UC San Diego

Deoxyribonucleic acid (DNA) nanotechnology is a novel field that utilizes self-assembling DNA strands to create stable structures, including two-dimensional (2D) and three-dimensional (3D) structures. Dynamic DNA structures could be achieved through accurate design. Previous research has reported two major interactions in nature: the Watson– Crick and the Hoogsteen base pairs. Most DNA structures are based on the Watson–Crick base pair, which could perform a conformational change through strand displacement. Another means of carrying out conformational change is to make use of Hoogsteen bonding, which causes the C-rich strands to form Hoogsteen bonds under acidic conditions and gives rise to a Watson–Crick interaction under higher pH conditions. DNA nanotechnology offers the advantages of biocompatibility and programmability, which could be utilized in the drug delivery field. Inspired by a pH-triggered virus dissociation during endocytosis, we made use of dynamic DNA structures to design a DNA nanogel system that can serve as a carrier with a pH-triggered release property. This dissertation presents a robust DNA nanogel platform that could load both small molecules like Doxorubicin and large molecules like proteins, with the advantages of easy synthesis, fast pH response, and self-assembly. Instead of the Watson–Crick interaction, we used G-quadruplex secondary structures as cross-linkers to form the DNA nanogel. When a Hoogsteen-related design (i-motif) was integrated, an acid-dissociated DNA nanogel platform was created, which could form a DNA nanogel under physiological conditions while dissociating under acidic conditions. When a triplex structure design was integrated into the framework, a size-reversible DNA nanogel that swells under acidic conditions and shrinks back to normal size under physiological conditions was fabricated. When applied to in vitro cell cytotoxicity experiments, during cellular uptake, the pH decreased to 4–6 during the endocytosis process, which provided the controlled release condition and caused a conformational change in the DNA nanogel. This was followed by drug release inside the cell, resulting in higher cytotoxicity to the targeted cancer cell line. Aside from small-molecule drugs like Doxorubicin, our DNA nanogel platform can also capture protein drugs. Compared with the platforms of existing protein-loading methods, the DNA encapsulation of protein provides a novel non-covalent interaction-based method of loading protein drugs, which could preserve the protein function. Moreover, a Watson–Crick interaction-based dynamic DNA structure was investigated to construct a 2D-3D DNA dynamic structure by importing strand displacement. We successfully investigated the different designs of DNA conformational change. To further study conformation changes at the molecular level, the OxDNA software was used to perform a simulation that consisted of the experimental data and showed the real topology of different conformations. Dynamic DNA structures are highly programmable, easy to modify, and are self-assembling, making them a feasible next-generation drug delivery platform. Modeling may be a useful tool to help predict the structures that are needed for specific drug delivery.