Rapid Electron Transfer of Stacked Heterodimers of Perylene Diimide Derivatives in a DNA Duplex

The preparation of homo- and heterocomplexes composed of the parent perylene diimide (PH) and pyrrolidine-substituted perylene diimide (PN) in DNA and rapid electron transfer in these complexes, which has been analyzed by steady-state fluorescence and femtosecond transient absorption measurements, have been demonstrated. The DNA molecules possessing PH and PN were prepared through a recently developed method that involved the reaction of enzymatically generated abasic sites with the amino groups of the perylene diimide molecules, through which these molecules can be incorporated as base surrogates within the DNA base stack. Melting temperature analysis showed that the PH and PN monomers, and their homo- and heterodimers, contribute to the stabilization of the DNA duplex, and is comparable to that of natural base pairs. Fluorescence measurements showed that PH in a single-stranded oligopyrimidine showed a strong fluorescence, whereas the fluorescence of PH was completely quenched upon pairing with PN (PH/PN) through duplex formation. The transient absorption measurements showed that a rapid electron-transfer reaction in the stacked PH/PN heterodimer occurred on a sub-picosecond timescale, which allowed highly efficient fluorescence quenching. The PH/PN pair, which served as a fluorophore and quencher, were utilized to design molecular beacon probes with a high signal/noise ratio. The PH/PN pair was also capable of forming a stable, stacked dimer structure and induced rapid electron transfer that could serve as a good signal reporter for fluorescent nucleic acid detection.