MITOMI: A Microfluidic Platform for In Vitro Characterization of Transcription Factor–DNA Interaction

  • Sylvie Rockel
  • Marcel Geertz
  • Sebastian J. Maerkl
Part of the Methods in Molecular Biology book series (MIMB, volume 786)

Abstract

Gene regulatory networks (GRNs) consist of transcription factors (TFs) that determine the level of gene expression by binding to specific DNA sequences. Mapping all TF–DNA interactions and elucidating their dynamics is a major goal to generate comprehensive models of GRNs. Measuring quantitative binding affinities of large sets of TF–DNA interactions requires the application of novel tools and methods. These tools need to cope with the difficulties related to the facts that TFs tend to be expressed at low levels in vivo, and often form only transient interactions with both DNA and their protein partners. Our approach describes a high-throughput microfluidic platform with a novel detection principle based on the mechanically induced trapping of molecular interactions (MITOMI). MITOMI allows the detection of transient and low-affinity TF–DNA interactions in high-throughput.

Key words

Microarrays Transcription factor binding sites High-throughput Binding affinities DNA array Protein array Surface chemistry Two-step PCR Microfluidics 

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Sylvie Rockel
    • 1
  • Marcel Geertz
    • 2
  • Sebastian J. Maerkl
    • 1
  1. 1.Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL)LausanneSwitzerland
  2. 2.Department of Molecular BiologyUniversity of GenevaGenevaSwitzerland

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