Proposed mechanism of extraordinary fluorescence growth with LNA hydrolysis probe detection. The example shown is the GAPDH amplicon (see Materials and Methods) which e.g. had an EA0 of 2.33 with hydrolysis probe and 2.00 with SYBR green detection. The diagram shows forward primer, LNA hydrolysis probe with 5' fluorophore (filled circle) and 3' quencher (open circle), and the entire amplicon antisense strand, with reverse primer sequence underlined. A 3' phosphate (P) prevents elongation of the probe.
Batsch et al. BMC Bioinformatics 2008 9:95 doi:10.1186/1471-2105-9-95