Heparin elution of transcription factors from DNA-Sepharose columns

A novel method using heparin for eluting transcription factors from DNA-Sep harose columns was characterized. CAAT enhancer binding protein (C/EBP) or lac repressor fusion proteins were both eluted with heparin from columns co ntaining specific DNA sequences coupled to cyanogen bromide activated Sepha rose. The amount of the lac repressor chimera which eluted from the column was shown to increase with increases in the mobile phase heparin concentrat ion. The elution of the protein was also shown to be dependent on the amoun t of DNA coupled to the column and more protein eluted from columns contain ing lesser amounts of DNA, These data suggest that heparin and DNA compete for binding to the protein; this competition causes elution. Comparison of heparin- and salt-eluted protein demonstrated the heparin-eluted fraction w as significantly purer and comparable to that obtained by elution with isop ropyl beta-D-thiogalactopyranoside, a lactose analog. Heparin elution repre sents an important new tool in the purification of transcription factors an d other DNA-binding proteins by DNA affinity chromatography. (C) 1999 Elsev ier Science B.V. All rights reserved.