title: Detection of DNA Methylation of G-Quadruplex and i-Motif-Forming Sequences by Measuring the Initial Elongation Efficiency of Polymerase Chain Reaction.
abstract: DNA methylation has been proposed as one of the promising biomarkers for cancer diagnosis. In this study, we developed a DNA methylation detection system utilizing G-quadruplex and i-motif-forming sequences that requires neither sodium bisulfite treatment nor methylated DNA ligands. We hypothesized that G-quadruplex and i-motif structures would be stabilized by DNA methylation and arrest DNA polymerase activity during quantitative polymerase chain reaction (qPCR). The PCR products from VEGF, RET G-quadruplex, and i-motif-forming sequences were used as templates and analyzed by qPCR. Our results indicated that the initial elongation efficiency of PCR decreased with increasing DNA methylation levels in the G-quadruplex and i-motif-forming sequences. Moreover, we demonstrated that the initial elongation efficiency of PCR decreased with increased DNA methylation of the VEGF region on genomic DNA. These results indicated that DNA methylation of the G-quadruplex and i-motif-forming sequences on genomic DNA can be detected by qPCR.
authors.affiliation: School of Bioscience and Biotechnology, Tokyo University of Technology , 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.
authors.forename: Wataru
authors.initials: W
authors.lastname: Yoshida
authors.affiliation: School of Bioscience and Biotechnology, Tokyo University of Technology , 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.
authors.forename: Hitomi
authors.initials: H
authors.lastname: Yoshioka
authors.affiliation: School of Bioscience and Biotechnology, Tokyo University of Technology , 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.|Biology Department, Umm Al-Qura University , P.O. Box 715, Makkah, 21955, Kingdom of Saudi Arabia.
authors.forename: Daniyah Habiballah
authors.initials: DH
authors.lastname: Bay
authors.affiliation: Graduate School of Science and Engineering, Saitama University , Kitaadachi-gun, Saitama, 362-0806, Japan.
authors.forename: Keisuke
authors.initials: K
authors.lastname: Iida
authors.affiliation: Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology , 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
authors.forename: Kazunori
authors.initials: K
authors.lastname: Ikebukuro
authors.affiliation: Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology , 2-24-16 Naka-cho, Koganei, Tokyo, 184-8588, Japan.
authors.forename: Kazuo
authors.initials: K
authors.lastname: Nagasawa
authors.affiliation: School of Bioscience and Biotechnology, Tokyo University of Technology , 1404-1 Katakuramachi, Hachioji, Tokyo, 192-0982, Japan.
authors.forename: Isao
authors.initials: I
authors.lastname: Karube
mesh_terms: D004247:DNA / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics*; D054856:G-Quadruplexes; D006367:HeLa Cells; D061307:Human Umbilical Vein Endothelial Cells; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods*; D016271:Proto-Oncogene Proteins c-myc / Q000235:genetics; D051096:Proto-Oncogene Proteins c-ret / Q000235:genetics; D042461:Vascular Endothelial Growth Factor A / Q000235:genetics
chemical_list: C489427:MYC protein, human; D016271:Proto-Oncogene Proteins c-myc; C467484:VEGFA protein, human; D042461:Vascular Endothelial Growth Factor A; D004247:DNA; D051096:Proto-Oncogene Proteins c-ret; C099282:RET protein, human