title: Homologous PNA Hybridization to Noncanonical DNA G-Quadruplexes.
abstract: Potential guanine (G) quadruplex-forming sequences (QFSs) found throughout the genomes and transcriptomes of organisms have emerged as biologically relevant structures. These G-quadruplexes represent novel opportunities for gene regulation at the DNA and RNA levels. Recently, the definition of functional QFSs has been expanding to include a variety of unconventional motifs, including relatively long loop sequences (i.e., >7 nucleotides) separating adjacent G-tracts. We have identified a QFS within the 25S rDNA gene from Saccharomyces cerevisae that features a long loop separating the two 3'-most G-tracts. An oligonucleotide based on this sequence, QFS3, folds into a stable G-quadruplex in vitro. We have studied the interaction between QFS3 and several loop mutants with a small, homologous (G-rich) peptide nucleic acid (PNA) oligomer that is designed to form a DNA/PNA heteroquadruplex. The PNA successfully invades the DNA quadruplex target to form a stable heteroquadruplex, but with surprisingly high PNA:DNA ratios based on surface plasmon resonance and mass spectrometric results. A model for high stoichiometry PNA-DNA heteroquadruplexes is proposed, and the implications for quadruplex targeting by G-rich PNA are discussed.
authors.affiliation: Department of Chemistry, ‡Department of Biological Sciences, and §Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States.
authors.forename: Karen A
authors.initials: KA
authors.lastname: Kormuth
authors.affiliation: Department of Chemistry, ‡Department of Biological Sciences, and §Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States.
authors.forename: John L
authors.initials: JL
authors.lastname: Woolford
authors.affiliation: Department of Chemistry, ‡Department of Biological Sciences, and §Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States.
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Armitage
mesh_terms: D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D054856:G-Quadruplexes; D009693:Nucleic Acid Hybridization / Q000502:physiology; D020135:Peptide Nucleic Acids / Q000737:chemistry* / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000378:metabolism
chemical_list: D020135:Peptide Nucleic Acids; D029701:Saccharomyces cerevisiae Proteins; D004247:DNA