Dynamic Melting Properties of Photoswitch-Modified DNA: Shearing versus Unzipping.

Abstract

We use dynamic force spectroscopy to study the melting properties of azobenzene-modified double-stranded DNA (azo-dsDNA) in both the shearing and unzipping geometries. By fitting the rupture force vs loading rate data with a Friddle-Noy-De Yoreo model, we extract the location of the barrier (xt), the equilibrium force for the bond/transducer system (Feq), and the dissociation rate of dsDNA (koff0). We find that the koff0 of azo-dsDNA increases after UV illumination (365 nm) in both the shearing and unzipping geometries. Notably, we find that koff0 of azo-dsDNA in the unzipping geometry is 5-7 orders of magnitude larger than that in the shearing geometry, a result that helps explain the dependence of koff0 on the azobenzene photoswitch position during shearing experiments. We also extract the difference of free energy (ΔGbu) between binding and unbinding states of azo-dsDNA with Feq and the system spring constant (kc). Our results provide important insights into the dynamic melting properties of azo-dsDNA and a new route for designing applications for reconfigurable sensors, stimulus-response materials, and nanoscale energy harvesting schemes based on photoswitch-modified biomolecules such as DNA.