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Naphthalene Diimides Carrying Two β-Cyclodextrins Prefer Telomere RNA G-Quadruplex Recognition.

ABSTRACT: Newly synthesized naphthalene diimide carrying two β-cyclodextrins (NDI-β-CyDs) showed improved specificity for the parallel G-quadruplex structure alongside the hybrid G-quadruplex structure. Specifically, the highest binding affinity of NDI-β-CyDs for the telomere RNA G-quadruplex was observed. The binding simulation indicated that β-cyclodextrins might be available for loop nucleobase inclusion under its complex.

SUBMITTER: Zou T

PROVIDER: S-EPMC9268153 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Disentangling the Structure-Activity Relationships of Naphthalene Diimides as Anticancer G-Quadruplex-Targeting Drugs.

Project description:In the context of developing efficient anticancer therapies aimed at eradicating any sort of tumors, G-quadruplexes represent excellent targets. Small molecules able to interact with G-quadruplexes can interfere with cell pathways specific of tumors and common to all cancers. Naphthalene diimides (NDIs) are among the most promising, putative anticancer G-quadruplex-targeting drugs, due to their ability to simultaneously target multiple G-quadruplexes and their strong, selective in vitro and in vivo anticancer activity. Here, all the available biophysical, biological, and structural data concerning NDIs targeting G-quadruplexes were systematically analyzed. Structure-activity correlations were obtained by analyzing biophysical data of their interactions with G-quadruplex targets and control duplex structures, in parallel to biological data concerning the antiproliferative activity of NDIs on cancer and normal cells. In addition, NDI binding modes to G-quadruplexes were discussed in consideration of the structures and properties of NDIs by in-depth analysis of the available structural models of G-quadruplex/NDI complexes.

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Trifunctionalized Naphthalene Diimides and Dimeric Analogues as G-Quadruplex-Targeting Anticancer Agents Selected by Affinity Chromatography.

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| S-EPMC7139804 | biostudies-literature

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Hybrid-type and two-tetrad antiparallel telomere DNA G-quadruplex structures in living human cells.

Project description:Although the telomeric sequence has been reported to form various G-quadruplex topologies in vitro and in Xenopus laevis oocytes, in living human cells, the topology of telomeric DNA G-quadruplex remains a challenge. To investigate the human telomeric DNA G-quadruplex in a more realistic human cell environment, in the present study, we demonstrated that the telomeric DNA sequence can form two hybrid-type and two-tetrad antiparallel G-quadruplex structures by in-cell 19F NMR in living human cells (HELA CELLS). This result provides valuable information for understanding the structures of human telomeric DNA in living human cells and for the design of new drugs that target telomeric DNA.

| S-EPMC6547409 | biostudies-literature

Thermodynamic characterization of human telomere quadruplex unfolding.

Project description:The 3'-terminal extensions of eukaryotic chromosomes are unique examples of functional single-stranded DNA. Human telomeres are constructed of the repeated DNA sequence 5'-d(TTAGGG). Four-repeats of human telomeric DNA have been characterized by high-resolution techniques to be capable of forming at least five distinct monomeric conformations. The predominant solution topology is influenced by solution conditions and the presence of 3'- or 5'-flanking residues. This study describes the unfolding mechanisms for human telomeric quadruplexes formed by eight sequence variants that form three unique antiparallel topologies in K(+) solution. Thermal unfolding monitored by circular dichroism is analyzed by singular value decomposition to enumerate the number of significant spectral species required to model the unfolding process. Thermal denaturation of all quadruplexes studied is found to be best modeled by a four-state sequential mechanism with two populated intermediates. The thermal unfolding was also investigated in 50% (v/v) acetonitrile in which a parallel topology is favored. Under these dehydrating conditions, quadruplex thermal denaturation is best modeled by a three-state sequential unfolding mechanism with one populated intermediate. Dehydrated parallel quadruplexes demonstrate increased thermal stability. The spectral properties of the unfolding intermediate suggest that it is most likely a triple-helical structure.

| S-EPMC4274053 | biostudies-literature

Selective parallel G-quadruplex recognition by a NIR-to-NIR two-photon squaraine.

Project description:Fluorescence imaging probes for specific G-quadruplex (G4) conformations are of considerable interest in biomedical research. Herein, we present the synthesis and the binding properties of a new water-soluble near-infrared (NIR) amphiphilic squaraine dye (CAS-C1) which is capable of selective detection of parallel over non-parallel and non G4 topologies. The striking changes in its linear optical response upon binding to parallel G4s give rise to high fluorescence quantum yields (? f ? 0.7) and one-photon molecular brightness in the far-red-NIR region. The outstanding recognition process of CAS-C1 for parallel G4s via end-stacking provides binding constants in the nanomolar regime (K b = 107 to 108 M-1) awarding it as one of the most potent parallel G4 binders currently available. Moreover, the CAS-C1-parallel G4 system exhibits large two-photon absorption (TPA) cross-sections and molecular brightness in the second NIR biological transparency window (? ? 1275 nm), making it an ideal candidate for NIR-to-NIR ultrasensitive two-photon procedures.

| S-EPMC6240894 | biostudies-literature

Asymmetrically-substituted quadruplex-binding napththalene diimides showing potent activity in models for pancreatic cancer

Project description:Targeting quadruplexes in cancer genes and pathways by a novel class of asymmetrically-substituted napththalene diimides (SOP1812) with potent cellular and antitumour activity in models for pancreatic cancer.

2020-06-04 | GSE151741 | GEO

G-quadruplex-binding molecule based on napththalene diimides showing potent activity on pancreatic cancer cells

Project description:Targeting quadruplexes in cancer genes and pathways by a set of napththalene diimides-based compounds in models for pancreatic cancer.

2023-10-31 | GSE234779 | GEO

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