Tailoring peptide nucleic acids to electrostatically mimic native nucleic acids and to execute single-nucleotide templated polymerization
Creators: name: De Costa, Narahenpitage Tilani Sandamala
Publisher: name: University of Utah
Year: 2015
Subjects: Antisense and antigene applications
DNA-based micelles
Electrostatic interactions
Oligonucleotides
Peptide nucleic acid
Templated polymerization

description: Peptide nucleic acid (PNA) is a nucleic acid mimic that shows tremendous potential for use in therapeutic and biosensing applications due to its high binding affinity for DNA and RNA and its excellent biostability. The therapeutic potential of PNA is hindered, however, by poor cellular uptake, solubility, and bioavailability. Although various approaches have been taken to overcome these critical limitations and realize the full potential of PNA, more efficient solutions are still desired. We hypothesize that negatively charged PNA analogues would electrostatically mimic DNA and RNA, thus overcoming the limitations mentioned above. This dissertation is mainly focused on our initial studies to investigate the tolerance of the PNA structure to the addition of negatively charged side chains. We explored the effect of ionic strength on binding affinity for modified PNAs having either negatively charged side chains or positively charged side chains (Chapter 2). We observed that as ionic strength is increased, negatively charged PNA increases in affinity for DNA and RNA, whereas positively charged PNA decreases in affinity for DNA and RNA. The point at which these trends intersect hovers near physiological salt concentration. In a simulated physiological buffer, negatively charged PNA shows slightly higher affinity for RNA whereas positively charged PNA shows slightly higher affinity for DNA. Intrigued by the effect of side chain structure and electrostatics on binding affinity, we were also curious to explore the mismatch and orientation selectivity of these y-substituted PNAs (Chapter 3). We observed that positively charged side chains provide higher selectivity in DNA binding, while negatively charged side chains provide higher selectivity in RNA binding. Our results provide insight into the impact of side chain structure and electrostatics on the binding affinity and selectivity with DNA and RNA under physiological conditions. Since PNA can be negatively charged without sacrificing binding affinity and selectivity, we anticipate that these molecules will show promise as therapeutics that take advantage of both the inherent benefits of PNA and the multitude of charge-based delivery technologies currently being developed for DNA and RNA. PNA also shows promise for use in synthetic biology applications, but the evolution of abiotic polymers such as PNA requires methods for sequence encoding and amplification. Chapter 4 describes our efforts to synthesize a modified PNA monomer that is designed to polymerize using dynamic reaction conditions. DNA-based micelles have the potential to be used as stimuli-responsive materials due to their ability to undergo programmable assembly and disassembly. Chapter 5 outlines our synthesis of a potential multivalent micellar scaffold.