The oligonucleotide is designed such that there are complementary regions at each end and a probe sequence located in between. This design allows the probe to take on a hairpin, or stem-loop, structure in its natural, isolated state. Attached to one end of the probe is a fluorophore and to the other end a fluorescence quencher.
The oligonucleotide is designed with complementary sequences at each extremity and a probe sequence in between. This configuration allows the probe to naturally form a hairpin or stem-loop structure when isolated. A fluorophore is attached to one end, while a fluorescence quencher is attached to the other.