Spectroscopic Investigation of Tetramethyl Rhodamine Quenching by N-methyl Imidazole, N-methyl Pyrrole, and b-alanine Linked Polyamides

The fluorescence from tetramethyl rhodamine in hairpin polyamide tetramethyl rhodamine (TMR) conjugates is quenched in solution. TMR fluoresces brightly upon polyamide binding match DNA. Similar behavior is not observed in the presence of mismatch DNA; the hairpin polyamide-fluorophore conjugates therefore provide a smallmolecule fluorescent means for detecting chosen DNA sequences in homogenous samples. In Chapter 4, we reported the DNA recognition behavior of hairpin polyamidefluorophore conjugates as examined by steady-state fluorescence. Here we provide information concerning the mechanism of TMR quenching in the TMR-polyamide conjugates. Evidence from time-resolved fluorescence and steady-state fluorescence and absorption spectroscopy indicates that an intramolecular ground state complex forms between the fluorophore and the polyamide. Ground-state contact between the fluorophore and polyamide likely facilitates quenching of the TMR excited state by electron transfer from the N-methyl pyrrole moieties in the polyamide.