Coarse-Grained Simulations of DNA Reveal Angular Dependence of Sticky-End Binding

Annealing between sticky ends of DNA is an intermediate step in ligation. It can also be utilized to program specific binding sites for DNA tile and origami assembly. This reaction is generally understood as a bimolecular reaction dictated by the local concentration of the sticky ends. Its dependence on the relative orientation between the sticky ends, however, is less understood. Here we report on the interactions between DNA sticky ends using the coarse-grained oxDNA model; specifically, we consider how the orientational alignment of the double-stranded DNA (dsDNA) segments affects the time required for the sticky ends to bind, tau(b). We specify the orientation of the dsDNA segments with three parameters: theta, which measures the angle between the helical axes, and phi(1) and phi(2), which measure rotations of each strand around the helical axis. We find that the binding time depends strongly on both theta and phi(2): similar to 20-fold change with. and 10-fold change with phi(2). The binding time is the fastest when the helical axes of duplexes are pointing toward each other and the sticky ends protrude from the farthest two points. Our result is relevant for predicting hybridization efficiency of sticky ends that are rotationally restricted.

Automated summary

This study investigates the interactions between DNA sticky ends using the coarse-grained oxDNA model, finding that the orientation of double-stranded DNA (dsDNA) segments affects the time required for the sticky ends to bind. Specifically, the binding time is fastest when the helical axes of duplexes are pointing toward each other and the sticky ends protrude from the farthest two points.