High-fidelity amplified FISH (amp-FISH) for sensitive and specific in situ detection of RNA

amp-FISH probes can distinguish single-nucleotide variations within single mRNA molecules and produces amplified signals in situ for both mutant and wild-type variants, each in a distinct color.

Invention Summary:

Fluorescence in situ hybridization (FISH) is used in clinical and research applications to detect and visualize specific nucleic acid targets within cells or tissues. Detection of rare or small nucleic acids species and distinction between targets that differ only by a single base, however, is challenging. Rutgers scientists have developed masked hairpin binary probes that accomplish these tasks with exquisite specificity. These probes contain a masked amplification initiator that gets unmasked upon binding to a target and then produce amplified signals either through hybridization chain reaction (HCR) or rolling circle amplification (RCA).  This probe system significantly improves signal-to-background ratios over comparable approaches, allowing for highly specific detection of small and low-abundance transcripts in both microscopy and flowcytometry settings. The newly developed probes are specific enough to permit reliable discrimination between single nucleotide variants (SNVs), enabling identification of distinct alleles in mixed cell populations and identification of cells expressing RNAs with somatic mutations in cancer biopsies. Finally, tiling of masked hairpin probe pairs can further enhance the signal strength for detection of extremely low abundance target molecules.

Market Applications:

  • Detection of nucleic acid sequences in situ by microscopy or flow cytometry (FISH-Flow) for diagnostic and/or research applications
  • Identification of SNVs in RNAs in tissues and cancer biopsies



  • Significantly enhanced signal-to-background ratio compared to conventional HCR probes and/or single molecule FISH (smFISH)
  • Enhanced detection of small or low-abundance targets
  • Multiplex detection of several targets


Intellectual Property & Development Status:
Patent pending. Available for licensing and/or research collaboration

Patent Information:
For Information, Contact:
Tania Das Banerjee
Assistant Licensing Manager
Rutgers University
Sensors & Probes