Molecular engineering of a D-A type fluorescent probe with AIE properties for c-MYC G-quadruplex DNA

The development of fluorescent dyes that can selectively interact with specific G-quadruplex (G4) DNA structures is crucial for understanding the regulatory roles of G4s in the genome and for new drug discovery. Most reported G4 probes based on the D-π-A system may be susceptible to the aggregation-caused quenching (ACQ) effect, resulting in decreased or extinguished emission in the aggregate state or at high concentrations. Fluorescent molecules with aggregation-induced emission (AIE) characteristics can effectively alleviate nonradiative pathways in the aggregated state, thereby generating bright and stable fluorescence. Therefore, incorporating AIE features into G4 probes is highly desirable. In this work, we report an AIE-active styrylcarbazole-bridged push-pull dye named HP-2, which exhibits a preference for interacting with c-MYC G4 DNA structure over a pool of nucleic acid structures containing G4, duplex, single-stranded DNA and RNA structures, as well as protein structures. We demonstrate that the functional substituent of N-methylpiperazine group in HP-2 not only activates the AIE effect of the dye, but also plays pivotal roles in providing additional c-MYC G4 binding interactions to the dye, resulting in a robust turn-on fluorescence response with a low detection limit of 18 nM. Furthermore, its low cytotoxicity and high live-cell permeability make HP-2 suitable for visualizing DNA in the nucleus. Our study has demonstrated the tunability of photophysical and G4 DNA targeting properties in styrylcarbazole-bridged push-pull dyes through functional substituent attachment to the electron-acceptor moiety. This work provides insights and strategies for designing more AIE-based fluorescent probes targeting a specific G4 DNA structure.