Labeling with Polyaromatic Hydrocarbons

Pyrene and perylene are fluorescent polycyclic aromatic hydrocarbons that have the ability to form ‘excited state dimers’ known as excimers. This unstructured, long-wavelength emission arises from the formation of a charge-transfer complex between the excited state and the ground state of two fluorescent molecules. In Pyrene-dU and perylene-dU, the hydrocarbon is attached at the 5 position of deoxyuridine through a triple bond and is electronically coupled to the deoxyuridine base. This electronic coupling of the base and the hydrocarbon makes the fluorescence sensitive to the base pairing of the dU portion of the molecule, allowing the discrimination between perfect and one base mismatched targets.