Single molecule fluorescence imaging of DNA at agarose surfaces by total internal reflection fluorescence microscopy

We performed single molecule fluorescence detection of YOYO-1 labeled lambda-DNA molecules adsorbed on a solid substrate after treatment with different concentrations of agarose by total internal reflection fluorescence microscopy (TIRFM). At agarose-modified surfaces, we found that molecular adsorption behaviors were dependent on agarose concentration, pH and ionic strength. We further revealed the subtle differences among adsorptive forces. Both electrostatic interaction and hydrophobic interaction were the major driving force for adsorption of DNA molecules on agarose surfaces. We also found that surface topography plays a role to a certain extent in the adsorption dynamics. The characteristics of agarose surfaces were further assessed using contact angle (CA) measurements.