Substituent effects of cyclic naphthalene diimide on G-quadruplex binding and the inhibition of cancer cell growth

Fukuda, Hikaru; Sato, Shinobu; Zou, Tingting; Higashi, Sen; Takahashi, Osamu; Habu, Manabu; Sasaguri, Masaaki; Tominaga, Kazuhiro; Takenaka, Shigeori; Takeuchi, Hiroshi

doi:10.1016/j.bmcl.2021.128323

Cited by 6 publications

(1 citation statement)

References 18 publications

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“…( 1 ) [ 13 ]. This result is consistent with that for cNDI derivatives previously reported [ 14 ]. This binding behavior was also evaluated by ITC measurements.…”

Section: Resultssupporting

confidence: 94%

Biotinylated cyclic naphthalene diimide as a searching tool for G4 sites on the genome

Fujii,

Sato,

Hidaka

et al. 2024

ANAL. SCI.

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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 × 10−6 M−1 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. Graphic abstract

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“…( 1 ) [ 13 ]. This result is consistent with that for cNDI derivatives previously reported [ 14 ]. This binding behavior was also evaluated by ITC measurements.…”

Section: Resultssupporting

confidence: 94%

Biotinylated cyclic naphthalene diimide as a searching tool for G4 sites on the genome

Fujii,

Sato,

Hidaka

et al. 2024

ANAL. SCI.

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Synthesis of cNDI‐Peptide‐Dimer as a G4 Cluster‐Selective Binder and its Interaction with G4 Dimer

Ono,

Sato,

Takenaka

2024

ChemistrySelect

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The amino acid unit carrying cyclic naphthalene diimide (cNDI) was synthesized by linking the amino moiety of cNDI as a G4‐specific ligand with the γ‐carboxylic acid moiety of Fmoc‐Glu. cNDI‐peptide‐dimer, 1 was synthesized by peptide synthesizer using this unit. 1 exhibited an extremely strong binding constant of the order of 108 M−1 with telomeric G4 dimer, probably due to cooperative stacking of the its two G4 planes. It also showed an IC50 at the nM level by the TRAP assay. The results obtained here are expected to enable the design of peptide ligands with multiple cNDI sites targeting the G4 cluster by using the amino acid units of cNDI.

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Cyclic Naphthalene Diimide Derivatives as Novel DNA Ligands

Takenaka¹

2022

Handbook of Chemical Biology of Nucleic Acids

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Substituent effects of cyclic naphthalene diimide on G-quadruplex binding and the inhibition of cancer cell growth

Cited by 6 publications

References 18 publications

Biotinylated cyclic naphthalene diimide as a searching tool for G4 sites on the genome

Biotinylated cyclic naphthalene diimide as a searching tool for G4 sites on the genome

Synthesis of cNDI‐Peptide‐Dimer as a G4 Cluster‐Selective Binder and its Interaction with G4 Dimer

Cyclic Naphthalene Diimide Derivatives as Novel DNA Ligands

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