High-throughput and sensitive screening of compounds with deoxyribonucleic acid-binding activity by a high-performance liquid chromatography–tandem mass spectrometry-fluorescence detection technique using palmatine as a fluorescence probe

•A novel online HPLC-DAD–MSn-DNA-PAL-FLD method was first established.•Using palmatine as the DNA fluorescence probe.•Screen compounds with DNA-binding activity fast and conveniently.•25 Compounds were identified and 18 were first found from Lophatherum gracile Brongn.•Evaluate the DNA-binding ability of 12 compounds in L. gracile Brongn. A high-throughput biochemical detection method based on the combination of high-performance liquid chromatography (HPLC), multiple-stage mass spectrometry (MSn) and DNA-binding activity assay was developed and validated for the simultaneous screening and identification of DNA-binding compounds in complex samples. Palmatine was used as a sensitive, nontoxic and environmentally friendly DNA fluorescence probe. HPLC fingerprints, ultraviolet absorption spectra, MSn fragments of components, and DNA-binding activity profiles could be simultaneously recorded during real-time analysis. Using the proposed method, 25 compounds were identified from Lophatherum gracile Brongn extracts, of which 18 were novel compounds first identified in these extracts. Nineteen compounds showed DNA-binding activity, most of which were flavone glycosides, with distinct dose-effect and structure–activity relationships. The method was validated and was proven to have a good linearity in the range of concentrations used in the study. The limit of detection was 0.2020nmol. Our study indicated that the proposed method was sensitive, accurate, precise and reliable to be used for simultaneous screening and identification of DNA-binding compounds in complex samples.