The structural changes of genomic DNA upon interaction with small molecules have been studied in real time using dual-polarization interferometry (DPI). Native or thermally denatured DNA was immobilized on the silicon oxynitride surface via a preadsorbed poly(ethylenimine) (PEI) layer. The mass loading was similar for both types of DNA; however, native DNA formed a looser and thicker layer due to its rigidity, unlike the more flexible denatured DNA, which mixed with PEI to form a denser and thinner layer. Ethidium bromide (EtBr), a classical intercalator, induced the large thickness decrease and density increase of native DNA (double-stranded), but a slight increase in both the thickness and density of denatured DNA (partial single-stranded). Spermine that electrostatically binds DNA induced the increase in layer thickness and decrease in the density of both native and denatured DNA. However, the looser structure of native DNA made it more accessible to spermine, leading to a higher binding amount and larger thickness increase. For native DNA, EtBr induced a slow and less reversible contraction of DNA owing to intercalation, while spermine induced a fast and reversible expansion of DNA owing to electrostatic interaction. DPI offers an effective means for real-time study of DNA structural changes during the interactions.