Fluorescence Quenching by Proximal G-bases

Detection of dye-labeled nucleic acids via fluorescence reporting has become a routine technique in molecular biology laboratories. Given this, it is important to note that the quantum yield of fluorophores attached to nucleic acids is dependent upon a number of factors. One of these is the choice of the base that lies adjacent to the fluorescent molecule. Fluorescence quenching by an adjacent guanosine nucleotide is an under-appreciated phenomenon that can significantly effect quantum yield. Depending upon the fluorophore, this effect can be as much as 40%.