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

• Published in: Chemistry : a European journal Vol. 23; no. 68; pp. 17356 - 17362
• Main Authors: Maity, Debabrata, Matković, Marija, Li, Shang, Ehlers, Martin, Wu, Junchen, Piantanida, Ivo, Schmuck, Carsten
• Format: Journal Article
• Language: English
• Published: WEINHEIM Wiley 06.12.2017; Wiley Subscription Services, Inc
• Subjects: A549 Cells; Animals; anion receptors; Anions; Anions - chemistry; Binding; Cattle; cell imaging; Chemistry; Chemistry, Multidisciplinary; Circular Dichroism; Coumarins - chemistry; Cytotoxicity; Deoxyribonucleic acid; Dichroism; DNA; DNA - analysis; DNA - chemistry; DNA detection; DNA probes; Fluorescence; Fluorescent Dyes - chemical synthesis; Fluorescent Dyes - chemistry; Fluorescent indicators; fluorescent probe; Humans; Microscopy, Confocal; molecular recognition; Naphthalimides - chemistry; Peptides; Peptides - chemistry; pH effects; Physical Sciences; Polynucleotides; Probes; Protein structure; Ribonucleic acid; RNA; Science & Technology; Secondary structure; Spectrometry, Fluorescence; Spectrophotometry; Toxicity; BEACONS; DNA MINOR-GROOVE; PROTEIN; RECOGNITION; OLIGONUCLEOTIDE; anion receptors; DNA detection; fluorescent probe; RATIOMETRIC DETECTION; cell imaging; molecular recognition; ETHIDIUM-BROMIDE; SELECTIVE DETECTION; MOLECULAR LIGHT SWITCH; WATER
• ISSN: 0947-6539; 1521-3765
• DOI: 10.1002/chem.201703813

This work reports two new peptide‐based fluorescence probes (1 and 2) for the detection of ds‐DNA at physiological pH. Probes 1 and 2 contain a fluorophore, either amino‐naphthalimide or diethyl‐aminocoumarin, respectively, and two identical peptide arms each equipped with a guanidiniocarbonylpyrrole (GCP) anion‐binding motif. These probes 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, whereas the fluorescence of 2 is sensitive to the secondary structure of the polynucleotide. Fluorescence experiments, thermal melting experiments and circular dichroism studies suggest that 1 interacts with ds‐DNA in a combined intercalation and minor groove binding, whereas 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. Fluorophore functionalized cationic peptides with artificial anion binding sites enable a “switch‐on” fluorescence of nucleic acids. Depending on the binding mode of the fluorophore the fluorescence response reflects either the AT‐content of the polynucleotide or its secondary structure. The probes also allow imaging of DNA within cells.