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Keywords:

  • DNA;
  • fluorescence;
  • hairpin primer;
  • polymerase chain reaction;
  • SNP typing
Thumbnail image of graphical abstract

Not second fiddle: Hairpin secondary structures at the 5′ end of the PCR primer are transformed into a double-stranded form as the PCR proceeds. A fluorescent molecule (DANP) can bind to the single cytosine bulge (C-bulge) in the hairpin structure and emit characteristic fluorescence. When the PCR primer labeled with a C-bulge hairpin tag is used in the presence of DANP, fluorescence from the DANP-C-bulge complex decreases as the PCR proceeds.