title: DNA-protein interactions: methods for detection and analysis.
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.
authors.affiliation: Department of Biotechnology, Jaypee Institute of Information Technology, A-10 Sector-62, Noida 201307, Uttar Pradesh, India.
authors.forename: Bipasha
authors.initials: B
authors.lastname: Dey
authors.forename: Sameer
authors.initials: S
authors.lastname: Thukral
authors.forename: Shruti
authors.initials: S
authors.lastname: Krishnan
authors.forename: Mainak
authors.initials: M
authors.lastname: Chakrobarty
authors.forename: Sahil
authors.initials: S
authors.lastname: Gupta
authors.forename: Chanchal
authors.initials: C
authors.lastname: Manghani
authors.forename: Vibha
authors.initials: V
authors.lastname: Rani
mesh_terms: D000818:Animals; D002151:Calorimetry; D047369:Chromatin Immunoprecipitation / Q000379:methods; D002942:Circular Dichroism; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry / Q000378:metabolism*; D018983:DNA Footprinting; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000378:metabolism*; D024202:Electrophoretic Mobility Shift Assay; D031541:Fluorescence Resonance Energy Transfer; D006801:Humans; D009682:Magnetic Resonance Spectroscopy; D018625:Microscopy, Atomic Force; D008958:Models, Molecular; D019151:Peptide Library; D011485:Protein Binding; D012984:Software; D020349:Surface Plasmon Resonance; D020798:Two-Hybrid System Techniques
chemical_list: D004268:DNA-Binding Proteins; D019151:Peptide Library; D004247:DNA