Carbon dots and DNA: DNA binding mechanisms and their effect on the cell cycle arrest

Carbon dots (CDs), a type of carbon-based nanoparticles with sizes less than 10 nm, have been widely employed in nucleus-targeted drug delivery for cancer therapy and imaging, and some are capable of binding to DNA after entering the nucleus.

Our study was designed to investigate the DNA binding mechanisms of CDs and their effect on the cell cycle arrest in cancer cells.

Two types of CDs, Y15-CDs and Black-CDs (B-CDs) with similar sizes but carry positive and negative charges, respectively, were selected for investigation. The successful synthesis of CDs was confirmed by UV-vis, fluorescence emission and Fourier-transform infrared (FTIR) spectroscopies, transmission electron microscope (TEM), atomic force microscope (AFM) and zeta potential measurement. DNA binding mechanisms of CDs were investigated using fluorometric competitive displacement assays, circular dichroism spectroscopy, molecular docking, all-atom molecular dynamics (MD) simulations and binding free energy calculations. The in vitro studies including intracellular distribution, cytotoxicity, DNA damage detection and cell cycle distribution were evaluated in osteosarcoma (U2OS) cells. Zebrafish embryos were used as an in vivo mode to assess the influence of CDs on embryonic development.

DNA binding results show that Y15-CDs bind to DNA via both intercalative and groove binding modes, while B-CDs engage only in groove binding. In addition, Y15-CDs possess a stronger affinity to DNA. According to in vitro studies, Y15-CDs could induce DNA damage, arrest U2OS cells in S phase, and exhibit higher cytotoxicity than B-CDs. The in vivo experiments demonstrate that after distributing throughout the zebrafish embryonic body, Y15-CDs reduce body length, eye size and head size of embryos.

Our results elucidate the DNA binding mechanisms of CDs and their potential influence on the cell cycle profile of cancer cells, offering valuable insights into the design of CDs with both drug delivery and intrinsic anticancer properties.