Supramolecular Recognition of Cytidine Phosphate in Nucleotides and RNA Sequences.

Supramolecular recognition of nucleotides would enable manipulating crucial biochemical pathways like transcription and translation directly and with high precision. Therefore, it offers great promise in medicinal applications, not least in treating cancer or viral infections. This work presents a universal supramolecular approach to target nucleoside phosphates in nucleotides and RNA.

Dye-functionalized phosphate-binding macrocycles: from nucleotide to G-quadruplex recognition and "turn-on" fluorescence sensing.

A novel strategy to design "turn-on" fluorescent receptors for G-quadruplexes of DNA is presented, which relies on the connection of phosphate binding macrocycles (PBM) with naphthalimide dyes. A new PBM-dye family was synthesized and evaluated in terms of binding and detection of nucleotides and DNA G-quadruplexes of different topologies.

Binding and Sensing Properties of a Hybrid Naphthalimide-Pyrene Aza-Cyclophane towards Nucleotides in an Aqueous Solution.

Selective recognition of nucleotides with synthetic receptors is an emerging direction to solve a series of nucleic acid-related challenges in biochemistry. Towards this goal, a new aza-cyclophane with two different dyes, naphthalimide and pyrene, connected through a triamine linker has been synthesized and studied for the ability to bind and detect nucleoside triphosphates in an aqueous solution. The receptor shows Foerster resonance energy transfer (FRET) in fluorescence spectra upon excitation in DMSO, which is diminished dramatically in the presence of water.

Control of Photoisomerization of an Azoazacryptand by Anion Binding and Cucurbit[8]uril Encapsulation in an Aqueous Solution.

Control of isomerization of a receptor bearing multiple light-switchable subunits in a confined space is critical for the design of synthetic molecular machines. Toward this goal, a new azacryptand containing three azobenzene subunits has been developed, and its photoisomerization in an aqueous solution has been studied depending on anion coordination and recognition by a larger host-cucurbit[8]uril (CB[8]). The cryptand in its hexaprotonated form shows considerable affinity for fluoride and perchlorate, which in turn affects the isomer distribution of the receptor under UV-light irradiation, stabilizing the isomers of the cryptand with -configurations.

Ratiometric Detection of ATP by Fluorescent Cyclophanes with Bellows-Type Sensing Mechanism.

Pyrene-based cyclophanes have been synthesized with the aim to realize a bellows-type sensing mechanism for the ratiometric detection of nucleotide concentrations in a buffered aqueous solution. The sensing mechanism involves the encapsulation of a nucleobase between two pyrene rings, which affects the monomer-excimer equilibrium of the receptor in the excited state. The nature of the spacer and its connection pattern to pyrene rings have been varied to achieve high selectivity for ATP.

Anthracene-Based Amido-Amine Cage Receptor for Anion Recognition under Neutral Aqueous Conditions.

A new amido-amine cage receptor, which combines 1,8-anthracene diacarboxamide subunit and a polyammonium azamacrocycle, is reported. Bearing both the hydrogen bond donor and the acceptor binding sites, the receptor is able to bind phosphate selectively under neutral (pH 7.2) aqueous conditions.

Anthracene-Based Amido-Amine Cage Receptor for Anion Recognition under Neutral Aqueous Conditions.

https://doi.org/10.1002/open.

Anthracene-Based Receptors with a Turn-on Fluorescence Response for Nitrate.

Herein we describe the design, synthesis, and anion binding properties of bicyclic receptors with two or three anthracenes, which show a turn-on fluorescence response in the presence of nitrate and chaotropic anions in a buffered aqueous solution. The receptor with two anthracenes binds nitrate with 10 M affinity and stabilizes it in the inner cavity though electrostatic, hydrogen bonding, and anion-π interactions.

Conformational Selection in Anion Recognition: cGMP-Selective Binding by a Naphthalimide-Functionalized Amido-Amine Macrocycle.

Amido-amine macrocycles with two and four naphthalimide dyes were designed to bind nucleoside monophosphates and oligonucleotides in an aqueous buffered solution. Anion-templated synthesis was used to direct the macrocyclization reaction to the [2+2] product, while high dilution conditions favored the formation of the [4+4] macrocycle with an unprecedented geometry, as revealed from the X-ray analysis. The [2+2] product was found to exhibit a remarkable binding strength and fluorescence response for cyclic guanosine monophosphate (cGMP) in an aqueous solution.

Molecular Receptors for Recognition and Sensing of Nucleotides.

Nucleotides are constituents of nucleic acids and they have a variety of functions in cellular metabolism. Synthetic receptors and sensors are required to reveal the role of nucleotides in living organisms and mechanisms of signal transduction events. In recent years, a large number of nucleotide-selective synthetic receptors have been devised, which utilize different molecular designs and sensing mechanisms.

Finding a receptor design for selective recognition of perrhenate and pertechnetate: hydrogen vs. halogen bonding.

Receptors bearing hydrogen and halogen bond donors for recognition of perrhenate and pertechnetate were designed and studied. Acyclic hosts with N-H and C-H binding sites showed the best selectivity for TcO4- and ReO4- over spherical and more basic tetrahedral anions.

Hybrid Macrocycles for Selective Binding and Sensing of Fluoride in Aqueous Solution.

Synthesis and anion binding properties of hybrid macrocycles containing ammonium and hydrogen bond donor groups are reported. Receptor properties were studied in a 10 mM MES buffer solution at pH 6.2, at which the receptors carry two positive charges at the secondary amine groups.

Selective recognition of oxalate in water: effect of pH on binding strength and sensing mechanisms.

Bicyclic receptors bearing anthracene as a strap were designed for selective oxalate binding in a buffered aqueous solution. The receptors were found to possess two mechanisms of fluorescence response depending on the pH of a buffered solution. Receptor 2 binds oxalate at pH 6.

Naphthalimide-Based Polyammonium Chemosensors for Anions: Study of Binding Properties and Sensing Mechanisms.

New naphthalimide-based receptors for anions have been synthesized. Efficient synthetic routes have been discovered to functionalize the naphthalimide core with branched polyamines. Binding and sensing properties of the receptors were studied by potentiometric, NMR and fluorescence titrations.

Design of anion-selective PET probes based on azacryptands: the effect of pH on binding and fluorescence properties.

Design of PET probes for anions working in an aqueous buffered solution is described. The design has been used to develop selective fluorescent probes for sulfate and pyrophosphate. The relationship between the selectivity of receptors towards anions, their conformation, fluorescence response and the pH of the solution has been studied in detail.