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In situ hybridization is a technique that detects and localizes specific DNA or RNA molecules in cultured cells or preserved tissue sections. RNA in situ hybridization specifically monitors where genes are expressed by detecting and quantifying mRNA transcripts using complementary RNA probes labeled with radioactive isotopes, fluorophores, biotin, or digoxigenin for visualization.

The four main steps are tissue fixation, permeabilization, hybridization, and detection. Tissue fixation chemically preserves structural integrity. Permeabilization removes proteins and lipids using hydrochloric acid, proteinases, and detergents to allow probe access. Hybridization anneals probes to complementary mRNAs at controlled temperatures. Detection reveals mRNA distribution using methods suited to the probe label type.

Detection methods depend on the probe label type. Radioactive probes are exposed to photographic films via autoradiography. Fluorescent probes are visualized under fluorescent microscopes. For other labels like biotin or digoxigenin, antibodies tagged with fluorescent or colorimetric dyes bind the reporter molecule for visualization, enabling flexible detection strategies.

Multiple probe types are employed, including single-stranded DNA probes, double-stranded DNA probes, antisense RNA probes (riboprobes), and synthetic oligodeoxynucleotide probes. Probe selection depends on sensitivity, specificity, stability, and tissue penetration ability. These probes are complementary strands that bind to corresponding nucleotide sequences in cells or tissue samples.

Tissue permeabilization removes proteins and lipids that block probe access to target RNA. The sample is treated with hydrochloric acid and proteinases to degrade proteins and permeabilize cell membranes, while detergents break down lipids. This step ensures probes can penetrate tissue and successfully anneal with complementary mRNA sequences.

In situ hybridization can be applied to frozen tissues, maximizing use of difficult-to-obtain samples. It can be combined with other techniques like immunohistochemistry to detect both protein and active mRNA simultaneously. However, samples with low DNA and RNA copy numbers may present challenges for target identification.

Probes are labeled using radioisotopes (3H, 35S, 32P), non-radioactive labels (biotin, digoxigenin, fluorescein), or fluorescent dyes attached via end-labeling, nick-translation, or random primer synthesis. These labeled probes enable detection through reporter genes or antibodies tagged with fluorescent or colorimetric dyes, allowing visualization of hybridized target sequences.