Ya we use 1M NaCl in lysis and 0.5M NaCl in washing buffer to avoid those contaminating DNAs and its consequencses. Have a look at the reference:

http://www.nature.com/nsmb/journal/v19/n10/full/nsmb.2378.html

That's quite a lot of salt, not sure but it might interfere with the GST interaction with the purification matrix. What about just treating your lysate with DNase? I do it often in bacterial extracts in order to get rid of DNA without sonicating or in cell extracts for IPs of chromatin proteins

Thank you Daniel. I already used DNase. DNA still exists since DNase may only cut it into small fragments. These fragments were also troublesome.

Ah ok.

I know that at least 500mM salt is probably ok, a lot of people use it for washing, so for binding might work too. There also a bunch of methods to get rid of DNA, namely using PEI, I have no experience with those. Refence here: http://wolfson.huji.ac.il/purification/tagproteinpurif/dna.html

Ya we use 1M NaCl in lysis and 0.5M NaCl in washing buffer to avoid those contaminating DNAs and its consequencses. Have a look at the reference:

http://www.nature.com/nsmb/journal/v19/n10/full/nsmb.2378.html

Thank you Ananda and Daniel. I will have a try.

I have used 500mM of NaCl for GST affinity purification. I have never tested higher concentration. So at least until 500mM it should work.

I have used up to 1M NaCl for GST (and polyhistidine) preps with no problems.

Hi Pengfei,

we have used 1M NaCl on Ni-NTA matrices for the same purpose. Our protein-DNA complex binds to E. coli DNA during expression and cell lysis and we loose approx. 90 % of the protein in the flow-trough. We have tried to increase DNaseI concentrations and incubation times, but DNaseI only digests DNA to oligonucleotides, which stick to the complex. Loading of the lysate on the column in the presence of 1 M NaCl solved the problem, so you should definitely give it a try.

Good luck, Magdalena