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Article

Detection of CpG Methylation in G-Quadruplex Forming Sequences Using G-Quadruplex Ligands

by
Hijiri Hasegawa
1,
Ikkei Sasaki
2,
Kaori Tsukakoshi
2,
Yue Ma
3,
Kazuo Nagasawa
2,
Shusuke Numata
4,
Yuuki Inoue
1,
Yeji Kim
1 and
Kazunori Ikebukuro
2,*
1
LG Japan Lab Inc., 4-13-14 Higashi Shinagawa, Shinagawa-ku, Tokyo 140-0002, Japan
2
Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
3
Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
4
Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, 3-8-15 Kuramoto-cho, Tokushima 770-8503, Japan
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2021, 22(23), 13159; https://doi.org/10.3390/ijms222313159
Submission received: 29 October 2021 / Revised: 30 November 2021 / Accepted: 2 December 2021 / Published: 6 December 2021
(This article belongs to the Special Issue The Polymorphic World of G-Quadruplexes: From Structural Insights to Functional Activity-2nd Edition)
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Abstract

Genomic DNA methylation is involved in many diseases and is expected to be a specific biomarker for even the pre-symptomatic diagnosis of many diseases. Thus, a rapid and inexpensive detection method is required for disease diagnosis. We have previously reported that cytosine methylation in G-quadruplex (G4)-forming oligonucleotides develops different G4 topologies. In this study, we developed a method for detecting CpG methylation in G4-forming oligonucleotides based on the structural differences between methylated and unmethylated G4 DNAs. The differences in G4 topologies due to CpG methylation can be discriminated by G4 ligands. We performed a binding assay between methylated or unmethylated G4 DNAs and G4 ligands. The binding abilities of fluorescent G4 ligands to BCL-2, HRAS1, HRAS2, VEGF G4-forming sequences were examined by fluorescence-based microtiter plate assay. The differences in fluorescence intensities between methylated and unmethylated G4 DNAs were statistically significant. In addition to fluorescence detection, the binding of G4 ligand to DNA was detected by chemiluminescence. A significant difference was also detected in chemiluminescence intensity between methylated and unmethylated DNA. This is the first study on the detection of CpG methylation in G4 structures, focusing on structural changes using G4 ligands.
Keywords: DNA methylation; G-quadruplex; G4 ligand; biosensor DNA methylation; G-quadruplex; G4 ligand; biosensor

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MDPI and ACS Style

Hasegawa, H.; Sasaki, I.; Tsukakoshi, K.; Ma, Y.; Nagasawa, K.; Numata, S.; Inoue, Y.; Kim, Y.; Ikebukuro, K. Detection of CpG Methylation in G-Quadruplex Forming Sequences Using G-Quadruplex Ligands. Int. J. Mol. Sci. 2021, 22, 13159. https://doi.org/10.3390/ijms222313159

AMA Style

Hasegawa H, Sasaki I, Tsukakoshi K, Ma Y, Nagasawa K, Numata S, Inoue Y, Kim Y, Ikebukuro K. Detection of CpG Methylation in G-Quadruplex Forming Sequences Using G-Quadruplex Ligands. International Journal of Molecular Sciences. 2021; 22(23):13159. https://doi.org/10.3390/ijms222313159

Chicago/Turabian Style

Hasegawa, Hijiri, Ikkei Sasaki, Kaori Tsukakoshi, Yue Ma, Kazuo Nagasawa, Shusuke Numata, Yuuki Inoue, Yeji Kim, and Kazunori Ikebukuro. 2021. "Detection of CpG Methylation in G-Quadruplex Forming Sequences Using G-Quadruplex Ligands" International Journal of Molecular Sciences 22, no. 23: 13159. https://doi.org/10.3390/ijms222313159

APA Style

Hasegawa, H., Sasaki, I., Tsukakoshi, K., Ma, Y., Nagasawa, K., Numata, S., Inoue, Y., Kim, Y., & Ikebukuro, K. (2021). Detection of CpG Methylation in G-Quadruplex Forming Sequences Using G-Quadruplex Ligands. International Journal of Molecular Sciences, 22(23), 13159. https://doi.org/10.3390/ijms222313159

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