Analysis of nucleoproteins by direct injection of dissolved nuclei or chromosomes into a high-performance liquid chromatographic system

This work describes the development of a method for fractionating the total nuclear proteins of Chinese hamster cells (line CHO) by high-performance liquid chromatography of whole nuclei or chromosomes. Nuclei or chromosomes were dissolved for 2 h in 6 M guanidine hydrochloride containing 0.2% trifluoroacetic acid (TFA). Residual particulates were removed by centrifugation, and a sample of the solution was passed through a Bio-Sil TSK guard column, followed by a Bio-Sil TSK 400 column, equilibrated with water containing 0.2% TFA. These columns fractionated the sample by adsorbing the DNA, passing the proteins near the exclusion limit, passing the guanidine at the inclusion limit, and passing an unidentified non-protein/non-DNA material after the inclusion limit. The protein peaks from the TSK columns were collected directly on a muBondapak CN reversed-phase column. The protein fractions were then eluted from the CN column with an acetonitrile gradient containing 0.2% TFA. Three other reversed-phase columns were examined for use with the TSK columns. The muBondapak C18 Radial-Pak column produced the best resolution of histone variants, while the Zorbax C8 column produced a better resolution of the non-histone proteins. The Nova-Pak C18 Radial-Pak column was found to be unsatisfactory for both classes of nucleoproteins.