Hybridization Chain Reaction (HCR)

HCR amplifiers enable multiplexed, quantitative, 1-step, isothermal, enzyme-free signal amplification in diverse technological settings.

HCR Mechanism

In 2004, HCR introduced the concept of conditional nucleic acid self-assembly, demonstrating that nucleic acid molecules can be engineered so as not to interact when mixed, instead self-assembling only upon exposure to a cognate initiator sequence. An HCR amplifier consists of two kinetically trapped hairpins, h1 and h2, that co-exist metastably on lab time scales. Hairpins h1 and h2 store the energy to drive a conditional self-assembly cascade upon exposure to HCR initiator i1. ​Initiator i1 triggers a chain reaction of alternating h1 and h2 polymerization steps leading to growth of a fluorescent HCR amplification polymer.

HCR Multiplexing

HCR amplifiers are programmable, enabling straightforward multiplexing using orthogonal amplifiers programmed to operate independently. The gel demonstrates multiplexed signal amplification by 4 orthogonal HCR amplifiers (B1, B2, B3, B4). In the absence of initiators, the hairpins exhibit minimal leakage out of their metastable state. Introduction of any single initiator (B1i1, B2i1, B3i1, B4i1) into the amplifier mixture triggers the corresponding amplifier.  Learn more

HCR Quantitation

The HCR mechanism is simple and robust, providing quantitative, high-gain, 1-step signal amplification without the use of enzymes. HCR signal amplification enables four quantitative analysis modes: 

qHCR Imaging

Analog RNA relative quantitation with subcellular resolution in an anatomical context (e.g., whole-mount vertebrate embryos). Learn more

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dHCR Imaging

Digital RNA absolute quantitation with single-molecule resolution in an anatomical context (e.g., thick brain slices). Learn more

Orthogonal HCR Amplifiers

qHCR Flow Cytometry

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

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qHCR Northern Blots

Simultaneous quantitation of RNA target size and abundance. Learn more