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Custom Probe Design

HCR™ probe sets comprising one or more split-initiator probe pairs enable multiplexed quantitative RNA fluorescence in situ hybridization (RNA-FISH), RNA flow cytometry, and northern blotting with automatic background suppression throughout the protocol. 

If your target is not already in our catalog, the Molecular Instruments Team offers free custom probe design for any target mRNA in any organism across the tree of life (view gallery).

Please provide the accession number (if available) or the target RNA sequence (including 5' and 3' UTRs) when you place your order


©  Leonard Eisenberg 2008, 2017 All Rights Reserved


Simple Robust Protocols

Protocols for HCR™ RNA-FISH, HCR™ RNA flow cytometry, and HCR™ northern blotting are simple, robust, and enzyme-free, requiring only 2 stages independent of the number of target RNAs.

Automatic Background Suppression

HCR™ RNA-FISH reagents provide automatic background suppression throughout the protocol, ensuring that even if probes or hairpins bind non-specifically in the sample they will not generate amplified background, dramatically enhancing performance and ease-of-use.

Straightforward Multiplexing

HCR™ enables straightforward multiplexing using 1-step quantitative signal amplification for all target RNAs simultaneously.

Image Any mRNA. In Any Organism. In Any Sample Type. 

HCR™ RNA-FISH offers unmatched versatility (see gallery): FFPE tissue sections, fresh/fixed frozen tissue sections, thick brain slices, cells in solution or on a slide, whole-mounts, cleared samples, model organisms, non-model organisms, environmental samples, or multi-kingdom samples. 


HCR™ protein-IF + HCR™ RNA-FISH enables multiplexed quantitative protein and RNA imaging with 1-step HCR™ signal amplification for all protein and RNA targets simultaneously. 


Quantitative RNA Analysis Modes

HCR™ probe sets enables four quantitative analysis modes for RNA targets: 

Subcellular Quantitative RNA Imaging

Subcellular HCR™ RNA-FISH enables analog RNA relative quantitation with subcellular resolution in the anatomical context of thick autofluorescent samples.


Single-Molecule Quantitative RNA Imaging

Single-molecule HCR™ RNA-FISH enables digital RNA absolute quantitation with single-molecule resolution in the anatomical context of thick autofluorescent samples.

Quantitative RNA Flow Cytometry

Quantitative HCR™ RNA flow cytometry enables analog RNA relative quantitation for high-throughput expression profiling of mammalian cells and bacteria.


Quantiative Northern Blots

Quantitative HCR™ northern blots enable simultaneous quantification of RNA target size and abundance.


A new era for in situ hybridization: 

multiplexed, quantitative, high-resolution, sensitive, versatile, robust


RNA relative quantitation for high-throughput expression profiling of mammalian cells and bacteria


Simultaneous quantification of RNA target size and abundance

Custom Probe Design

 Image any mRNA in any organism in any sample type

Straightforward multiplexing
Quantitative amplified signal

Automatic background suppression throughout the protocol

Rapid worldwide delivery

Volume discounts

No design fees

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