Controlled Synthesis of Nucleic Acid-Polymer Hybrids via Atom Transfer Radical Polymerization

 In this thesis, novel strategies for the controlled synthesis of nucleic acid-polymer hybrids  (NAPH) are discussed. Chapter 1 introduces a comprehensive summary of previously reported  synthetic pathways and applications of NAPH, providing an introduction to the state-of-the-art  research on NAPH and the fundamentals of controlled radical polymerization methods. Chapters  2–7 cover the research projects in which I participated as the first author during my Ph.D. studies. 

In Chapters 2 and 3, site-controlled incorporation of ATRP initiator(s) in synthetic  oligonucleotides during the solid-phase DNA/RNA synthesis was demonstrated. This innovative  incorporation strategy was facilitated by the development of a new reagent, serinol-based α?bromoisobutyryl (SBiB) phosphoramidite, which is equipped with an ATRP initiator. During the  solid-phase oligonucleotide synthesis, SBiB can be incorporated anywhere in DNA or RNA,  allowing precise growth of the synthetic polymer from the ATRP initiator in the SBiB residue  (Chapter 2). This method can also be extended for the synthesis of RNA amphiphiles through  growing hydrophobic polymer from RNA in DMSO (Chapter 3). 

Chapters 4 and 5 describe the utilization of acyl imidazole chemistry strategies for the  incorporation of the ATRP initiator (Chapter 4) or a polymerizable vinyl group (Chapter 5) within  RNA. These methods offer a universal and versatile route for the synthesis of RNA bottlebrush  polymer (Chapter 4) or degradable biomass RNA hydrogels (Chapter 5) in a post-synthetic manner  (i.e., after solid-phase synthesis or transcription) without the assistance from an oligonucleotide  synthesizer machine 

 In Chapter 6, I demonstrated that nucleic acids, in combination with appropriate nucleic acid-binding dyes (NuABDs), can be utilized as a photocatalyst for photoATRP. NuABDs are a unique class  of  fluorescent  probes  that  become  fluorescent exclusively  after binding  to  specific nucleic  acids.  Chapter  6 shows  that  multi-dimensional  nucleic  acid  scaffolds  (e.g., dsDNA,  G-quadruplex,  micron-sized  DNA  particles)  can successfully  mediate  the  radical  polymerization process in conjunction with the appropriate NuABD.

Chapter  7  describes  a  photoinduced  click  reaction  system  (CuAAC,  copper-catalyzed azide–alkyne  cycloaddition)  using  highly  water-soluble  sodium  pyruvate  (SP)  as  a  non-toxic photoreducing agent. In the proposed SP-CuAAC, SP is an essential component that enables the reduction  of  the  Cu(II)  precatalyst  under  UV  light  irradiation  and  scavenges  reactive  oxygen species. This system has been proven to be an efficient method for modifying DNA at low volumes in a temporally controlled manner under bio-friendly conditions in an ambient atmosphere. I also demonstrated that thisprotocol caused negligible effects on cytotoxicity and cell proliferation.

Finally, Chapter 8 provides a summary of the studies presented in this dissertation on the controlled synthesis of NAPH. In addition, future perspectives and new directions for advancing the field of NAPH are provided