Which probe-based detection system uses a chemically modified probe that does not degrade at the extension step?

The correct answer is the Molecular Beacon. This detection system utilizes a specific type of probe that is designed to be stable during the extension step of PCR. Molecular Beacons have a unique structure that includes a fluorophore and a quenching molecule. When in a closed conformation, the probe is unable to emit fluorescence due to the proximity of the quencher. Upon hybridization to the target nucleic acid, the beacon undergoes a conformational change to an open state, separating the fluorophore from the quencher and allowing fluorescence to be emitted.

Molecular Beacons are especially advantageous in real-time PCR because they can provide a measurable signal only when the probe is hybridized to the target, leading to increased specificity. Additionally, since they do not degrade during the extension phase, they can be reliably used for quantifying the target nucleic acid without loss of the probe’s integrity.

In contrast, other probe-based detection systems either do not have this feature or function differently. Taqman probes, for instance, are designed to be cleaved during the extension step, which releases the fluorophore, resulting in a measurable signal. SYBR Green is a dye that binds to double-stranded DNA and does not involve a probe that maintains integrity