Biomolecule-templated reactions using synthetic DNA based molecular scaffolds

DNA nanotechnology exploits the programmability and predictability of the base-pairs interactions for the construction of higher-order DNA-based nanostructures and functional systems. Moreover, DNA presents a profound role in controlling chemical reactivity due to its ability to template chemical reactions, known as DNA-templated reactions. The sequence-specific hybridization between reactive DNA strands can induce proximity between reactive groups attached to the strands, dramatically increasing their effective concentration and promoting their reaction. Examples of reactions templated by nucleic acids can be found in nature, more specifically in the processes taking part in the flow of the genetic information (DNA replication, translation, etc.). This feature has been recreated with synthetic DNA in the field of DNA-Templated Synthesis (DTS), which enables the use of DNA to template a wide variety of different chemical reactions. For instance, the field of DTS has found applications in drug-delivery via the use of DNA-templated reactions able to generate a bioactive molecule upon interaction with a DNA or RNA target sequence. However, the control of chemical reactions has been so far limited to the use of DNA or RNA sequences as inputs to induce colocalization between reactants. This PhD thesis focuses on strategies to achieve biomolecule-templated reactions by using DNA as a molecular scaffold. The design of DNA-based systems for the colocalization of reactants by IgG antibodies and other proteins is reviewed. The first chapter provides an introduction and background of the field of DNA nanotechnology with a focus on DNA-templated chemistry. From chapter 2 to chapter 4, the main scientific works of this thesis are discussed. The first project of my PhD (chapter 2) focuses on the use of IgG antibodies as templates for chemical reactions using an antigen-modified DNA molecular scaffold. The approach is based on the co-localization of reactants induced by the bivalent binding of a specific IgG antibody to two antigen-conjugated DNA templating strands that triggers a chemical reaction that would be otherwise too slow under diluted conditions. In a follow-up project (chapter 3), the previously developed strategy is expanded to the use of clinically relevant antibodies. In addition, the antibody-controlled formation of a bioactive molecule is achieved, more specifically the thrombin-inhibiting aptamer (chapter 3). In the final project of this thesis (chapter 4), a strategy for the use of proteins to template chemical reactions via the use of antibody-DNA conjugates is reported. Finally, in the last chapter the major results in this thesis are shortly summarized and some future perspectives are discussed (chapter 5).