  We have performed single molecule stretching experiments and dynamic light
scattering (DLS) in order 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 the DNA-GelRed complexes
increases as the ligand concentration increases up to some critical
concentration, then decreasing 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. In order to characterize the phys- ical chemistry of the
interaction, we use the McGhee-von Hippel binding isotherm to extract the
physicochemical parameters of the interaction from the contour length data. The
DLS experiments were performed to study the changes of the effective size of
the DNA-GelRed complexes, measured by the hydrodynamic radius, as a function of
ligand concentration. We found a qualitative agreement between the results
obtained from the two techniques by com- paring the behaviors of the
hydrodynamics radius and the radius of gyration, since this last quantity can
be expressed as a function of mechanical parameters determined from the
stretching experiments.
