protein.
Ion exchange chromatography should remove most of the contaminating polymerized nucleic acid that's left after nuclease treatment. Low molecular weight oligonucleotides and nucleotides will be removed by gel filtration chromatography and dialysis, and will also be removed during metal affinity chromatography or any other affinity chromatography.
So you mean DNA and RNA (polymers), not (d)NTPs (monomers)?
To break down DNA and RNA, any mechanical disturbance will help (stirring, mixing) or anion exchange chromatography (nucleic acids bind very strongly). Also salting out with ammonium sulphate till 20% saturation shall remove nucleic acids.
As for nucleotides, you will get rid of them during any chromatography, during dialysis or ultrafiltration and similar techniques. And of course gel filtration chromatography as already mentioned by Adam.
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