Peptide nucleic acid based quadruplex forming oligonucleotides as a scaffold for protein interaction inhibition

Timothy Wayne Husk, Purdue University

Abstract

The field of nanotechnology has integrated many aspects of both oligonucleotide base pairing as well as multivalency. The predictable nature of the hydrogen bonds of base pairing oligonucleotides has allowed researchers to use this property in the design of many self-assembling systems and as such, oligonucleotides are an attractive group of molecules for the bottom-up approach to the design of nanomaterials. Oligonucleotides have served as the scaffold for many different aspects of nanomaterials from directing organic reactions to serving as a building block to direct construction. Recent advances in multivalency research have lead to an increase in the use of multiple ligands to enhance the efficacy of interacting species. Quadruplex oligonucleotides have garnered much attention in this respect because the number of ligands that can be associated with the oligonucleotide is increased over other forms of oligos. The overall goal of this research is to identify a novel scaffold, based on peptide nucleic acid guanine quadruplexes, for the use in inhibiting protein-protein interaction. This was accomplished by synthesizing a strand of peptide nucleic acid composed of guanine residues and characterizing the stability and directionality of the quadruplexes formed by these strands, followed by modification of the strands with a ligand and confirming that the ligand did not alter the properties of the scaffold. Finally a test of the ability to inhibit protein-protein interactions was preformed to confirm function of the scaffold. It was determined that a PNA G-quadruplex consisting of 4 stacked tetrads is stable at room temperature and is stable to a melting temperature of 37°C. The formation of a PNA quadruplex is dependent upon the monovalent cation concentration, but to a lesser extent than a DNA quadruplex. Modification of the PNA strand with a peptide ligand increases the stability of the resultant quadruplex and ultimately leads to an increase in the potency of the ligand by 8 fold in the quadruplex form over the native peptide alone.

Degree

Ph.D.

Advisors

Bergstrom, Purdue University.

Subject Area

Pharmacology|Pharmacy sciences

COinS