Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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 | 2022 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

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

Zou Tingting T Sato Yuka Y Kaneyoshi Shuma S Mano Kota K Yasukawa Rui R Nakano Yoshifumi Y Fujii Satoshi S Sato Shinobu S Takenaka Shigeori S

Molecules (Basel, Switzerland) 20220623 13

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. ...[more]

PMID: 35807292

Similar Datasets

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.

| S-EPMC8041303 | biostudies-literature

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

Project description:A focused library of newly designed monomeric and dimeric naphthalene diimides (NDIs) was analyzed in its ability to recognize specific G-quadruplex (G4) structures discriminating duplex DNA. The best G4 ligands-according to an affinity chromatography-based screening method named G4-CPG-were tested on human cancer and healthy cells, inducing DNA damage at telomeres, and in parallel, showing selective antiproliferative activity on HeLa cancer cells with IC50 values in the low nanomolar range. CD and fluorescence spectroscopy studies allowed detailed investigation of the interaction in solution with different G4 and duplex DNA models of the most promising NDI of the series, as determined by combining the biophysical and biological assays' data.

| S-EPMC7139804 | biostudies-literature

Naphthalene diimides with improved solubility for visible light photoredox catalysis.

Project description:Five core-substituted naphthalene diimides bearing two dialkylamino groups were synthesized as potential visible light photoredox catalysts and characterized by methods of optical spectroscopy and electrochemistry in comparison with one unsubstituted naphthalene diimide as reference. The core-substituted naphthalene diimides differ by the alkyl groups at the imide nitrogens and at the nitrogens of the two substituents at the core in order to enhance their solubility in DMF and thereby enhance their photoredox catalytic potential. The 1-ethylpropyl group as rather short and branched alkyl substituent at the imide nitrogen and the n-propyl group as short and unbranched one at the core amines yielded the best solubilities. The electron-donating diaminoalkyl substituents together with the electron-deficient aromatic core of the naphthalene diimides increase the charge-transfer character of their photoexcited states and thus shift their absorption into the visible light (500-650 nm). The excited state reduction potential was estimated to be approximately +1.0 V (vs SCE) which is sufficient to photocatalyze typical organic reactions. The photoredox catalytic activity in the visible light range was tested by the α-alkylation of 1-octanal as benchmark reaction. Irradiations were performed with LEDs in the visible light range between 520 nm and 640 nm. The irradiation by visible light together with the use of an organic dye instead of a transition metal complex as photoredox catalyst improve the sustainability and make photoredox catalysis "greener".

| S-EPMC6720061 | biostudies-literature

Performance of TDDFT Vertical Excitation Energies of Core-Substituted Naphthalene Diimides.

Project description:We have evaluated the performance of various density functionals, covering generalized gradient approximation (GGA), global hybrid (GH) and range-separated hybrid (RSH), using time dependent density functional theory (TDDFT) for computing vertical excitation energies against experimental absorption maximum (λmax ) for a set of 10 different core-substituted naphthalene diimides (cNDI) recorded in dichloromethane. The computed excitation in case of GH PBE0 is most accurate while the trend is most systematic with RSH LCY-BLYP compared to λmax . We highlight the importance of including solvent effects for optimal agreement with the λmax . Increasing the basis set size from TZ2P to QZ4P has a negligible influence on the computed excitation energies. Notably, RSH CAMY-B3LYP gave the least error for charge-transfer excitation. The poorest agreement with λmax is obtained with semi-local GGA functionals. Use of the optimally-tuned RSH LCY-BLYP* is not recommended because of the high computational cost and marginal improvement in results.

| S-EPMC7317478 | biostudies-literature

Antiparallel RNA G-quadruplex Formed by Human Telomere RNA Containing 8-Bromoguanosine.

Project description:In this study, by combining nuclear magnetic resonance (NMR), circular dichroism (CD), liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS), and gel electrophoresis, we report an unusual topological structure of the RNA G-quadruplex motif formed by human telomere RNA r(UAGGGU) containing 8-bromoguanosine. Results showed that the RNA sequence formed an antiparallel tetramolecular G-quadruplex, in which each pair of diagonal strands run in opposite directions. Furthermore, guanosines were observed both in syn- and anti-conformations. In addition, two of these G-quadruplex subunits were found to be stacking on top of each other, forming a dimeric RNA G-quadruplex. Our findings provide a new insight into the behavior of RNA G-quadruplex structures.

| S-EPMC5532209 | biostudies-literature

Polymorph Screening of Core-Chlorinated Naphthalene Diimides with Different Fluoroalkyl Side-Chain Lengths.

Project description:In this work, naphthalenediimide (NDI) derivatives are widely studied for their semiconducting properties and the influence of the side-chain length on the crystal packing is reported, along with the thermal properties of three core-chlorinated NDIs with different fluoroalkyl side-chain lengths (CF3-NDI, C3F7-NDI and C4F9-NDI). The introduction of fluorinated substituents at the imide nitrogen and addition of strong electron-withdrawing groups at the NDI core are used to improve the NDI derivatives air stability. The new compound, CF3-NDI, was deeply analyzed and compared to the well-known C3F7-NDI and C4F9-NDI, leading to the discovery and solution of two different crystal phases, form α and solvate form, and a solid solution of CF3-NDI and CF3-NDI-OH, formed by the decomposition in DMSO.

| S-EPMC11434339 | biostudies-literature

Recognition of G-quadruplex RNA by a crucial RNA methyltransferase component, METTL14.

Project description:N6-methyladenosine (m6A) is an important epitranscriptomic chemical modification that is mainly catalyzed by the METTL3/METTL14 RNA methyltransferase heterodimer. Although m6A is found at the consensus sequence of 5'-DRACH-3' in various transcripts, the mechanism by which METTL3/METTL14 determines its target is unclear. This study aimed to clarify the RNA binding property of METTL3/METTL14. We found that the methyltransferase heterodimer itself has a binding preference for RNA G-quadruplex (rG4) structures, which are non-canonical four-stranded structures formed by G-rich sequences, via the METTL14 RGG repeats. Additionally, the methyltransferase heterodimer selectively methylated adenosines close to the rG4 sequences. These results suggest a possible process for direct recruitment of METTL3/METTL14 to specific methylation sites, especially near the G4-forming regions. This study is the first to report the RNA binding preference of the m6A writer complex for the rG4 structure and provides insights into the role of rG4 in epitranscriptomic regulation.

| S-EPMC8755082 | biostudies-literature

π-Extended Diaza[7]helicenes by Hybridization of Naphthalene Diimides and Hexa-peri-hexabenzocoronenes.

Project description:The synthesis of an unprecedented, π-extended hexabenzocorene (HBC)-based diaza[7]helicene is presented. The target compound was synthesized by an ortho-fusion of two naphthalene diimide (NDI) units to a HBC-skeleton. A combination of Diels-Alder and Scholl-type oxidation reactions involving a symmetric di-NDI-tolane precursor were crucial for the very selective formation of the helical superstructure via a hexaphenyl-benzene (HPB) derivative. The formation of the diaza[7]helicene moiety in the final Scholl oxidation is favoured, affording the symmetric π-extended helicene as the major product as a pair of enantiomers. The separation of the enantiomers was successfully accomplished by HPLC involving a chiral stationary phase. The absolute configuration of the enantiomers was assigned by comparison of circular dichroism spectra with quantum mechanical calculations.

| S-EPMC7898888 | biostudies-literature

Fluorinated Naphthalene Diimides as Buried Electron Transport Materials Achieve Over 23% Efficient Perovskite Solar Cells.

Project description:Naphthalene diimides (NDI) are widely serving as the skeleton to construct electron transport materials (ETMs) for optoelectronic devices. However, most of the reported NDI-based ETMs suffer from poor interfaces with the perovskite which deteriorates the carrier extraction and device stability. Here, a representative design concept for editing the peripheral groups of NDI molecules to achieve multifunctional properties is introduced. The resulting molecule 2,7-bis(2,2,3,3,4,4,4-heptafluorobutyl)benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetraone (NDI-C4F) incorporated with hydrophobic fluorine units contributes to the prevention of excessive molecular aggregation, the improvement of surface wettability and the formation of strong chemical coordination with perovskite precursors. All these features favor retarding the perovskite crystallization and achieving superior buried interfaces, which subsequently promote charge collection and improve the structural compatibility between perovskite and ETMs. The corresponding PSCs based on low-temperature processed NDI-C4F yield a record efficiency of 23.21%, which is the highest reported value for organic ETMs in n-i-p PSCs. More encouragingly, the unencapsulated devices with NDI-C4F demonstrate extraordinary stability by retaining over 90% of their initial PCEs after 2600 h in air. This work provides an alternative molecular strategy to engineer the buried interfaces and can trigger further development of organic ETMs toward reliable PSCs.

| S-EPMC11423218 | biostudies-literature

Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP.

Project description:Fragile X Mental Retardation Protein (FMRP) is a regulatory RNA binding protein that plays a central role in the development of several human disorders including Fragile X Syndrome (FXS) and autism. FMRP uses an arginine-glycine-rich (RGG) motif for specific interactions with guanine (G)-quadruplexes, mRNA elements implicated in the disease-associated regulation of specific mRNAs. Here we report the 2.8-Å crystal structure of the complex between the human FMRP RGG peptide bound to the in vitro selected G-rich RNA. In this model system, the RNA adopts an intramolecular K(+)-stabilized G-quadruplex structure composed of three G-quartets and a mixed tetrad connected to an RNA duplex. The RGG peptide specifically binds to the duplex-quadruplex junction, the mixed tetrad, and the duplex region of the RNA through shape complementarity, cation-π interactions, and multiple hydrogen bonds. Many of these interactions critically depend on a type I β-turn, a secondary structure element whose formation was not previously recognized in the RGG motif of FMRP. RNA mutagenesis and footprinting experiments indicate that interactions of the peptide with the duplex-quadruplex junction and the duplex of RNA are equally important for affinity and specificity of the RGG-RNA complex formation. These results suggest that specific binding of cellular RNAs by FMRP may involve hydrogen bonding with RNA duplexes and that RNA duplex recognition can be a characteristic RNA binding feature for RGG motifs in other proteins.

| S-EPMC4593078 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data