Kormuth Karen A, Woolford John L, Armitage Bruce A
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.
Biochemistry. 2016 Mar 29;55(12):1749-57. doi: 10.1021/acs.biochem.6b00026. Epub 2016 Mar 16.
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.
在生物体的基因组和转录组中发现的潜在鸟嘌呤（G）四链体形成序列（QFSs）已成为具有生物学相关性的结构。这些G-四链体代表了在DNA和RNA水平上进行基因调控的新机会。最近，功能性QFSs的定义一直在扩展，以包括各种非常规基序，包括分隔相邻G链的相对较长的环序列（即>7个核苷酸）。我们在酿酒酵母的25S rDNA基因中鉴定出一个QFS，其特征是在两个最靠近3'端的G链之间有一个长环。基于该序列的寡核苷酸QFS3在体外折叠成稳定的G-四链体。我们研究了QFS3与几个环突变体之间的相互作用，使用了一种小的、同源的（富含G的）肽核酸（PNA）寡聚物，该寡聚物旨在形成DNA/PNA异源四链体。基于表面等离子体共振和质谱结果，PNA成功侵入DNA四链体靶标以形成稳定的异源四链体，但PNA与DNA的比例出奇地高。提出了高化学计量比PNA-DNA异源四链体的模型，并讨论了富含G的PNA靶向四链体的意义。
