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DNA–protein interactions: methods for detection and analysis

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Abstract

DNA-binding proteins control various cellular processes such as recombination, replication and transcription. This review is aimed to summarize some of the most commonly used techniques to determine DNA–protein interactions. In vitro techniques such as footprinting assays, electrophoretic mobility shift assay, southwestern blotting, yeast one-hybrid assay, phage display and proximity ligation assay have been discussed. The highly versatile in vivo techniques such as chromatin immunoprecipitation and its variants, DNA adenine methyl transferase identification as well as 3C and chip-loop assay have also been summarized. In addition, some in silico tools have been reviewed to provide computational basis for determining DNA–protein interactions. Biophysical techniques like fluorescence resonance energy transfer (FRET) techniques, FRET–FLIM, circular dichroism, atomic force microscopy, nuclear magnetic resonance, surface plasmon resonance, etc. have also been highlighted.

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Acknowledgments

This study was supported by the research grant awarded to Dr. Vibha Rani by the Department of Science and Technology, Government of India (SR/FT/LS-006/2009: Sept 4, 2009). We acknowledge Jaypee Institute of Information Technology, Deemed to be University for providing the infrastructural support.

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  1. Department of Biotechnology, Jaypee Institute of Information Technology, A-10 Sector-62, Noida, 201307, Uttar Pradesh, India

    Bipasha Dey, Sameer Thukral, Shruti Krishnan, Mainak Chakrobarty, Sahil Gupta, Chanchal Manghani & Vibha Rani

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  1. Bipasha Dey
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  2. Sameer Thukral
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  3. Shruti Krishnan
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  7. Vibha Rani
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Correspondence to Vibha Rani.

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All the authors have contributed equally.

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Dey, B., Thukral, S., Krishnan, S. et al. DNA–protein interactions: methods for detection and analysis. Mol Cell Biochem 365, 279–299 (2012). https://doi.org/10.1007/s11010-012-1269-z

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