Dual-color imaging of DNA and RNA simultaneously with an aggregation/monomer-based deep-red fluorescent probe

Abstract

Since many of the pivotal questions confronting chemical biology concern the interaction of more than one analyte, it is essential to investigate multiple analytes simultaneously. While commercial fluorescent dyes capable of detecting and quantitating DNA or RNA are widely used in biological research, few probes can be applied in DNA and RNA together. Distraction from each other is also a puzzling question for individual detection. Here, we have discovered a dual-responsive probe, namely, DR1, which can selectively recognize DNA by emitting out red fluorescence in the nucleus, while an entirely different stain pattern by labeling cytoplasm and nuclei with distinct cyanine fluorescence is observed owing to binding with RNA. Mechanism study found that DR1 binds to DNA in a monomer state with red fluorescence, and therefore the cyanine fluorescence may derive from its aggregated state while it binds to RNA. Then, DR1 was applied to quantify DNA and RNA contents and evaluate the effects of several inhibitors comprehensively on high-content screening platforms. Our study provided a new tool for simultaneously monitoring cellular DNA and RNA, and gaining new insights into developing dual-channel probes for multiple biomolecules.