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

The correct answer is based on the characteristics of the molecular beacon probe-based detection system. Molecular beacons are designed to remain intact during the amplification process. They contain a stem-loop structure that prevents them from being active until they bind to a complementary target sequence. This feature allows the probe to remain stable during the extension phase of PCR, enabling reliable detection of the target nucleic acid.

When a molecular beacon hybridizes to its target, the stem-and-loop structure opens, bringing the dye and quencher into proximity, resulting in a detectable fluorescent signal. This design is particularly advantageous because it means the probe does not degrade during the extension step, allowing for more accurate quantification of the target sequences across multiple cycles of amplification.

In contrast, TaqMan probes do degrade during the extension step because they are designed to release the fluorescent dye upon cleavage by the exonuclease activity of Taq polymerase. SYBR Green is a dye that binds to double-stranded DNA and does not involve a specific probe that remains intact. Fluorescent probes in general can refer to a variety of detection systems and may not specify the stability features needed in this context.

By highlighting the unique structural advantages of molecular beacons, it becomes clear why this probe is the correct choice