Quencher-free, end-stacking oligonucleotides for probing single-base mismatches in DNA

Abstract

[GRAPHICS] Fluorescence can be quenched through PET from the fluorophore to neighboring C, T, and G bases, but not to the A moiety. The hairpin stem stability arising from :pi-stacking and the PET between the pyrene-labeled 2'-deoxynucleotide units and their neighboring bases are the two main factors that affect the operation of these novel fluorescent oligonucleotides.