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Related Concept Videos

Protein Networks02:26

Protein Networks

An organism can have thousands of different proteins, and these proteins must cooperate to ensure the health of an organism. Proteins bind to other proteins and form complexes to carry out their functions. Many proteins interact with multiple other proteins creating a complex network of protein interactions.
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Protein-protein Interfaces02:04

Protein-protein Interfaces

Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a polypeptide...
Protein-Drug Binding: Determination Methods01:22

Protein-Drug Binding: Determination Methods

Determining protein-drug binding can be achieved through indirect and direct methods, each providing valuable insights into the interaction between proteins and drugs.
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...

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Analyzing DNA-Protein Interactions with Streptavidin-Based Biolayer Interferometry
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Analyzing DNA-Protein Interactions with Streptavidin-Based Biolayer Interferometry

Published on: January 17, 2025

DNA-protein interactions: methods for detection and analysis.

Bipasha Dey1, Sameer Thukral, Shruti Krishnan

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

Molecular and Cellular Biochemistry
|March 9, 2012
PubMed
Summary
This summary is machine-generated.

This review summarizes key techniques for studying DNA-protein interactions, essential for understanding cellular processes like transcription. It covers in vitro, in vivo, in silico, and biophysical methods for analyzing these crucial molecular interactions.

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Last Updated: May 24, 2026

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In-vivo Detection of Protein-protein Interactions on Micro-patterned Surfaces

Published on: March 19, 2010

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • DNA-binding proteins are critical regulators of fundamental cellular processes, including DNA replication, transcription, and recombination.
  • Understanding the intricate mechanisms of DNA-protein interactions is vital for deciphering gene regulation and cellular function.

Purpose of the Study:

  • To provide a comprehensive overview of diverse methodologies used to investigate DNA-protein interactions.
  • To highlight the strengths and applications of various experimental and computational approaches.

Main Methods:

  • In vitro techniques: Footprinting assays, electrophoretic mobility shift assay (EMSA), southwestern blotting, yeast one-hybrid assay, phage display, proximity ligation assay.
  • In vivo techniques: Chromatin immunoprecipitation (ChIP) and its variants, DNA adenine methyl transferase identification (DamID), 3C, ChIP-loop assay.
  • In silico and biophysical methods: Computational tools, fluorescence resonance energy transfer (FRET), circular dichroism, atomic force microscopy (AFM), nuclear magnetic resonance (NMR), surface plasmon resonance (SPR).

Main Results:

  • The review systematically categorizes and describes a wide array of techniques for analyzing DNA-protein interactions.
  • It emphasizes the versatility and applicability of both established and advanced methods across different biological contexts.

Conclusions:

  • A broad spectrum of techniques, spanning in vitro, in vivo, in silico, and biophysical approaches, are available for characterizing DNA-protein interactions.
  • The selection of an appropriate method depends on the specific research question and the biological system under investigation.