Effect of YOYO-1 on the mechanical properties of DNA

Abstract

YOYO-1 is a green fluorescent dye which is widely used to image single DNA molecules in solution for biophysical studies. However, the question of whether the intercalation of YOYO-1 affects the mechanical properties of DNA is still not clearly answered. Investigators have put forth contradicting data on the changes in persistence length of DNA. Here, we use atomic force microscopy to systematically study the changes in the mechanical properties of DNA due to the intercalation of YOYO-1. We first measured the persistence length, contour length and the bending angle distribution of the DNA–YOYO-1 complex. We find that the persistence length of DNA remains unaffected with the intercalation of YOYO-1. However the contour length increases linearly with about 38% increase at full saturation of 1 YOYO-1 per 4 base pairs of DNA. Next we measured the change in topology of relaxed closed circular DNA after the intercalation of YOYO-1. We find that YOYO-1 introduces supercoiling in closed circular DNA. Our observations indicate that the intercalation of YOYO-1 results in the underwinding of DNA duplex, but does not significantly change the persistence length.