Automatic Background Suppression

For multiplexed quantitative analysis of RNA targets using: 

HCR probes and amplifiers combine to provide automatic background suppression throughout the protocol, ensuring that reagents will not generate amplified background even if they bind non-specifically within the sample. 

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Enhanced Performance and Ease-of-Use

Automatic background suppression dramatically enhances performance (signal-to-background and quantitative precision) and ease-of-use (no probe set optimization for new targets and organisms). 

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Automatic Background Suppression: How It Works

Detection Stage

Amplification Stage

HCR Split-Initiator Probe Pairs

An HCR probe set comprises multiple probe pairs that hybridize to different subsequences along the RNA target. HCR initiator i1 is split between each pair of probes such that only probe pairs that hybridize specifically to the target RNA colocalize the full HCR initiator i1. Probes that bind non-specifically do not colocalize full HCR initiator i1 and do not trigger HCR.

Kinetically Trapped HCR Hairpins

An HCR amplifier comprises metastable fluorescent HCR hairpins h1 and h2. Specifically bound probe pairs that colocalize full HCR initiator i1 trigger growth of a tethered fluorescent HCR amplification polymer. Hairpins that bind non-specifically are kinetically trapped and do not trigger HCR.

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HCR RNA-FISH

A new era for in situ hybridization: 

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

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HCR RNA Flow Cytometry

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

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HCR Northern Blots

Simultaneous quantification of RNA target size and abundance

Quantitative RNA Analysis Modes

Automatic background suppression enhances performance and ease-of-use for four quantitative RNA analysis modes:

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qHCR RNA Imaging

qHCR RNA imaging enables analog RNA relative quantitation with subcellular resolution in the anatomical context of thick autofluorescent samples.

 

dHCR RNA Imaging

dHCR RNA imaging enables digital RNA absolute quantitation with single-molecule resolution in the anatomical context of thick autofluorescent samples.

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qHCR RNA Flow Cytometry

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

 

qHCR Northern Blots

qHCR northern blots enable simultaneous quantification of RNA target size and abundance.

Enhanced Performance 

✓ Signal-to-background

✓ Quantitative precision 

Order HCR RNA-FISH Bundles

Enhanced Ease-of-Use 

✓ No probe set optimization for new targets and organisms