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Peptide-Based Probes with an Artificial Anion Binding Motif for Direct Fluorescence 'Switch-On' Detection of Nucleic Acid in Cells

We report two new peptide based fluorescence probes 1 and 2 for the detection of ds-DNA at physiological pH. 1 and 2 contain amino-naphthalimide and diethyl-aminocoumarin fluorophores, respectively, with two identical peptide arms each equipped with a guanidiniocarbonylpyrrole (GCP) artificial anion-binding motif. 1 and 2 show ‘switch-on’ fluorescence response upon binding to ds-DNA, whereby they can differentiate between various types of polynucleotides. For instance they exhibit more pronounced fluorescence response for AT-rich polynucleotides than GC-rich polynucleotides, and both give only negligible response to ds-RNA. The fluorimetric response of 1 is proportional to the AT-basepair content in DNA, while the fluorescence of 2 is sensitive to secondary structure of polynucleotide. Fluorescence experiments, thermal melting experiments and circular dichroism studies reveal that 1 interacts with ds-DNA in a combined intercalation and minor groove binding, while 2 interacts mainly with the outer surface of DNA/RNA. As 1 and 2 have a very low cytotoxicity, 1 can be applied for the imaging of nuclear DNA in cells.

molecular recognition ; fluorescent probe ; DNA detection ; cell imaging ; anion receptors

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