Browse
Submit Data
Databases
API
Help

Dataset Information

28 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

A photoresponsive supramolecular G-quadruplex.

ABSTRACT: Photoirradiation of a hexadecameric supramolecular G-quadruplex leads to a diastereoselective [2 + 2] cyclodimerization of half of its constituent subunits, which in turn shifts the equilibrium toward the formation of a precise heteromeric octamer.

SUBMITTER: Rivera JM

PROVIDER: S-EPMC3766467 | biostudies-literature | 2013 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

A photoresponsive supramolecular G-quadruplex.

Rivera José M JM Silva-Brenes Diana D

Organic letters 20130503 10

Photoirradiation of a hexadecameric supramolecular G-quadruplex leads to a diastereoselective [2 + 2] cyclodimerization of half of its constituent subunits, which in turn shifts the equilibrium toward the formation of a precise heteromeric octamer. ...[more]

PMID: 23642252

Similar Datasets

Photoresponsive supramolecular complexes as efficient DNA regulator.

Project description:Two supramolecular complexes of trans-1?CB[8] and trans-2?CB[8] were successfully achieved by the controlled selective complexation process of cucurbit[8]uril (CB[8]) with hetero-guest pair containing azobenzene and bispyridinium moieties in aqueous solution, exhibiting the reversibly light-driven movements of CB[8] upon the photocontrollable isomerization of azophenyl axle components. Significantly, the obtained bistable supramolecular complexes and their corresponding [2]pseudorotaxanes could act as a promising concentrator and cleavage agent to regulate the binding behaviors with DNA molecules.

| S-EPMC3936212 | biostudies-literature

Photoresponsive supramolecular coordination polyelectrolyte as smart anticounterfeiting inks.

Project description:While photoluminescence printing is a widely applied anticounterfeiting technique, there are still challenges in developing new generation anticounterfeiting materials with high security. Here we report the construction of a photoresponsive supramolecular coordination polyelectrolyte (SCP) through hierarchical self-assembly of lanthanide ion, bis-ligand and diarylethene unit, driven by metal-ligand coordination and ionic interaction. Owing to the conformation-dependent photochromic fluorescence resonance energy transfer between the lanthanide donor and diarylethene acceptor, the ring-closure/ring-opening isomerization of the diarylethene unit leads to a photoreversible luminescence on/off switch in the SCP. The SCP is then utilized as security ink to print various patterns, through which photoreversible multiple information patterns with visible/invisible transformations are realized by simply alternating the irradiation with UV and visible light. This work demonstrates the possibility of developing a new class of smart anticounterfeiting materials, which could be operated in a noninvasive manner with a higher level of security.

| S-EPMC7921134 | biostudies-literature

A Photoresponsive Stiff-Stilbene Ligand Fuels the Reversible Unfolding of G-Quadruplex DNA.

Project description:The polymorphic nature of G-quadruplex (G4) DNA structures points to a range of potential applications in nanodevices and an opportunity to control G4 in biological settings. Light is an attractive means for the regulation of oligonucleotide structure as it can be delivered with high spatiotemporal precision. However, surprisingly little attention has been devoted towards the development of ligands for G4 that allow photoregulation of G4 folding. We report a novel G4-binding chemotype derived from stiff-stilbene. Surprisingly however, whilst the ligand induces high stabilization in the potassium form of human telomeric DNA, it causes the unfolding of the same G4 sequence in sodium buffer. This effect can be reversed on demand by irradiation with 400 nm light through deactivation of the ligand by photo-oxidation. By fuelling the system with the photolabile ligand, the conformation of G4 DNA was switched five times.

| S-EPMC6563076 | biostudies-literature

Mechanistic Insights into the Self-Assembly of an Acid-Sensitive Photoresponsive Supramolecular Polymer.

Project description:The supramolecular polymerization of an acid-sensitive pyridyl-based ligand (L1 ) bearing a photoresponsive azobenzene moiety was elucidated by mechanistic studies. Addition of trifluoroacetic acid (TFA) led to the transformation of the antiparallel H-bonded fibers of L1 in methylcyclohexane into superhelical braid-like fibers stabilized by H-bonding of parallel-stacked monomer units. Interestingly, L1 dimers held together by unconventional pyridine-TFA N⋅⋅⋅H⋅⋅⋅O bridges represent the main structural elements of the assembly. UV-light irradiation caused a strain-driven disassembly and subsequent aggregate reconstruction, which ultimately led to short fibers. The results allowed to understand the mechanism of mutual influence of acid and light stimuli on supramolecular polymerization processes, thus opening up new possibilities to design advanced stimuli-triggered supramolecular systems.

| S-EPMC7187368 | biostudies-literature

Chiral metallo-supramolecular complexes selectively recognize human telomeric G-quadruplex DNA.

Project description:Here, we report the first example that one enantiomer of a supramolecular cylinder can selectively stabilize human telomeric G-quadruplex DNA. The P-enantiomer of this cylinder has a strong preference for G-quadruplex over duplex DNA and, in the presence of sodium, can convert G-quadruplexes from an antiparallel to a hybrid structure. The compound's chiral selectivity and its ability to discriminate quadruplex DNA have been studied by DNA melting, circular dichroism, gel electrophoresis, fluorescence spectroscopy and S1 nuclease cleavage. The chiral supramolecular complex has both small molecular chemical features and the large size of a zinc-finger-like DNA-binding motif. The complex is also convenient to synthesize and separate enantiomers. These results provide new insights into the development of chiral anticancer agents for targeting G-quadruplex DNA.

| S-EPMC2553577 | biostudies-literature

An aquatic host-guest complex between a supramolecular G-quadruplex and the anticancer drug doxorubicin.

Project description:We describe the synthesis of a fluorescent deoxyguanosine derivative that co-assembles (in water) with an unlabeled analogue into a heteromeric supramolecular G-quadruplex, which forms a host-guest complex with doxorubicin as evidenced by FRET experiments.

| S-EPMC3646657 | biostudies-literature

Reversible manipulation of the G-quadruplex structures and enzymatic reactions through supramolecular host-guest interactions.

Project description:Supramolecular chemistry addresses intermolecular forces and consequently promises great flexibility and precision. Biological systems are often the inspirations for supramolecular research. The G-quadruplex (G4) belongs to one of the most important secondary structures in nucleic acids. Until recently, the supramolecular manipulation of the G4 has not been reported. The present study is the first to disclose a supramolecular switch for the reversible control of human telomere G4s. Moreover, this supramolecular switch has been successfully used to manipulate an enzymatic reaction. Using various methods, we show that cucurbit[7]uril preferably locks and encapsulates the positively charged piperidines of Razo through supramolecular interactions. They can switch the conformations of the DNA inhibitor between a flexible state and the rigid G4 and are therefore responsible for the reversible control of the thrombin activity. Thus, our findings open a promising route and exhibit potential applications in future studies of chemical biology.

| S-EPMC5389557 | biostudies-literature

Rational design of supramolecular hemin/G-quadruplex-dopamine aptamer nucleoapzyme systems with superior catalytic performance.

Project description:The rational design of a set of hemin/G-quadruplex (hGQ)-dopamine binding aptamer (DBA) conjugates, acting as nucleoapzymes, is described. The nucleoapzyme constructs consist of a hGQ DNAzyme as a catalytic unit and DBA as a substrate binding unit that are brought into spatial proximity by a duplex scaffold composed of complementary oligonucleotide strands. When the hGQ unit is linked to the duplex scaffold via a single-strand DNA tether of variable length, the resulting nucleoapzymes reveal a moderate catalytic enhancement toward the H2O2-mediated oxidation of dopamine to aminochrome as compared to the process stimulated by the separated hGQ and DBA units (5-7 fold enhancement). This limited enhancement is attributed to inappropriate spatial positioning of the hGQ in respect to the dopamine binding site, and/or to the flexibility of the tether that links the hGQ catalytic site to the double-stranded scaffold. To solve this, rigidification of the hGQ/DBA conjugates by triplex oligonucleotide structures that anchor the hGQ to a duplex domain associated with the DBA units was achieved. By the sequential, programmed, triplex-controlled rigidification of the hGQ/DBA structure, a nucleoapzyme with superior catalytic activity toward the oxidation of dopamine to aminochrome is identified (30-fold catalytic enhancement). Molecular dynamics simulations reveal that in the resulting highly active rigidified nucleoapzyme structure, the hGQ catalytic site is positioned in spatial proximity to the opening of the DBA substrate binding site, thus rationalizing and supporting the enhanced catalytic functions of the system. Finally, the most active nucleoapzyme system was subjected to fuel- and anti-fuel strands that separate and re-assemble the nucleoapzyme structure, allowing "ON" and "OFF" switching of the nucleoapzyme catalytic functions.

| S-EPMC6005209 | biostudies-literature

Photoresponsive nanoscale columnar transistors.

Project description:This study reports a general methodology for making stable high-performance photosensitive field effect transistors (FET) from self-assembled columns of polycyclic aromatic hydrocarbons by using single-walled carbon nanotubes (SWNTs) as point contacts. In particular, the molecules used in this work are liquid crystalline materials of tetra(dodecyloxy)hexabenzocoronenes (HBCs) that are able to self-organize into columnar nanostructures with a diameter similar to that of SWNTs and then form nanoscale columnar transistors. To rule out potential artifacts, 2 different structural approaches were used to construct devices. One approach is to coat thin films of HBCs onto the devices with the SWNT-metal junctions protected by hydrogensilsesquioxane resin (HSQ), and the other is to place a droplet of HBC exactly on the nanogaps of SWNT electrodes. Both types of devices showed typical FET behaviors, indicating that SWNT-molecule-SWNT nanojunctions are responsible for the electrical characteristics of the devices. After thermally annealing the devices, HBC molecules assembled into columnar structures and formed more efficacious transistors with increased current modulation and higher gate efficiency. More interestingly, when the devices were exposed to visible light, photocurrents with an on/off ratio of >3 orders of magnitude were observed. This study demonstrates that stimuli-responsive nanoscale transistors have the potential applications in ultrasensitive devices for environmental sensing and solar energy harvesting.

| S-EPMC2630108 | biostudies-literature

Verification of specific G-quadruplex structure by using a novel cyanine dye supramolecular assembly: II. The binding characterization with specific intramolecular G-quadruplex and the recognizing mechanism.

Project description:The supramolecular assembly of a novel cyanine dye, 3,3'-di(3-sulfopropyl)-4,5,4',5'-dibenzo-9-ethyl-thiacarbocyanine triethylammonium salt (ETC) was designed to verify specific intramolecular G-quadruplexes from duplex and single-strand DNAs. Spectral results have shown that ETC presented two major distinct signatures with specific intramolecular G-quadruplexes in vitro: (i) dramatic changes in the absorption spectra (including disappearance of absorption peak around 660 nm and appearance of independent new peak around 584 nm); (ii) approximately 70 times enhancement of fluorescence signal at 600 nm. Furthermore, based on (1)H-nuclear magnetic resonance and circular dichroism results, the preferring binding of ETC to specific intramolecular G-quadruplexes probably result from end-stacking, and the loop structure nearby also plays an important role.

| S-EPMC2817466 | 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