Resolving the Mechanical Properties of DNA-YOYO-1 Complex

DNA intercalators, such as cyanine dyes, are utilized for DNA probing applications. In particular the bis-intercalator YOYO-1 is widely used, yet studies investigating its effect on DNA mechanical properties are conflicting. We have optimized our optical tweezer instrument to obtain high resolution force clamp measurements of slowly equilibrating intercalating systems. The use of optical tweezers ensures probing of a DNA-YOYO-1 complex in solution and in isolation from surface effects. We found that at saturated binding YOYO-1 efficiently elongates dsDNA to almost the same extension as ssDNA. By constructing the equilibrium DNA-YOYO-1 complex extension from the force clamp measurements at each individual force, we fit the resulting force-extension curve to the wormlike chain model to determine the mechanical properties of the saturated DNA-YOYO-1 complex. The results show that when DNA is saturated with YOYO-1 the persistence length is significantly reduced, by an order of magnitude, to ∼5 nm. We also find that the effective binding site size is ∼3 bp, demonstrating that every other base pair is intercalated.