I am working on tobacco mosaic virus in vitro and in vivo encapsidation. I mainly used PEG8000 to precipitate encapsidated virions. I am wondering if it's possible that PEG can also precipitate free, non-assembled coat protein discs? The reason I ask is I happen to see a weak band on SDS-PAGE regarding one control sample(with only free coat protein, no viral genome) after PEG precipitation. Just wonder if that's normal or I had some contamination problems?
Dear Tommy. depending on pH and ionic strength the RNA-free coat protein preparation can form assemblies of various symmetry an size. particles resembling the virus are one of the possibilities. with PEG precipitation you are basically crowding out the solvent - water and the least soluble species will gradually fall out of the solution. The larger the particle the more likely it is to be precipitated, but this method is by no means specific only to large particles. You will precipitate also smaller discs and other proteins unrelated to tmv. depends on your sample. If you suspect RNA contamination I would suggest doing RT-PCR, that should be pretty sensitive.
PEG will not have selective precipitation, so it is possibly a contaminant
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