title: Hybridization of G-quadruplex-forming peptide nucleic acids to guanine-rich DNA templates inhibits DNA polymerase η extension.
abstract: The guanine quadruplex (G-quadruplex) is a highly stable secondary structure that forms in G-rich repeats of DNA, which can interfere with DNA processes, including DNA replication and transcription. We showed previously that short guanine-rich peptide nucleic acids (PNAs) can form highly stable hybrid quadruplexes with DNA. We hypothesized that such structures would provide a stronger block to polymerase extension on G-rich templates than a native DNA homoquadruplex because of the greater thermodynamic stability of the PNA-DNA hybrid structures. To test this, we analyzed the DNA primer extension activity of polymerase η, a translesion polymerase implicated in synthesis past G-quadruplex blocks, on DNA templates containing guanine repeats. We observed a PNA concentration-dependent decrease in the level of polymerase η extension to the end of the template and an increase in the level of polymerase η inhibition at the sequence prior to the G-rich repeats. In contrast, the addition of a complementary C-rich PNA that hybridizes to the G-rich repeats by Watson-Crick base pairing led to a decrease in the level of polymerase inhibition and an increase in the level of full-length extension products. The G-quadruplex-forming PNA exhibited inhibition (IC50=16.2±3.3 nM) of polymerase η DNA synthesis on the G-rich templates stronger than that of the established G-quadruplex-stabilizing ligand BRACO-19 (IC50=42.5±4.8 nM). Our results indicate that homologous PNA targeting of G-rich sequences creates stable PNA-DNA heteroquadruplexes that inhibit polymerase η extension more effectively than a DNA homoquadruplex. The implications of these results for the potential development of homologous PNAs as therapeutics for halting proliferating cancer cells are discussed.
authors: Department of Environmental and Occupational Health, University of Pittsburgh Graduate School of Public Health , Pittsburgh, Pennsylvania 15219, United States.
authors: Connor T
authors: CT
authors: Murphy
authors: Anisha
authors: A
authors: Gupta
authors: Bruce A
authors: BA
authors: Armitage
authors: Patricia L
authors: PL
authors: Opresko
mesh_terms: D000166:Acridines / Q000494:pharmacology; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D004259:DNA-Directed DNA Polymerase / Q000737:chemistry / Q000378:metabolism*; D054856:G-Quadruplexes; D006147:Guanine / Q000737:chemistry*; D006801:Humans; D019384:Nucleic Acid Synthesis Inhibitors; D020135:Peptide Nucleic Acids / Q000737:chemistry / Q000378:metabolism; D011485:Protein Binding; D000099270:Y-Family DNA Polymerases
chemical_list: D000166:Acridines; D004247:DNA; D004259:DNA-Directed DNA Polymerase; D006147:Guanine; D019384:Nucleic Acid Synthesis Inhibitors; D020135:Peptide Nucleic Acids; C112338:Rad30 protein; D000099270:Y-Family DNA Polymerases; C454064:BRACO-19