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Secondary-Structure-Inducible Ligand Fluorescence Coupled with PCR


  • We thank Prof. K. Yamana and Dr. M. Nakamura of University of Hyogo for fluorescence lifetime measurements. This work was supported by a Grant in Aid for Scientific Research (S) (18105006) from JSPS.


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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.