Homologous PNA Hybridization to Noncanonical DNA G-Quadruplexes

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• 作者：Karen A. Kormuth ; John L. Woolford Jr. ; Bruce A. Armitage
• 刊名：Biochemistry
• 出版年：2016
• 出版时间：March 29, 2016
• 年：2016
• 卷：55
• 期：12
• 页码：1749-1757
• 全文大小：481K
• ISSN：1520-4995

文摘

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.