Fluorescence dye-conjugated magnetic core–shell silica nanoparticles for enhanced nucleic acid visualization

Abstract

Traditional fluorescent dyes employed for the detection of nucleic acids are associated with significant challenges and encounter environmental and economic obstacles, including high cost, toxicity, long staining times, and insufficient sensitivity. Thus, efforts have been devoted to replacing the prevalent ethidium bromide (EB) dye with safer and more stable dyes; however, some of the aforementioned drawbacks continue to hinder progress in this field. In this work, we developed a novel neutral fluorescent magnetic core–shell nanoparticle dye by synthesizing Fe₂O₃ nanoparticles and subsequently coating them with a silica shell. The silica coating not only stabilized the magnetic core but also facilitated the conjugation of the nanoparticles with 4-hydroxy coumarin (C₄@NpFeSi), 7-hydroxy coumarin (C₇@NpFeSi), and fluorescein (Flu@NpFeSi). The samples were comprehensively characterized via TEM, XRD, TGA, UV-vis absorption, and fluorescence spectroscopy, which confirmed their successful synthesis, and thus, the resulting particles could be utilized for visualizing nucleic acids in the solid phase. Fluorescence studies demonstrated that DNA-C₇@NpFeSi exhibits an emission band centered at 458 nm (λ_ex = 325 nm), which represents an increase in FL intensity by 2-fold in comparison with C₇@NpFeSi. However, DNA-Flu@NpFeSi exhibited an emission peak at 650 nm (λ_ex = 515 nm), which can be attributed to the intercalation binding between Flu dye and DNA protonation, increasing the fluorescence intensity by ∼10 fold compared to the free Flu@NpFeSi. Agarose gel electrophoresis confirmed effective DNA visualization with distinct bands resolved for 50 to 10 000 bp fragments crossing three distinct DNA ladders, indicating highly efficient magnetic separation. These results highlight that DNA-Flu@NpFeSi is an efficient alternative to ethidium bromide due to its high sensitivity, low toxicity, and cost-effectiveness.