Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Protein Networks02:26

Protein Networks

4.2K
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,...
4.2K
Protein-protein Interfaces02:04

Protein-protein Interfaces

14.1K
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...
14.1K
Conservation of Protein Domains Over Different Proteins02:26

Conservation of Protein Domains Over Different Proteins

13.4K
Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
A limited set of protein domains often duplicate and recombine during evolution. These domains can be organized in different combinations to...
13.4K
Conserved Binding Sites01:49

Conserved Binding Sites

4.7K
Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
4.7K
Protein Organization01:24

Protein Organization

8.1K
Proteins are polymers of amino acid residues. They are versatile and responsible for different cellular functions, including DNA replication, molecular transport, catalysis, and structural support. Proteins have a hierarchical structure comprising at least three levels of organization: primary, secondary, and tertiary structure. Some large proteins have a quaternary structure where individual protein subunits are linked together.
The primary structure of a protein is its amino acid sequence....
8.1K
Evolutionary Relationships through Genome Comparisons02:54

Evolutionary Relationships through Genome Comparisons

6.5K
Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
6.5K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

A review on the function of arabinogalactan-proteins during pollen grain development.

Plant reproduction·2025
Same author

The peri-germ cell membrane: poorly characterized but key interface for plant reproduction.

Nature plants·2024
Same author

HISTONE DEACETYLASE19 Controls Ovule Number Determination and Transmitting Tract Differentiation.

Plant physiology·2023
Same author

Type II arabinogalactans initiated by hydroxyproline-O-galactosyltransferases play important roles in pollen-pistil interactions.

The Plant journal : for cell and molecular biology·2023
Same author

The best CRISPR/Cas9 versus RNA interference approaches for Arabinogalactan proteins' study.

Molecular biology reports·2020
Same author

In silico and expression analyses of fasciclin-like arabinogalactan proteins reveal functional conservation during embryo and seed development.

Plant reproduction·2019

Related Experiment Video

Updated: Oct 27, 2025

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.8K

DNA-protein interaction studies: a historical and comparative analysis.

Ricardo André Campos Ferraz1,2, Ana Lúcia Gonçalves Lopes1,2, Jessy Ariana Faria da Silva2,3

  • 1Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal.

Plant Methods
|July 24, 2021
PubMed
Summary

Choosing the right method to study DNA-protein interactions is crucial. This review guides researchers by comparing various techniques based on their strengths, weaknesses, and applications for characterizing these vital molecular interactions.

Keywords:
ChIPDNA-footprintingDNA–protein interactionEMSASELEXSPR

More Related Videos

Visualization of Protein-protein Interaction in Nuclear and Cytoplasmic Fractions by Co-immunoprecipitation and In Situ Proximity Ligation Assay
10:05

Visualization of Protein-protein Interaction in Nuclear and Cytoplasmic Fractions by Co-immunoprecipitation and In Situ Proximity Ligation Assay

Published on: January 16, 2017

13.0K
Analyzing DNA-Protein Interactions with Streptavidin-Based Biolayer Interferometry
08:07

Analyzing DNA-Protein Interactions with Streptavidin-Based Biolayer Interferometry

Published on: January 17, 2025

1.8K

Related Experiment Videos

Last Updated: Oct 27, 2025

Analyzing and Building Nucleic Acid Structures with 3DNA
16:24

Analyzing and Building Nucleic Acid Structures with 3DNA

Published on: April 26, 2013

20.8K
Visualization of Protein-protein Interaction in Nuclear and Cytoplasmic Fractions by Co-immunoprecipitation and In Situ Proximity Ligation Assay
10:05

Visualization of Protein-protein Interaction in Nuclear and Cytoplasmic Fractions by Co-immunoprecipitation and In Situ Proximity Ligation Assay

Published on: January 16, 2017

13.0K
Analyzing DNA-Protein Interactions with Streptavidin-Based Biolayer Interferometry
08:07

Analyzing DNA-Protein Interactions with Streptavidin-Based Biolayer Interferometry

Published on: January 17, 2025

1.8K

Area of Science:

  • Molecular Biology
  • Biochemistry
  • Genetics

Background:

  • DNA-protein interactions are fundamental to cellular processes like transcription and DNA modification.
  • Numerous techniques exist to study these interactions, making method selection challenging.
  • A comprehensive overview of available methods is needed to guide researchers.

Purpose of the Study:

  • To provide a historical context of DNA-protein interaction studies.
  • To compile and compare various techniques for studying DNA-protein interactions.
  • To assist research teams in selecting the most appropriate method based on their objectives and resources.

Main Methods:

  • Review of established and advanced techniques for DNA-protein interaction analysis.
  • Comparison of methods including filter binding assay, EMSA, DNA-footprinting, SPR, spectroscopy, and ChIP-seq.
  • Evaluation of advantages, disadvantages, and recent applications of each technique.

Main Results:

  • Filter binding assay and EMSA are effective for initial in vitro identification of DNA-binding proteins.
  • DNA-footprinting offers a reliable approach for identifying DNA-binding sites, with base analogue methods providing higher precision.
  • SPR and spectroscopy offer greater sensitivity for binding kinetics and affinities compared to filter binding assays and EMSA.
  • ChIP-seq is the preferred method for high-resolution, genome-wide studies of DNA-protein interactions.

Conclusions:

  • The selection of a DNA-protein interaction study technique requires careful consideration of experimental goals, available resources, and desired precision.
  • Different techniques offer varying levels of accuracy and are suited for specific research questions.
  • This review serves as a guide to aid researchers in navigating the diverse landscape of DNA-protein interaction analysis methods.