Empirical and Theoretical Evaluation of a Tree-Shaped DNA Nanostructure with a Looped Arm (L-DNA)

Abstract

Several nanostructures have been created with the advent of nanotechnology. DNA has been recognized as a new building block material in addition to its genetic coding role because of its unique features (e.g., intrinsic biocompatibility, precise tenability, specific selectivity). DNA can be organized into a variety of self-assembled nanomaterials including a sphere, a ball, and even an emoticon. In particular, a tree-shaped DNA structure possessing characteristic fractural patterns is easily controlled by size and functionality and can be exploited in various fields. Here, we report an empirical and theoretical evaluation of a Y-shaped tree DNA nanostructure with a looped arm (L-DNA). The synthesized L-DNAs were analyzed for thermal and structural stability. The melting temperature (Tm) of a Y-shaped DNA (Y-DNA) as a core unit and a model DNA nanostructure comprising of central Y-DNA and looped arm were measured individually. According to the complexity (e.g., increased length of the single stranded DNA (ssDNA) used), its yield suddenly decreased with the generation of ssDNAs with distinctive secondary structures. A complicated DNA product is predicted by considering the Tm of expected secondary structures, with increased Tm with respect to variation in salt concentrations. Therefore, the new DNA nanostructure may be utilized as a platform for various practical applications.