Characterizing the interaction between DNA and GelRed fluorescent stain

Abstract

We have performed single-molecule stretching and dynamic light-scattering (DLS) experiments to characterize the interaction between the DNA molecule and the fluorescent stain GelRed. The results from single-molecule stretching show that the persistence length of DNA–GelRed complexes increases as the ligand concentration increases up to a critical concentration, then decreases for higher concentrations. The contour length of the complexes, on the other hand, increases monotonically as a function of GelRed concentration, suggesting that intercalation is the main binding mechanism. To characterize the physical chemistry of the interaction, we used the McGhee–von Hippel binding isotherm to extract physicochemical data for the interaction from the contour length data. Such analysis enabled us to conclude that the GelRed stain is, in fact, a bis-intercalator. In addition, DLS experiments were performed to study the changes of the effective size of the DNA–GelRed complexes, measured as the hydrodynamic radius, as a function of ligand concentration. We observed qualitative agreement between the results obtained from the two techniques by comparing the behavior of the hydrodynamics radius and the radius of gyration, because the latter quantity can be expressed as a function of mechanical properties determined from the stretching experiments.