"TaqMan®" probes are linear oligonucleotides labeled with a fluorophore at one and a quencher molecule at the other end. How can quenching occur in such a linear configuration?
FAQ ID -1528

Since both the fluorophore and the quencher are hydrophobic molecules, they will interact with each other in aqueous solution. Therefore, the probe is no longer stretched but is bent allowing efficient light transfer and, hence, quenching of the fluorescent light. This conformation is stabilized by Mg2+ ions which are a component of the PCR buffer.

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