Elucidating Protein: DNA Complex by Oligonucleotide DNA Affinity Purification

  • Teddy T. C. Yang
  • Chi-Wing ChowEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 809)


Transcription factors recruit a wide variety of associated co-factors to regulate gene expression. These co-factors include protein kinases, phosphatases, deacetylases, methylases, and ubiquitin ligases, etc. To identify novel protein kinases associated with transcription factor NFAT, we took advantage of the increased ability of DNA binding and used an oligonucleotide affinity-binding approach. Coupling with in-gel kinase assays to detect phosphotransferase activity, we were able to identify p90 ribosomal S6 kinase (RSK) and p70 S6 kinase (S6K) that are present in the NFAT:DNA complex. We further demonstrated that RSK and S6K binds to and physically interacts with NFATc4. Similar oligonucleotide affinity-binding approach can be coupled with other enzymatic reactions, such as dephosphorylation, deacetylation, methylation, ubiquitination, etc. Mass spectrometry can also be carried out to systemically identify these transcription co-factors in the protein:DNA complex. Lastly, gene-specific enhancer elements can also be devised based on their respective sequence to identify distinctive protein:DNA complexes.

Key words

Transcription activation complex Oligonucleotide DNA affinity purification Transcription factor NFAT Transcription co-factors Protein kinases 



The authors would like to acknowledge the past and current members of the Chow laboratory for their input, discussion, and trouble shooting of the protocol.


  1. 1.
    Durand DB, Shaw JP, Bush MR, Replogle RE, Belagaje R and Crabtree GR (1988) Characterization of antigen receptor response elements within the interleukin-2 enhancer. Mol Cell Biol 8:1715–24.PubMedGoogle Scholar
  2. 2.
    Crabtree GR and EN Olson (2002) NFAT signaling: choreographing the social lives of cells. Cell 109 Suppl:S67–79.PubMedCrossRefGoogle Scholar
  3. 3.
    Hogan PG, Chen L, Nardone J and Rao A (2003) Transcriptional regulation by calcium, calcineurin, and NFAT. Genes Dev 17:2205–32.PubMedCrossRefGoogle Scholar
  4. 4.
    Olabisi OA, Soto-Nieves N, Nieves E, Yang TT, Yang X, Yu RY, Suk HY, Macian F and Chow CW (2008) Regulation of transcription factor NFAT by ADP-ribosylation. Mol Cell Biol 28:2860–71.PubMedCrossRefGoogle Scholar
  5. 5.
    Yang TT and Chow CW (2003) Transcription cooperation by NFAT.C/EBP composite enhancer complex. J Biol Chem 278:1587485.PubMedCrossRefGoogle Scholar
  6. 6.
    Yang TT, Xiong Q, Graef IA, Crabtree GR and Chow CW (2005) Recruitment of the extracellular signal-regulated kinase/ribosomal S6 kinase signaling pathway to the NFATc4 transcription activation complex. Mol Cell Biol 25:90720.PubMedCrossRefGoogle Scholar
  7. 7.
    Kao SC, Wu H, Xie J, Chang CP, Ranish JA, Graef IA and Crabtree GR (2009) Calcineurin/NFAT Signaling Is Required for Neuregulin-Regulated Schwann Cell Differentiation. Science 323:651–654.PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  1. 1.Department of Molecular PharmacologyAlbert Einstein College of MedicineBronxUSA

Personalised recommendations