DNA OR NUCLEOTIDE CONTAMINATION OF PROTEIN - I NEED TO GET THIS FRAGEMENTED DNA OUT OF MY SMALL PROTEIN (Feb/19/2006 )

IN BREAKING DOWN MY CELLS AND PURIFYING MY PROTEIN, I HAVE ALSO BROKEN DOWN DNA SIGNIGICANTLY AND ITS ALL OVER MY PURIFIED PROTEIN AFTER GEL FILTRATION. THE SOLN ACTUALLY LOOKS BROWN. MY NEXT TWO STEPS ARE ION EXCHANGE AND REVERSE PHASE CHROMATOGRAPHY AND I DONT WANT IT GETTING IN THE WAY. CAN ANYONE THINK OF A WAY OF GETTING RID OF THIS A260 PEAK.

JBC

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Dnase treatment? But then you might have to repurify

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try benzonase treatment

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You could try sonicating your sample, as well. Sonication will generally cleave DNA, but leave protein more or less alone.

If your protein just likes DNA, though, you might get pieces sticking to it regardless of how you try to remove it.

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what you can do is take the protein fraction and load it on a DNA affinity column with the appropriate cut off (pores ). after centrifugation you take the fraction in your tube and the dna stays on the column. you can also do DNAse reaction on your sample, but the reaction temp' is 37 and your protein could be affected (activity wise).
another solution is to percipitate the DNA and only use the liquid fraction above.
daphna

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