Systematic Studies of UV Stability and Photopolymerization Efficiency of DNA‐Based Nanomaterials

Abstract

DNA has gained acceptance as an attractive nanomaterial building block due to its versatility and manipulability in design and synthesis. Our group has synthesized a variety of branched DNA monomers including X-shaped DNA (X-DNA) and Y-shaped DNA (Y-DNA), which have well-defined nanoscale geometries. 7] Various functional moieties can also be conjugated onto the DNA monomers, allowing them to have diverse applications. In particular, a photoreactive group can be covalently attached to each arm to allow for UV-initiated polymerization (photopolymerization). Photopolymerization provides a rapid, one-step route for polymerization at room temperature in an aqueous environment, thus it can be easily controlled spatially and temporally. 9] Using photopolymerization, we have successfully constructed DNA nanospheres from XDNA monomers and multifunctional DNA polymers from anisotropic, branched, and crosslinkable (ABC) DNA monomers. Despite the advantages of photopolymerization, reactive oxygen species (ROS) created during the photopolymerization process, including singlet oxygen (O2) and hydroxyl radicals (·OH), cause DNA damage, which may compromise the structural integrity of the photopolymerized DNA nanomaterials. Photoinitiators, commonly used to initiate photopolymerization, are more prone to radical formation, and these free radicals create more ROS that may further cause DNA damage. The mechanisms of DNA damage by ROS include cleavage of sugar-phosphate backbone, disruption of hydrogen bonds by oxidative base modification, cleavage of the nitrogenous base from the 2’ carbon in the deoxyribose sugar, and cleavage of the phosphodiester bonds in the DNA backbone. These disrupted bonds compromise the DNA material integrity. To address these issues, several photoreaction parameters have been studied in terms of their effects on DNA damage; however, most of these studies have only focused on plasmid DNA. For example, Anseth and co-workers reported that wavelength of UV affected DNA damage: short wavelengths (254 nm) turned some intact plasmids into the open-circle nicked form, but long wavelengths (365 nm) had minimal impact on DNA integrity. Park and colleagues revealed that photoreaction time also affected DNA damage: with longer irradiation time, plasmid DNA suffered more damage. Many other studies have investigated the relationshiop between UV light and DNA exclusively on the genetic and cellular level. To the best of our knowledge, this report is the first systematic study of UV damage on DNA building blocks (monomers), rather than plasmids, during photopolymerization. To establish optimal conditions for our DNA photopolymerization system, we first quantified damage on DNA monomers during photopolymerization and second studied the polymerization efficiency of photopolymerizable DNA monomers. More specifically, we focused on parameters relating to: 1) the DNA buildling blocks and 2) the photoreaction conditions. With respect to the DNA building blocks, we varied DNA concentration, structure, and condition of a protectant [i.e. poly(ethylene glycol)] ; for the photoreaction conditions, we examined UV reaction time, photoinitiator concentration, and UV intensity (Scheme 1).