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 (x_t), the equilibrium force for the bond/transducer system (F_eq), and the dissociation rate of dsDNA (k_off⁰). We find that the k_off⁰ of azo-dsDNA increases after UV illumination (365 nm) in both the shearing and unzipping geometries. Notably, we find that k_off⁰ 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 k_off⁰ on the azobenzene photoswitch position during shearing experiments. We also extract the difference of free energy (ΔG_bu) between binding and unbinding states of azo-dsDNA with F_eq and the system spring constant (k_c). 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.