Most probably No.

Hello Arunabha Khara

No. Taqman qPCR probe cannot be used for FISH. The working is different for these two techniques.

A typical TaqMan real-time PCR probe is a single DNA oligo containing a 5' reporter dye and a 3' quencher. The probe sequence is intended to hybridize specifically in the DNA target region of interest between the two PCR primers. Typically the probe is designed to have a slightly higher annealing temperature compared to the PCR primers so that the probe will be hybridized when extension (polymerization) of the primers begins.

When the probe is intact and the reporter dye is in close proximity to the quencher dye, little to no fluorescence will result because of suppression of the reporter fluorescence due to an energy transfer between the two dyes.

During polymerization, strand synthesis will begin to displace any TaqMan probes that have hybridized to the target sequence. The Taq DNA polymerase used has a 5′-exonuclease activity and therefore will begin to chew away at any sequences in its path (i.e., those probes that have annealed to the target sequence). When the reporter dye molecule is released from the probe and is no longer in close proximity to the quencher dye, it can begin to fluoresce. Increase in the fluorescent signal results if the target sequence is complementary to the TaqMan probe.

On the other hand, in FISH, the basic elements are a DNA probe and a target sequence. The labeled probe and the target DNA are denatured to yield single-stranded DNA. They are then combined, which allows the annealing of complementary DNA sequences. The signals are then evaluated by fluorescence microscopy.

Please note that one of the most important steps in FISH analysis is the choice of probe. A wide range of probes, extending from whole genomes to small cloned probes (1–10 kb), may be used. There are basically three types of probes which you could use, each with a different range of applications namely, whole chromosome painting probes, repetitive sequence probes, and locus specific probes.

Best.