electrophoresis
Definition
Electrophoresis is a laboratory technique that separates charged biomolecules—including DNA, RNA, proteins, and other macromolecules—based on their size, charge, and shape by applying an electric field through a gel or liquid medium. Molecules migrate through the matrix at different rates, with smaller or more highly charged molecules typically moving faster. Common variants include agarose gel electrophoresis for nucleic acids, SDS-PAGE for proteins, and capillary electrophoresis for high-resolution separations. This foundational technique is essential for molecular biology applications including quality control of PCR products, protein purification verification, mutation detection, and quantitative analysis of biomolecules. Electrophoresis results inform downstream analyses like Western blotting, sequencing, and mass spectrometry.
Visualize electrophoresis in Nodes Bio
Researchers can visualize protein complexes or gene products identified through electrophoresis as nodes within interaction networks. By mapping electrophoretically separated proteins to their interaction partners, researchers can explore how post-translational modifications affect network topology, identify co-migrating protein complexes, or trace pathway connections between differentially expressed bands across experimental conditions in Nodes Bio's network environment.
Visualization Ideas:
- Protein-protein interaction networks from co-migrating electrophoretic bands
- Pathway enrichment maps connecting differentially expressed proteins identified via 2D electrophoresis
- Gene regulatory networks linking DNA fragments separated by pulsed-field gel electrophoresis
Example Use Case
A cancer research team uses 2D gel electrophoresis to separate proteins from tumor versus normal tissue samples, identifying 15 differentially expressed protein spots. After mass spectrometry identification, they input these proteins into Nodes Bio to map their interaction networks and pathway enrichments. The visualization reveals that 8 proteins cluster within the PI3K/AKT signaling pathway, suggesting this pathway's dysregulation in tumor progression. This network-level insight guides their selection of targeted therapeutic candidates for validation studies.