Fast Track in der operativen Medizin
Größtmögliche Schonung des Patienten bei operativen Eingriffen, eine effiziente Schmerztherapie und Beschleunigung der postoperativen Rekonvaleszenz - dies alles verbirgt sich hinter dem Begriff "Fast-Track-Rehabilitation". Mit diesem Buch ist erstmals ei
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DNA–protein interactions: methods for detection and analysis Bipasha Dey • Sameer Thukral • Shruti Krishnan Mainak Chakrobarty • Sahil Gupta • Chanchal Manghani • Vibha Rani
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Received: 24 September 2011 / Accepted: 16 February 2012 / Published online: 8 March 2012 Ó Springer Science+Business Media, LLC. 2012
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. Keywords DNA–protein interactions Footprinting Electrophoretic mobility shift assay Southwestern blotting Phage display Yeast one-hybrid assay Chromatin immunoprecipitation assay Biophysical techniques
All the authors have contributed equally. B. Dey S. Thukral S. Krishnan M. Chakrobarty S. Gupta C. Manghani V. Rani (&) Department of Biotechnology, Jaypee Institute of Information Technology, A-10 Sector-62, Noida 201307, Uttar Pradesh, India e-mail: [email protected]
Introduction Association of DNA with proteins is a phenomenon of utmost importance. In effect, almost all aspects of cellular function, such as transcriptional regulation, chromosome maintenance, replication and DNA repair depend on the interaction of proteins with DNA. Activation of genes by DNA-binding proteins is a fundamental regulatory mechanism involving the chromatin modifying and transcription complexes to initiate the RNA synthesis [1]. Such DNA-binding proteins have diverse roles and may function as structural proteins making up the nucleosome, enzymes modulating chromatin structure to control gene expression, transcription factors, and also as cofactors. One of the most widely studied examples of DNAbinding proteins is the transcription factor. TFs association with DNA is considered to be extremely critical in development processes and in response to environmental stresses. Also, in humans their dysfunction can contribute to the progression of various diseases [2]. In view of such an important role played by DNA– protein interactions, various techniques have evolved over the years to elucidate them. Each technique, with its own advantages and drawbacks, serves a very specific purpose. In brief, the techniques cater either of the two
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