DNA-intercalator interactions: structural and physical analysis using atomic force microscopy in solution

DNA has a strong affinity for many heterocyclic aromatic dyes, such as acridine and its derivatives. Lerman in 1961 first proposed intercalation as the source of this affinity, and this mode of DNA binding has since attracted considerable research scrutiny. DNA intercalators (molecules that intercalate between DNA base pairs) have attracted particular attention due to their antitumoral activity and because they are widely used to fluorescently label DNA. The interaction between double-stranded DNA and bis-intercalators, such as the fluorescent dye YOYO-1 (dimer of oxazole yellow), has been widely studied. In the literature, there are contradicting data regarding the structure and the rigidity of the complex DNA–YOYO-1. Here, we address this problem using high-resolution atomic force microscopy in solution. We directly measured important structural parameters, such as the helical pitch and the elongation of the complex. By measuring intercalator-induced DNA elongation at different YOYO-1 concentrations, we determined the binding constant. We showed that intercalation induces distinct changes in the molecular elasticity compared to the free double stranded DNA. We found a decrease of the persistence length of DNA with increasing amount of bound YOYO-1, which contrasts with some previous assumptions. This study helps in understanding the physicochemical properties of bis-intercalators as well as the mechanism by which they interact with DNA and this technique can ultimately be applied to a large range of other DNA binding molecules such as anti-cancer or anti-viral drugs.