I have tried using UV crosslinking with MyOne magnetic streptavidin beads. It is a giving lot of non-specific background, making it impossible to see any clear cut different protein band. Same with formaldehyde. I have tried 4-Thio UTP but it does not work. I have another problem that my RNA polymerase is a mutant one from Durascribe, which does not take many modified bases.
We don't know absolutely anything about the protein we're trying to pull out. We are trying to find out the target of this RNA aptamer, biding to whole cell.
Do you have any idea, if these 2'-O-methyl ribonucleotides incorporated by Durascribe RNA polymerase?
Trans-diamminedichloroplatinum(II) could be useful in your case, especially as X-linking is reversible. see Tukalo et al. Biochemistry, 1987, 26 (16), pp 5200–5208
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