Magnetic DNA Affinity Purification of a Cellular Transcription Factor

The Epstein-Barr viral nuclear antigen 2 (EBNA2) plays a key role during establishment and maintenance of B-cell immortalization after Epstein-Barr virus (EBV) infection (1 ). EBNA2 acts as a transcriptional activator of cellular and viral genes (2 –8 ) and is tethered to EBNA2 responsive promoter elements by interaction with a cellular DNA binding protein (9 ,10 ). We purified this transcription factor by classical chromatographic methods, however, instead of the usual final DNA affinity column step, we applied a magnetic DNA affinity purification protocol. This increased the purity of the transcription factor from about 0.01% to almost homogeneity and allowed subsequent identification of the protein as RBP-Jκ (11 ).