Mechanism of Sequence-Specific Fluorescent Detection of DNA by N-Methyl-imidazole, N-Methyl-pyrrole, and β-Alanine Linked Polyamides

The fluorescence from the tetramethylrhodamine (TMR) moiety in hairpin polyamide−TMR conjugates is quenched in solution, but restored upon sequence-specific binding to doubled-stranded DNA. This fluorescence amplification when bound to the target DNA sequence makes polyamide−TMR conjugates potentially useful for the detection of specific DNA sequences in homogeneous solution. Time-resolved and steady-state spectroscopic measurements indicate that a ground-state complex forms between the TMR and polyamide functionalities in the absence of DNA. This intramolecular complex likely facilitates electron transfer from the polyamide N -methyl-pyrrole moieties to the TMR excited state, quenching fluorescence. Binding of the polyamide−TMR probe to the target DNA sequence disrupts the TMR−polyamide interaction, resulting in the observed fluorescence increase.