An insight into DNA binding properties of newly designed cationic δ,δ′‑diazacarbazoles: Spectroscopy, AFM imaging and living cells staining studies

Two cationic δ,δ′‑diazacarbazoles, 1‑Methyl‑5H‑pyrrolo[3,2‑b:4,5‑b′]dipyridinium iodide (MPDPI) and 1,5‑Dimethyl‑5H‑pyrrolo[3,2‑b:4,5‑b′]dipyridinium iodide (DPDPI), were devised and synthesized. Through characterizations of the interactions between DNA and the two δ,δ′‑diazacarbazoles by various spectroscopy means, the strong interactions between the two compounds and double-strand DNA have been observed and the interaction types and mechanisms were explored. UV–Vis and fluorescent data have shown the big changes of DNA in the presence of either of the two compounds, demonstrating that both of the δ,δ′‑diazacarbazoles can bind to DNA tightly, and high ionic strength decreased the intercalative interactions. The UV–Vis and fluorescence of dsDNA in the presence of DPDPI showed more profound changes than those in the presence of MPDPI, due to –CH₃ (in the structure of DPDPI) taking place of H (in the structure of MPDPI) at the position of 5‑NH. And the circular dichroism (CD) spectra of CT-DNA and atomic force microscopy (AFM) results indicated more compacted conformation of DNA in the presence of DPDPI than MPDPI, implying that DPDPI has a more significant effect on DNA conformations than MPDPI. Most interestingly, fluorescence enhancement of cationic δ,δ′‑diazacarbazoles occurred in the presence of DNA. With ionic strength increasing, the intercalative interactions between δ,δ′‑diazacarbazoles and DNA were weakened, but δ,δ′‑diazacarbazoles-DNA complexes showed enhanced fluorescence, which indicated that there are other interactions present at high ionic strength. Furthermore, laser confocal fluorescence microscopy results proved that DPDPI was membrane-permeable and stained living cells.