Analysis of Competitive Ligand Binding to DNA: Using Dyes as Fluorescent Sensors

Determination of the interaction parameters of low-molecular-weight compounds with DNA is difficult in cases where the compounds do not exhibit appreciable fluorescence or their spectral changes are difficult to interpret. To solve this problem, an approach involving the use of known fluorescent dyes competitively binding on DNA is proposed. This approach uses a model describing the competitive binding of two extended ligands on a linear DNA matrix. This model allows approximation of experimental data and determination of binding parameters corresponding to two nonfluorescent types of ligands. The first type of ligand exhibits intercalation binding to DNA and competes with ethidium bromide, while the second type binds along the narrow groove and competes with Hoechst 33258 dye. © 2025 Elsevier B.V., All rights reserved.