A multi-parametric flow cytometric assay to analyze DNA-protein interactions

Mandana Arbab, Shaun Mahony, Hyunjii Cho, Joel M. Chick, P. Alexander Rolfe, John Peter Van Hoff, Viveca W.S. Morris, Steven P. Gygi, Richard L. Maas, David K. Gifford, Richard I. Sherwood

Research output: Contribution to journalArticlepeer-review

3 Scopus citations


Interactions between DNA and transcription factors (TFs) guide cellular function and development, yet the complexities of gene regulation are still far from being understood. Such understanding is limited by a paucity of techniques with which to probe DNA-protein interactions. We have devised magnetic protein immobilization on enhancer DNA (MagPIE), a simple, rapid, multi-parametric assay using flow cytometric immunofluorescence to reveal interactions among TFs, chromatin structure and DNA. In MagPIE, synthesized DNA is bound to magnetic beads, which are then incubated with nuclear lysate, permitting sequence-specific binding by TFs, histones and methylation by native lysate factors that can be optionally inhibited with small molecules. Lysate protein-DNA binding is monitored by flow cytometric immunofluorescence, which allows for accurate comparative measurement of TF-DNA affinity. Combinatorial fluorescent staining allows simultaneous analysis of sequence-specific TF-DNA interaction and chromatin modification. MagPIE provides a simple and robust method to analyze complex epigenetic interactions in vitro.

Original languageEnglish (US)
Pages (from-to)e38
JournalNucleic acids research
Issue number2
StatePublished - Jan 2013

All Science Journal Classification (ASJC) codes

  • Genetics


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