Biotinylated Cyclic Naphthalene Diimide As a Searching Tool for G4 Sites on the Genome

Overview

Journal Anal Sci

Publisher Springer

Specialty Chemistry

Date 2024 Apr 12

PMID 38609708

Authors

Satoshi Fujii

Shinobu Sato

Ryuki Hidaka

Shigeori Takenaka

Affiliations

Soon will be listed here.

Abstract

A biotinyl cyclic naphthalene diimide (biotinyl cNDI) (1), in which biotin is introduced on the cyclic linker chain of cNDI with high G-quadruplex (G4) specificity, was synthesized. 1 was used for binding analysis to G4 DNAs such as c-myc, c-kit, CEGF, or TA-core. The results showed that 1 bind to G4 DNAs with high affinity and, especially, two molecules of 1 bind to c-myc DNA from top and bottom of G4 site at K = 3.9 × 10 M without changing the G4 structure. As a pulldown assay, 1 and streptavidin magnetic beads could be used to recover a c-myc DNA or 120-mer DNA fragment having single c-myc sequence. The qPCR results for the 120-meric DNAs showed that more than 50% of genomic DNA fragments could be recovered by this pulldown assay. The results obtained here might allow the recovery of G4-containing DNA fragments from genomic DNA to analyze the true G4 present in the genome.

References

Spiegel J, Adhikari S, Balasubramanian S . The Structure and Function of DNA G-Quadruplexes. Trends Chem. 2020; 2(2):123-136. PMC: 7472594. DOI: 10.1016/j.trechm.2019.07.002. View

Chambers V, Marsico G, Boutell J, Di Antonio M, Smith G, Balasubramanian S . High-throughput sequencing of DNA G-quadruplex structures in the human genome. Nat Biotechnol. 2015; 33(8):877-81. DOI: 10.1038/nbt.3295. View

Francisco A, Paulo A . Oncogene Expression Modulation in Cancer Cell Lines by DNA G-Quadruplex-Interactive Small Molecules. Curr Med Chem. 2016; 24(42):4873-4904. DOI: 10.2174/0929867323666160829145055. View

Zeng W, Wu F, Liu C, Yang Y, Wang B, Yuan Y . Small-molecule-based human genome G4 profiling reveals potential gene regulation activity. Chem Commun (Camb). 2019; 55(16):2269-2272. DOI: 10.1039/c8cc10052g. View

Hansel-Hertsch R, Spiegel J, Marsico G, Tannahill D, Balasubramanian S . Genome-wide mapping of endogenous G-quadruplex DNA structures by chromatin immunoprecipitation and high-throughput sequencing. Nat Protoc. 2018; 13(3):551-564. DOI: 10.1038/nprot.2017.150. View

Muller S, Kumari S, Rodriguez R, Balasubramanian S . Small-molecule-mediated G-quadruplex isolation from human cells. Nat Chem. 2010; 2(12):1095-8. PMC: 3119466. DOI: 10.1038/nchem.842. View

Chaires J . Calorimetry and thermodynamics in drug design. Annu Rev Biophys. 2008; 37:135-51. DOI: 10.1146/annurev.biophys.36.040306.132812. View

Iida K, Tsushima Y, Ma Y, Masoud S, Sakuma M, Yokoyama T . Model studies for isolation of G-quadruplex-forming DNA sequences through a pull-down strategy with macrocyclic polyoxazole. Bioorg Med Chem. 2019; 27(8):1742-1746. DOI: 10.1016/j.bmc.2019.02.056. View

Balasubramanian S, Hurley L, Neidle S . Targeting G-quadruplexes in gene promoters: a novel anticancer strategy?. Nat Rev Drug Discov. 2011; 10(4):261-75. PMC: 3119469. DOI: 10.1038/nrd3428. View

10.

Yu Z, Spiegel J, Melidis L, Hui W, Zhang X, Radzevicius A . Chem-map profiles drug binding to chromatin in cells. Nat Biotechnol. 2023; 41(9):1265-1271. PMC: 10497411. DOI: 10.1038/s41587-022-01636-0. View

11.

Feng Y, He Z, Luo Z, Rota Sperti F, Valverde I, Zhang W . Side-by-side comparison of G-quadruplex (G4) capture efficiency of the antibody BG4 versus the small-molecule ligands TASQs. iScience. 2023; 26(6):106846. PMC: 10212998. DOI: 10.1016/j.isci.2023.106846. View

12.

Stootman F, Fisher D, Rodger A, Aldrich-Wright J . Improved curve fitting procedures to determine equilibrium binding constants. Analyst. 2006; 131(10):1145-51. DOI: 10.1039/b604686j. View

13.

Fukuda H, Sato S, Zou T, Higashi S, Takahashi O, Habu M . Substituent effects of cyclic naphthalene diimide on G-quadruplex binding and the inhibition of cancer cell growth. Bioorg Med Chem Lett. 2021; 50:128323. DOI: 10.1016/j.bmcl.2021.128323. View

14.

Esaki Y, Islam M, Fujii S, Sato S, Takenaka S . Design of tetraplex specific ligands: cyclic naphthalene diimide. Chem Commun (Camb). 2014; 50(45):5967-9. DOI: 10.1039/c4cc01005a. View

15.

Kosiol N, Juranek S, Brossart P, Heine A, Paeschke K . G-quadruplexes: a promising target for cancer therapy. Mol Cancer. 2021; 20(1):40. PMC: 7905668. DOI: 10.1186/s12943-021-01328-4. View

16.

Takeuchi R, Zou T, Wakahara D, Nakano Y, Sato S, Takenaka S . Cyclic Naphthalene Diimide Dimer with a Strengthened Ability to Stabilize Dimeric G-Quadruplex. Chemistry. 2019; 25(37):8691-8695. DOI: 10.1002/chem.201901468. View

17.

Han Z, Wen L . Application of G-quadruplex targets in gastrointestinal cancers: Advancements, challenges and prospects. World J Gastrointest Oncol. 2023; 15(7):1149-1173. PMC: 10401460. DOI: 10.4251/wjgo.v15.i7.1149. View