I am working with a protocol that requires cell pellet resuspension in 6 M guanidinium. I did not make this protocol, so I don't know how they came to this optimization. I keep getting very viscous lysate which I think is due to the DNA. With the Gdm in the solution, it will denature a nuclease which bars me from that method. Is there a way to remove the DNA from solution after I lyse the cells while keeping the high Gdm concentration? I generally resuspend in 50 mL of buffer (50 mM Tris, pH 8.0, 500 mM NaCl, 20 mM imidazole, 1 mM TCEP).
It looks like you are planning to purify a protein by Ni- or Co- metal affinity chromatography (else, why 20 mM imidazole ?). The only reason to add guanidinium is if your protein is insoluble and forms granules. At any rate, I wouldn't use guanidine hydrochloride for lysis. Mechanical lysis (French press, sonication) would be preferable if you have access to it, or even chemical lysis with lysozyme plus a mild detergent such as Triton X-100. After that, you can treat the lysate with a DNase (preferably Benzonase™ rather than pancreatic DNase, as the latter may be contaminated with proteases). If the protein is insoluble, you can then pellet it by centrifugation and solubilize it by taking up the pellet in the guanidinium buffer prior to loading on the IMAC resin. Alternatively, if the protein is soluble, you can load the DNase-treated lysate directly onto the IMAC resin and proceed with the purification, which has the advantage of yielding a native protein.
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