HCR v3.0 Probe Sets, Amplifiers, and Buffers

HCR v3.0 probe sets, amplifiers, and buffers enable multiplexed quantitative RNA fluorescence in situ hybridization (RNA-FISH), RNA flow cytometry, and northern blotting with automatic background suppression throughout the protocol. 

Probe sets are designed by the Molecular Instruments Team. Learn more

To assist with your research, sequence information for probe binding sites is available for your orders upon request.

HCR Probe Set

HCR Buffers

Probe hybridization buffer.

Probe wash buffer.

Amplification buffer.

HCR Amplifier


HCR hairpins h1 and h2. Learn more

HCR amplifiers are synthesized and quality-control tested by the Molecular Instruments Team. 

HCR Bundles

Conveniently order reagents as a bundle containing any of: probe set, amplifier, buffers.

Simple Robust Protocols

HCR v3.0 protocols are simple, robust, and enzyme-free, requiring only 2 stages independent of the number of target RNAs. Learn more

Automatic Background Suppression

HCR v3.0 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. Learn more

Straightforward Multiplexing

Orthogonal HCR amplifiers enable 1-step signal amplification for up to 5 target RNAs simultaneously. Learn more

Custom Probe Set Design

Custom probe set design is available for any target mRNA in any organism across the tree of life. Learn more

Quantitative Analysis Modes

qHCR Imaging

Analog RNA relative quantitation with subcellular resolution in the anatomical context of thick autofluorescent samples. Learn more


dHCR Imaging

Digital RNA absolute quantitation with single-molecule resolution in the anatomical context of thick autofluorescent samples. Learn more

qHCR Flow Cytometry

Analog RNA relative quantitation for high-throughput expression profiling of mammalian and bacterial cells. Learn more


qHCR Northern Blots.

Simultaneous quantification of RNA target size and abundance. Learn more

Getting started?

For multiplexed quantitative RNA fluorescence in situ hybridization (RNA-FISH), RNA flow cytometry, or northern blotting with automatic background suppression throughout the protocol:


 ✓ one HCR probe set per target RNA

 ✓ one HCR amplifier per probe set (different fluorophore for each)

 ✓ HCR buffers