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Related Concept Videos

In-situ Hybridization02:31

In-situ Hybridization

In situ hybridization (ISH) is a technique used to detect and localize specific DNA or RNA molecules in cells, tissue, or tissue sections using a labeled probe. The technique was first used in 1969 for the investigation of nucleic acids. It is currently an essential tool in scientific research and clinical settings, especially for diagnostic purposes.
Types of probes and labels
A probe is a complementary strand of DNA or RNA that binds to corresponding nucleotide sequences in a cell. Many...
Southern Blot02:57

Southern Blot

Agarose gel electrophoresis is very useful in separating DNA fragments by size. Running a DNA ladder containing fragments of the known length alongside the sample helps determine the approximate length of the sample DNA fragments. However, additional steps are needed to verify the sequence identity of the sample DNA fragments.
Denatured DNA fragments must be transferred onto a carrier membrane from the gel to make it accessible to a probe - a small ssDNA fragment complementary to the target DNA...

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Related Experiment Video

Updated: May 8, 2026

Hybridization Chain Reaction RNA Whole-Mount Fluorescence In situ Hybridization of Chemosensory Genes in Mosquito Olfactory Appendages
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Hybridization Chain Reaction RNA Whole-Mount Fluorescence In situ Hybridization of Chemosensory Genes in Mosquito Olfactory Appendages

Published on: November 17, 2023

Methodological framework for chromogenic mRNA detection using in situ hybridization chain reaction.

Mitsuru Yashiro1,2, Yousuke Tsuneoka3, Yusuke Atsumi1,2

  • 1Department of Anatomy, Faculty of Medicine, Toho University, Tokyo, Japan.

Histochemistry and Cell Biology
|May 6, 2026
PubMed
Summary

A new chromogenic in situ hybridization chain reaction (HCR) method allows sensitive visualization of single mRNA molecules. This bright-field technique overcomes limitations of fluorescence HCR in routine pathology and autofluorescent tissues.

Keywords:
Chromogenic stainingISH–IHC combinationIn situ HCRRegional markerSingle-molecule ISH

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Radioactive in situ Hybridization for Detecting Diverse Gene Expression Patterns in Tissue
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Last Updated: May 8, 2026

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Radioactive in situ Hybridization for Detecting Diverse Gene Expression Patterns in Tissue
17:38

Radioactive in situ Hybridization for Detecting Diverse Gene Expression Patterns in Tissue

Published on: April 27, 2012

Area of Science:

  • Molecular Biology
  • Histology
  • Biochemistry

Background:

  • In situ hybridization chain reaction (HCR) is a sensitive single-molecule mRNA detection method.
  • Conventional fluorescence HCR is limited in routine pathology and autofluorescent tissues.

Purpose of the Study:

  • To develop a chromogenic in situ HCR protocol for sensitive mRNA detection.
  • To expand HCR utility in histology and pathology.

Main Methods:

  • Established a chromogenic in situ HCR protocol using short hairpin DNA and indirect hapten labeling.
  • Validated the protocol on mouse tissues (brain, kidney, liver) and different section types.
  • Demonstrated duplex staining and combined mRNA-protein visualization.

Main Results:

  • Achieved sensitivity comparable to fluorescent HCR.
  • Enabled clear visualization of low-abundance transcripts (Oxtr, Esr1).
  • Showcased versatility in multiplexing and combining with immunohistochemistry.

Conclusions:

  • Chromogenic in situ HCR offers high sensitivity with practical bright-field detection advantages.
  • This method enhances HCR applicability in histological research and routine diagnostics.