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. According to binding studies, the receptor has a preference to bind ATP (adenosine triphosphate) and CTP (cytidine triphosphate) with a "turn-on" fluorescence response. Two separate emission bands of dyes allow one to detect nucleotides in a ratiometric manner in a broad concentration range of 10-5-10-3 M. Spectroscopic measurements and quantum chemical calculations suggest the formation of receptor-nucleotide complexes, which are stabilized by dispersion interactions between a nucleobase and dyes, while hydrogen bonding interactions of nucleobases with the amine linkers are responsible for selectivity.

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. The 1,8-substituted pyrene-based cyclophane with the 2,2'-diaminodiethylamine spacer demonstrates the best selectivity for ATP showing a 50-fold increase in the monomer-excimer emission ratio upon saturation with the nucleotide. The receptor can detect ATP within the biological concentrations range over a wide pH range. NMR and spectroscopic studies have revealed the importance of hydrogen bonding and stacking interactions for achieving a required receptor selectivity. The probe has been successfully applied for the real-time monitoring of creatine kinase activity.

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 Z-configurations. CB[8] was found to be able to encapsulate the isomers of the cryptand by forming a Matryoshka-type complex. The irradiation of a 10:1 CB[8]-cryptand mixture has led to a selective conversion of the cryptand to the E,E,Z isomer inside CB[8]. It has been demonstrated that the addition of fluoride to the resulted complex induces the release of the cryptand as a major E,E,E isomer, while other studied anions were ineffective in this reaction. To our knowledge, this work presents a first example of a host-controlled photoisomerization of an anion receptor bearing multiple switching azobenzenes that model the function of naturally occurring chaperones.

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. This Minireview presents recent progress in the design of synthetic molecular receptors for selective recognition of nucleotides in aqueous solution. The binding properties of receptors and the origins of their selectivity for a particular nucleotide are discussed.

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. To our knowledge, this is the first synthetic receptor for cGMP, which also demonstrates a high preference to bind guanine-rich sequences accomplished by a strong fluorescence quenching. The receptor conformation is very sensitive to the guest structure in an aqueous solution, thus modeling the adaptive behavior of proteins. The study of synthetic systems with a detectable conformational equilibrium represents a great potential for understanding highly specific and tightly regulated interactions in biological systems.

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. Receptor 1 was found to bind fluoride with the highest affinity (105 M-1) and selectivity among the synthesized receptors. It was the only receptor that demonstrated fluorescence increase upon addition of fluoride. Other titration experiments with halides and oxyanions led to an anion-induced aggregation and fluorescence quenching. The mechanism of the particular turn-on fluorescence for fluoride was explained by the ability of receptor 1 to encapsulate several fluoride anions. Multiple anion coordination resulted in the protonation of the tertiary amine group and subsequent hindering of the PET process. 1H and 19F NMR titrations, single-crystal X-ray structure of chloride complex, and DFT calculation suggest that 1 can perfectly accommodate two fluoride anions in the inner cavity but only one chloride, keeping the second chloride in the outer coordination sphere. Thus, the importance of size selectivity, which is reflected in a collective behavior of molecules in an aqueous solution, represents a new strategy for the design of highly selective probes for fluoride functioning in an aqueous solution.

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. The receptors bind selectively to the pyrophosphate anion in buffered aqueous solutions. The receptors with more than six amine groups in the structure demonstrated the highest affinities for pyrophosphate. The fluorescence response towards anions was found to be dependent on the position of the amine groups relative to the naphthalimide core, and on the pH of the buffered solution. Three sensing mechanisms have been found that explain fluorescence responses of receptors towards anions in an aqueous solution.

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. The artificial active site in new receptors simultaneously realizes several binding and sensing mechanisms: encapsulation of a nucleobase via dispersion and hydrogen bonding interactions, recognition of the phosphate residue, and a self-reporting feature-"turn-on" fluorescence. Key to the high selectivity is the conscious separation of phosphate- and nucleobase-binding sites by introducing specific spacers in the receptor structure. We have tuned the spacers to achieve high binding affinity and selectivity for cytidine 5' triphosphate coupled to a record 60-fold fluorescence enhancement. The resulting structures are also the first functional models of poly(rC)-binding protein coordinating specifically to C-rich RNA oligomers, e.g., the 5'-AUCCC(C/U) sequence present in poliovirus type 1 and the human transcriptome. The receptors bind to RNA in human ovarian cells A2780, causing strong cytotoxicity at 800 nM. The performance, self-reporting property, and tunability of our approach open up a promising and unique avenue for sequence-specific RNA binding in cells by using low-molecular-weight artificial receptors.

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.

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

Invited for this month's cover picture is the group of Evgeny A. Kataev at the Technical University Chemnitz. The cover picture shows the authors' association of fluorescence anion sensing with pearl hunting - the activity of recovering pearls from wild molluscs. In the presented work, the group of Kataev has developed a new water-soluble amido-amine azacryptand bearing a fluorescence anthracene dicarboxamide fragment. With the help of the fluorescent receptors (a hand) one can catch the phosphate anion (a glowing pearl) and visualize this binding event. The recognition of phosphate and oxalate has led to a fluorescent enhancement in a selective manner. Read the full text of their Communication at https://doi.org/10.1002/open.201900309.

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. The recognition events for phosphate and dicarboxylates are accomplished by a fluorescence enhancement in the anthracene emission. As revealed by experimental and theoretical studies, phosphate and oxalate show different recognition modes. Phosphate demonstrates hydrogen bond acceptor properties, while the coordination of oxalate favours the protonation of the receptor.

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 103 M-1 affinity and stabilizes it in the inner cavity though electrostatic, hydrogen bonding, and anion-π interactions.

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.

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.

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 6.2 showing a 10-fold fluorescence enhancement and a two orders of magnitude selectivity over other anions.