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Analysis of DNA–protein interactions: from nitrocellulose filter binding assays to microarray studies

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Abstract

Determination of the sequence of the human genome and knowledge of the genetic code have allowed rapid progress in the identification of mammalian proteins. However, far less is known about the molecular mechanisms that control expression of human genes and about the variations in gene expression that underlie many pathological states, including cancer. This is caused in part by lack of information about the binding specificities of DNA-binding proteins and particularly regulative important molecules such as transcription factors. It is consequently crucial to develop new technologies or improve existing ones for the analysis of DNA–protein interaction in order to identify and characterise DNA response elements and the related transcription factors or other DNA-binding proteins. The techniques that are currently available vary with respect to the type of result that can be expected from the assay: a mere qualitative demonstration of binding; the identification of response element sequences at high throughput; or a quantitative characterisation of affinities. This article gives an overview of early and recent methodologies applied to such ends.

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Acknowledgements

We are grateful to Christian Kraus for provision of Fig. 4. Work on protein–DNA interaction in our laboratory is funded by the German Federal Ministry of Education and Research (BMBF) as part of the NGFNplus PaCaNet project as well as the Regulatory Genomics and DropTop projects funded by the European Commission. R.H. is supported by a PhD fellowship of the Egyptian Government.

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  1. Division of Functional Genome Analysis, Deutsches Krebsforschungszentrum (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany

    Reham Helwa & Jörg D. Hoheisel

  2. Molecular Cell Biology Laboratory, Zoology Department, Faculty of Science, Ain Shams University, Cairo, 11566, Egypt

    Reham Helwa

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  1. Reham Helwa
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Correspondence to Reham Helwa.

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Published in the special issue Focus on Bioanalysis with guest editors Antje J. Baeumner, Günter Gauglitz, and Frieder W. Scheller.

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Helwa, R., Hoheisel, J.D. Analysis of DNA–protein interactions: from nitrocellulose filter binding assays to microarray studies. Anal Bioanal Chem 398, 2551–2561 (2010). https://doi.org/10.1007/s00216-010-4096-7

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