Pattern-based sensing of nucleotides in aqueous solution with a multicomponent indicator displacement assay

A Fluorescence Sensor Array Based on Zinc(II)-Carboxyamidoquinolines: Toward Quantitative Detection of ATP*

The newly prepared fluorescent carboxyamidoquinolines (1-3) and their Zn(II) complexes (Zn@1-Zn@3) were used to bind and sense various phosphate anions utilizing a relay mechanism, in which the Zn(II) ion migrates from the Zn@1-Zn@3 complexes to the phosphate, namely adenosine 5'-triphosphate (ATP) and pyrophosphate (PPi), a process accompanied by a dramatic change in fluorescence. Zn@1-Zn@3 assemblies interact with adenine nucleotide phosphates while displaying an analyte-specific response. This process was investigated using UV-vis, fluorescence, and NMR spectroscopy. It is shown that the different binding selectivity and the corresponding fluorescence response enable differentiation of adenosine 5'-triphosphate (ATP), adenosine 5'-diphosphate (ADP), pyrophosphate (PPi), and phosphate (Pi). The cross-reactive nature of the carboxyamidoquinolines-Zn(II) sensors in conjunction with linear discriminant analysis (LDA) was utilized in a simple fluorescence chemosensor array that allows for the identification of ATP, ADP, PPi, and Pi from 8 other anions including adenosine 5'-monophosphate (AMP) with 100 % correct classification. Furthermore, the support vector machine algorithm, a machine learning method, allowed for highly accurate quantitation of ATP in the range of 5-100 μM concentration in unknown samples with error <2.5 %.

Fluorescent carbon nanodots-based artificial tongue for determining and discriminating cigarettes

Smoking can cause cigarette-related diseases and pose serious threat to human health. Its dangers can be effectively controlled by discriminating cigarettes and monitoring cigarette quality. Herein, a kind of artificial tongue technique based on the indicator displacement assay (IDA) was developed and applied to determine and discriminate cigarettes and their main ingredients (saccharides, organic acids and nicotine). This method was constructed using carbon nanodots (CDs) as a fluorescent indicator and various concentrations of silver ion (Ag⁺) as a fluorescent regulator. A cigarette extracting solution was prepared to interact with an artificial tongue and produce fluorescence fingerprints. Twenty-nine kinds of cigarettes can be well discriminated in terms of category (flue-cured cigarette, blended cigarette and cigar), brand, origin (domestic or foreign cigarettes) after processing and visualizing the response fingerprints. The artificial tongue fluorescent sensor array can sensitively detect nine kinds of tobacco-based chemical ingredients and discriminate them between different concentrations. The as-prepared fluorescent artificial tongue is a promising platform for monitoring cigarette quality and controlling the harmful effects of smoking because of its cheap material requirements, simple operation, and good performance.

Exploiting complexity to implement function in chemical systems

This feature article reflects a personal overview of the importance of complexity as an additional parameter to be considered in chemical research, being illustrated with selected examples in molecular recognition and catalysis.

Boronic Acid Appended Naphthyl-Pyridinium Receptors as Chemosensors for Sugars

There remains a need in clinics and research to have simple and sensitive detection systems that allow the detection and quantification of sugar markers of biomedical relevance such as sugars lactulose and mannitol for noninvasive gut permeability assessment. We have prepared a new class of boronic acid-appended naphthyl-pyridinium receptor compounds as chemosensors. These were studied for their ability to act as modular internal charge transfer (ICT) fluorescent probes or donor/acceptor pair ensembles where the receptor compound can act as a quencher for an anionic dye. As an ICT sensor, fluorescence intensity increased upon diol recognition, which stems from the neutralization of the pyridinium nitrogen that is perturbing the chromophoric properties. We found these ICT probes provide good sensitivity for disaccharide lactulose with low micromolar detection and quantification limits. In addition, their ability to form a non-fluorescent ground state complex with anionic reporter dyes, such as HPTS or TSPP, was examined as probes for various sugars. We have identified three receptor/quencher compounds with high quenching efficiency for anionic dyes. Subsequently, a range of sugars and sugar derivatives were tested for chemosenstivity of our probes. This study illustrates an approach for designing boronic acid-based chemoreceptors for the recognition and quantification of sugars and sugar derivatives.

Single-system based discriminative optical sensors: different strategies and versatile applications

Discriminative optical sensors with pattern recognition properties and high-throughput ability have been widely developed as they can distinguish multiple chemically similar analytes. Compared to traditional sensor arrays composed of a series of sensor elements, single-system based discriminative sensors using an array of optical changes at different wavelengths to provide input signals have drawn intensive attention recently. On the one hand, they can provide discrimination ability that is lack in using selective sensors; on the other hand, they can simplify the complex data acquisition process accompanied by multiple-element-based sensor arrays and reduce consumption of sensor samples. This tutorial review gives an overview of the development of single-system based discriminative optical sensors. Different strategies for the construction of single-system based discriminative sensors including dynamic combinatorial libraries, cross-reactive conjugated polymers, DNA G-quadruplex ensembles, combinatorial fluorescent molecular sensors, and fluorophore/surfactant aggregate ensembles are particularly introduced.

Array-based sensing of purine derivatives with fluorescent dyes

Natural and synthetic purine derivatives such as caffeine, theophylline, 6-mercaptopurine and 8-chlorotheophylline are important drugs. Due to the structural similarity of these compounds, it is intrinsically difficult to prepare chemosensors for their selective optical detection. Here, we describe a sensor array which can be used to differentiate pharmacologically important purine derivatives with good accuracy. The array is composed of four polysufonated fluorescent dyes, all of which can bind purines viaπ-stacking interactions. The complexation of the analytes results in partial quenching of the fluorescence. The fluorescence response of the four dyes provides a characteristic signal pattern, enabling the identification of thirteen purine derivatives at low millimolar concentration. Furthermore, it is possible to use the array for obtaining information about the quantity and purity of purine samples.

Dynamic combinatorial/covalent chemistry: a tool to read, generate and modulate the bioactivity of compounds and compound mixtures

Reversible covalent bond formation under thermodynamic control adds reactivity to self-assembled supramolecular systems, and is therefore an ideal tool to assess complexity of chemical and biological systems. Dynamic combinatorial/covalent chemistry (DCC) has been used to read structural information by selectively assembling receptors with the optimum molecular fit around a given template from a mixture of reversibly reacting building blocks. This technique allows access to efficient sensing devices and the generation of new biomolecules, such as small molecule receptor binders for drug discovery, but also larger biomimetic polymers and macromolecules with particular three-dimensional structural architectures. Adding a kinetic factor to a thermodynamically controlled equilibrium results in dynamic resolution and in self-sorting and self-replicating systems, all of which are of major importance in biological systems. Furthermore, the temporary modification of bioactive compounds by reversible combinatorial/covalent derivatisation allows control of their release and facilitates their transport across amphiphilic self-assembled systems such as artificial membranes or cell walls. The goal of this review is to give a conceptual overview of how the impact of DCC on supramolecular assemblies at different levels can allow us to understand, predict and modulate the complexity of biological systems.

A facile approach to cross-reactive colorimetric sensor arrays: an application in the recognition of the 20 natural amino acids

A very facile approach for the design and fabrication of a colorimetric sensor array, by using only a single indicator–receptor couple at various ratios and concentrations, is described for the first time.

Experimental and theoretical methods for the analyses of dynamic combinatorial libraries

Progresses in spatial and temporal analytical tools open new avenues for the study and control of increasingly complex chemical systems.

Pattern-based sensing of nucleotides with functionalized gold nanoparticles

A sensing system has been obtained by self-assembly of multiple fluorescent indicators and monolayer protected gold nanoparticles. The system is able to discriminate between each of the eight nucleotides NDP and NTP (N = A, T, G, C) in a quantitative manner at micromolar concentrations.

Zn(II)-cyclam based chromogenic sensors for recognition of ATP in aqueous solution under physiological conditions and their application as viable staining agents for microorganism

Two chromogenic complexes, L.Zn (where L is (E)-4-((4-(1,4,8,11-tetraazacyclotetradecan-1-ylsulfonyl)phenyl)diazenyl)-N,N-dimethylaniline) and its [2]pseudorotaxane form (α-CD.L.Zn), were found to bind preferentially to adenosine triphosphate (ATP), among all other common anions and biologically important phosphate (AMP, ADP, pyrophosphate, and phosphate) ions in aqueous HEPES buffer medium of pH 7.2. Studies with live cell cultures of prokaryotic microbes revealed that binding of these two reagents to intercellular ATP, produced in situ, could be used in delineating the gram-positive and the gram-negative bacteria. More importantly, these dyes were found to be nontoxic to living microbes (eukaryotes and prokaryotes) and could be used for studying the cell growth dynamics. Binding to these two viable staining agents to intercellular ATP was also confirmed by spectroscopic studies on cell growth in the presence of different respiratory inhibitors that influence the intercellular ATP generation.

Synthesis of phototrappable shape-shifting molecules for adaptive guest binding

We have designed and synthesized oligosubstituted bullvalenes 1 and 2 as adaptive molecules that can change their shapes in order to bind tightly to a suitable guest. By incorporation of a photolabile o-nitroveratryloxycarbonate (NVOC) group into bullvalenes 1 and 2, tightly binding species can be selectively isolated from a population of hundreds of interconverting structural isomers. Spontaneous strain-assisted Cope rearrangements allow these shape-shifting molecules to exist in a dynamic equilibrium of configurationally distinct valence isomers, as revealed by dynamic NMR and HPLC studies. When NVOC bullvalenes 1 and 2 were exposed to UV light, the cleavage of the NVOC group resulted in a mixture of static isomers of the corresponding bullvalone. Binding studies of NVOC bisporphyrin bullvalene 1 demonstrated that the dynamic isomeric equilibrium shifted in the presence of C(60), favoring configurations with more favorable binding affinities. Irradiation of a mixture of 1 and C(60) with UV light and isolation of the major static isomer yielded an isomer of bisporphyrin bullvalone with a binding affinity for C(60) that was ∼2 times larger than that of the nonadapted isomer bisporphyrin bullvalone 41.

A general approach to differential sensing using synthetic molecular receptors

Differential sensing is continuing to develop as an alternative to traditional, selective chemosensing techniques. This technique takes a cue from how the human senses of taste and smell operate in order to obtain qualitative and even quantitative data on single analytes and mixtures. Whereas classical chemosensing techniques inspired by the 'lock-and-key' approach depend on the development of a selective receptor for a target analyte, pattern-based sensing depends on the development of an array of cross-reactive receptors, which produce a collection of responses upon the array's interaction with a target analyte. This review focuses on an approach to differential sensing that diversifies synthetic receptors to be used in an array via appending combinatorial peptidic arms, metal ions, and indicators to a core binding unit.

Enzyme-amplified array sensing of proteins in solution and in biofluids

We have developed an enzyme-nanoparticle sensor array where the sensitivity is amplified through enzymatic catalysis. In this approach cationic gold nanoparticles are electrostatically bound to an enzyme (beta-galactosidase, beta-Gal), inhibiting enzyme activity. Analyte proteins release the beta-Gal, restoring activity and providing an amplified readout of the binding event. Using this strategy we have been able to identify proteins in buffer at a concentration of 1 nM, substantially lower than current strategies for array-based protein sensing. Moreover, we have obtained identical sensitivity in studies where the proteins are spiked into the complex protein matrix provided by desalted human urine ( approximately 1.5 muM total protein; spiked protein concentrations were 0.067% of the overall protein concentration), demonstrating the potential of the method for diagnostic applications.

A simple approach for the discrimination of nucleotides based on a water-soluble polythiophene derivative

A sensor based on an array of wavelengths of a cationic poythiophene derivative was applied to discriminate fifteen nucleotides along with monophosphate and pyrophosphate with 100% confidence limits.

Recognition of phospho sugars and nucleotides with an array of boronic acid appended bipyridinium salts

The solution-phase sensor array of three cationic bis-boronic acid appended benzyl viologens (BBV) and the anionic fluorescent dye, 8-hydroxypyrene-1,3,6-trisulfonic acid trisodium salt (HPTS), is able to discriminate among five phospho sugars, four nucleotides and three neutral saccharides in aqueous buffered solution at low mM concentrations. Linear discriminant analysis, principal component analysis, and hierachical cluster analysis studies showed the "discrimination limit" (lowest analyte concentration where the discrimination is still 100%) to be 4mM. Calculated K(b) and F(max)/F(0) values from binding curves of the three BBVs with 1-12 were also used to perform multi-variate analyses with very good discrimination results.