Threshold Detection Using Indicator-Displacement Assays: An Application in the Analysis of Malate in Pinot Noir Grapes

Indicator displacement assays: from concept to recent developments

Overcoming the synthetic burden related to covalently connected receptors with appropriate indicators for sensing various analytes via an indicator spacer receptor (ISR) approach, the indicator displacement assay (IDA) seems to be a very sophisticated and versatile supramolecular sensing paradigm, and it has taken the phenomenon of molecular recognition to the next level in the realm of host-guest chemistry. Due to the unavailability of a comprehensive report on what has been done in the last decade in relation to IDAs, we decided to set down this account illustrating diverse indicator displacement assays (IDAs) in detail from the concept stage to recent developments relating to the detection of cationic, anionic, and neutral analytes. The authors conclude this account with future perspectives and highlight the limitations and challenges relating to IDAs which need to be overcome in order to realize the full potential of this popular sensing phenomenon. While we were finalizing our account for publication, a tutorial review by the research groups of Anslyn, Sessler, and Sun was published, which focuses mainly on diverse aspects of the chemistry related to IDAs. As can be seen, our review, besides discussing various basic IDA concepts, has a vast collection of information published in the past decade and hence, hopefully, will be very informative for the supramolecular community. We believe that this work will offer new insights for the construction of novel sensors operating through the IDA approach.

Reaction-based indicator displacement assay (RIA) for the development of a triggered release system capable of biofilm inhibition

Here, a reaction-based indicator displacement hydrogel assay (RIA) was developed for the detection of hydrogen peroxide (H2O2) via the oxidative release of the optical reporter Alizarin Red S (ARS). In the presence of H2O2, the RIA system displayed potent biofilm inhibition for Methicillin-resistant Staphylococcus aureus (MRSA), as shown through an in vitro assay quantifying antimicrobial efficacy. This work demonstrated the potential of H2O2-responsive hydrogels containing a covalently bound diol-based drug for controlled drug release.

Poly(p-phenyleneethynylene)-based tongues discriminate fruit juices

We describe a simple optoelectronic tongue, consisting of a positively charged, fluorescent poly(para-phenyleneethynylene), P2, that reacts to fruit juices, when employed at three different pH-values (pH 3, 7, 13). This minimal tongue identifies and discriminates 14 different commercially available apple juices, 6 different grape juices and 5 different black currant juices from each other. A similar, negatively charged fluorescent polymer, P1, also achieved discrimination, but the analyte concentration had to be increased by a factor of 50. A mixture of black currant juice and red grape juice is identified as red grape juice, for specific combinations of grape and black currant juices. A mixture of red and green grape juice passes as red grape juice in our sensing system when it contains more than 70% of red grape juice. The data were obtained by fluorescence quenching of the conjugated polymers and processed by linear discriminant analysis of the collected data.

Fluorescence "Turn-On" Indicator Displacement Assay-Based Sensing of Nitroexplosive 2,4,6-Trinitrophenol in Aqueous Media via a Polyelectrolyte and Dye Complex

A water-soluble nonfluorescent cationic conjugated polyelectrolyte poly(1,1'-((1,4-phenylenebis(oxy))bis(propane-3,1-diyl))bis(pyridin-1-ium)bromide) (PPPy) was specifically synthesized via an economical method of oxidative coupling polymerization in high yields. PPPy selectively recognized nitroexplosive picric acid (PA) by fluorescence "turn-on" in the presence of closely related nitroexplosive compounds, namely, 2,4,6-trinitrotoluene, 2,4-dinitrophenol, and 4-nitrophenol via fluorescence indicator displacement assay (IDA) technique in water at pH 7.0. The polymer PPPy was characterized by NMR spectroscopy, gel permeable chromatography, UV-vis spectroscopy. The polymer PPPy forms an electrostatic complex with uranine dye. This ensemble scheme was utilized to detect PA with a limit of detection value of 295 nM (solution state) and 0.22 ppm (vapor state) through IDA, a phenomenon that is very different from the widely reported Förster resonance energy transfer, photoinduced electron transfer, ground-state charge transfer and inner filter effect based probes used for nitroexplosive PA detection.

Fingerprinting antibiotics with PAE-based fluorescent sensor arrays

We outline an evolution process for tongue elements composed of poly(p-aryleneethynylene)s (PAE) and detergents, resulting in a chemical tongue (24 elements) that discerns antibiotics. Cross-breeding of this new tongue with tongue elements that consist of simple poly(p-phenyleneethynylene)s (PPE) at different pH-values leads to an enlarged sensor array, composed of 30 elements. This tongue was pruned, employing principal component analysis. We find that a filial tongue featuring three elements from each original array (i.e. a six element tongue) is superior to either of the prior tongues and the composite tongue in the discrimination of structurally different antibiotics. Such a selection process should be general and give an idea how to successfully generate powerful low-selectivity sensor elements and configure them into discriminative chemical tongues.

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.

Chemical analog-to-digital signal conversion based on robust threshold chemistry and its evaluation in the context of microfluidics-based quantitative assays

In this article, we describe a nonlinear threshold chemistry based on enzymatic inhibition and demonstrate how it can be coupled with microfluidics to convert a chemical concentration (analog input) into patterns of ON or OFF reaction outcomes (chemical digital readout). Quantification of small changes in concentration is needed in a number of assays, such as that for cystatin C, where a 1.5-fold increase in concentration may indicate the presence of acute kidney injury or progression of chronic kidney disease. We developed an analog-to-digital chemical signal conversion that gives visual readout and applied it to an assay for cystatin C as a model target. The threshold chemistry is based on enzymatic inhibition and gives sharper responses with tighter inhibition. The chemistry described here uses acetylcholinesterase (AChE) and produces an unambiguous color change when the input is above a predetermined threshold concentration. An input gives a pattern of ON/OFF responses when subjected to a monotonic sequence of threshold concentrations, revealing the input concentration at the point of transition from OFF to ON outcomes. We demonstrated that this threshold chemistry can detect a 1.30-fold increase in concentration at 22 °C and that it is robust to experimental fluctuations: it provided the same output despite changes in temperature (22-34 °C) and readout time (10-fold range). We applied this threshold chemistry to diagnostics by coupling it with a traditional sandwich immunoassay for serum cystatin C. Because one quantitative measurement comprises several assays, each with its own threshold concentration, we used a microfluidic SlipChip device to process 12 assays in parallel, detecting a 1.5-fold increase (from 0.64 (49 nM) to 0.96 mg/L (74 nM)) of cystatin C in serum. We also demonstrated applicability to analysis of patient serum samples and the ability to image results using a cell phone camera. This work indicates that combining developments in nonlinear chemistries with microfluidics may lead to development of user-friendly diagnostic assays with simple readouts.

In-situ generation of differential sensors that fingerprint kinases and the cellular response to their expression

Mitogen-activated protein (MAP) kinases are responsible for many cellular functions, and their malfunction manifests itself in several human diseases. Usually, monitoring the phosphorylation states of MAP kinases in vitro requires the preparation and purification of the proteins or Western blotting. Herein, we report an array sensing approach for the differentiation of MAP kinases and their phosphorylated counterparts in vitro. This technique utilizes a library of differential receptors created in situ containing peptides known for affinity to MAP kinases, and a Zn(II)-dipicolylamine complex that binds phosphate groups on proteins. An indicator-displacement assay signals the binding of the individual receptors to the kinases, while chemometrics is used to create a fingerprint for the kinases and their state of activity. For example, linear discriminant analysis correctly identified kinase activity with a classification accuracy of 97.5% in vitro, while the cellular response to kinase expression was classified with 100% accuracy.

Supramolecular displacement-mediated activation of a silent fluorescence probe for label-free ligand screening

We report a new approach for the rapid screening of analyte binding affinities for a target protein. We demonstrate that a molecular probe, with a pro-fluorophore substrate and ligand moieties, can be hindered from enzymatic access when bound to the target protein. When analytes displace the probe from the protein's binding pocket, a fluorescence profile is generated. This profile is used to discriminate analytes based on their relative binding affinities.

Discrimination and classification of ginsenosides and ginsengs using bis-boronic acid receptors in dynamic multicomponent indicator displacement sensor arrays

Ginsenosides are complex natural products with a diverse array of biological activities, but their molecular recognition and sensing is challenging. A library of simple bis-boronic acid-based receptors with various spacers was synthesized for the sensing of ginsenosides. The incorporation of two boronic acids allowed the pairing of two indicators, which can simultaneously bind the receptors or two saccharides within the ginsenosides. A cross-reactive sensing array was therefore constructed using the receptors in conjunction with different pairs of indicators. LDA plots created from the colorimetric response of the hosts and indicator pairs reveal excellent classification of the ginsenosides, and the corresponding loading plots reveal the cross-reactivity of the receptors. In addition, several commercial ginseng extracts were unambiguously classified using the same sensing array. The assay reported here should be applicable to the analysis of other large saccharide-based natural products.

Using ratiometric indicator-displacement assays in semi-quantitative colorimetric determination of chloride, bromide, and iodide anions

A ratiometric indicator-displacement assay (RIDA) array has been developed for the semi-quantitative colorimetric determination of chloride, bromide, and iodide anions. Determinations of these halide anions follow the displacement reaction using the chelate compound of (2-(3,5-dibromo-2-pyridylazo)-5-(diethylamino)phenol) (3,5-Br2-PADAP) and heavy metal salts as colorimetric reagent. Different from regular silver nitrate titrations, the chloride, bromide, and iodide anions compete with the 3,5-Br2-PADAP ligand and change the colour of the 3,5-Br2-PADAP-metal chelate compound dramatically. These clearer colour changes make the semi-quantitative colorimetric determination of chloride, bromide, and iodide anions possible. The colour changes are imaged using a conventional flatbed scanner, and digitized. After statistical analysis, these colour changes in the RIDA array provide facile identification of chloride, bromide, and iodide anions at a wide concentration range (10 μM to 10 mM) without any misclassification. The RIDA array is able to discriminate without misclassifications among seven concentrations of chloride, bromide, and iodide anions. No shelf life issue exists because the chelating compounds react with halide anions directly without any pre-immobilizations.

Intelligent chiral sensing based on supramolecular and interfacial concepts

Of the known intelligently-operating systems, the majority can undoubtedly be classed as being of biological origin. One of the notable differences between biological and artificial systems is the important fact that biological materials consist mostly of chiral molecules. While most biochemical processes routinely discriminate chiral molecules, differentiation between chiral molecules in artificial systems is currently one of the challenging subjects in the field of molecular recognition. Therefore, one of the important challenges for intelligent man-made sensors is to prepare a sensing system that can discriminate chiral molecules. Because intermolecular interactions and detection at surfaces are respectively parts of supramolecular chemistry and interfacial science, chiral sensing based on supramolecular and interfacial concepts is a significant topic. In this review, we briefly summarize recent advances in these fields, including supramolecular hosts for color detection on chiral sensing, indicator-displacement assays, kinetic resolution in supramolecular reactions with analyses by mass spectrometry, use of chiral shape-defined polymers, such as dynamic helical polymers, molecular imprinting, thin films on surfaces of devices such as QCM, functional electrodes, FET, and SPR, the combined technique of magnetic resonance imaging and immunoassay, and chiral detection using scanning tunneling microscopy and cantilever technology. In addition, we will discuss novel concepts in recent research including the use of achiral reagents for chiral sensing with NMR, and mechanical control of chiral sensing. The importance of integration of chiral sensing systems with rapidly developing nanotechnology and nanomaterials is also emphasized.

Molecular recognition and self-assembly special feature: A general protocol for creating high-throughput screening assays for reaction yield and enantiomeric excess applied to hydrobenzoin

A general approach to high-throughput screening of enantiomeric excess (ee) and concentration was developed by using indicator displacement assays (IDAs), and the protocol was then applied to the vicinal diol hydrobenzoin. The method involves the sequential utilization of what we define herein as screening, training, and analysis plates. Several enantioselective boronic acid-based receptors were screened by using 96-well plates, both for their ability to discriminate the enantiomers of hydrobenzoin and to find their optimal pairing with indicators resulting in the largest optical responses. The best receptor/indicator combination was then used to train an artificial neural network to determine concentration and ee. To prove the practicality of the developed protocol, analysis plates were created containing true unknown samples of hydrobenzoin generated by established Sharpless asymmetric dihydroxylation reactions, and the best ligand was correctly identified.

Using enantioselective indicator displacement assays to determine the enantiomeric excess of alpha-amino acids

Enantioselective indicator displacement assays (eIDAs) were used for the determination of enantiomeric excess (ee) of alpha-amino acids as an alternative to the labor-intensive technique of chromatography. In this study, eIDAs were implemented by the use of two chiral receptors [(Cu(II)(1)](2+), [Cu(II)(2)](2+)) in conjunction with the indicator chrome azurol S. The two receptors were able to enantioselectively discriminate 13 of the 17 analyzed alpha-amino acids. Enantiomeric excess calibration curves were made using both receptors and then used to analyze true test samples to check the system's ability to determine ee accurately. The proposed method uses a conventional UV-vis spectrophotometer to monitor the colorimetric signal, which allows for a potential high-throughput screening (HTS) method for determining ee. The techniques created consistently produced results accurate enough for rapid preliminary determination of ee.

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.

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

A multicomponent indicator displacement assay (MIDA) based on an organometallic receptor and three dyes can be used for the identification and quantification of nucleotides in aqueous solution at neutral pH.

Tapping into Boron/?-Hydroxycarboxylic Acid Interactions in Sensing and Catalysis

Whereas interaction of boron acids (boric and boronic) with diols and neutral sugar ligands has received much global research attention in recent years, the binding of simple α-hydroxycarboxylic and sugar acids by boron has received less attention. Applications of boron-based fluorescent sensors and chemoselective catalysts targeting this functional motif have appeared only in the past 5 years. The present synopsis will focus on rapid developments that have occurred in both areas during this half decade.

Designed Boronate Ligands for Glucose-Selective Holographic Sensors

In this study, 2-acrylamidophenylboronate (2-APB) was synthesised and its ability to bind with glucose was investigated both in solution and when integrated into a holographic sensor. Multiple forms of 2-APB, resulting from the neighbouring effect of the amido group with the boronic acid through an intramolecular B--O-coordinated interaction, were shown to exist in solution by using multinuclear NMR spectrometry. It was found that 2-APB predominantly adopts a zwitterionic tetrahedral form at physiological pH values. The complex formation of 2-APB with glucose and lactate was investigated in DMSO; 2-APB favours binding with glucose rather than lactate and generates a five-membered-ring complex. Furthermore, a 2-APB-based holographic sensor displayed a significant response to glucose with little interference from lactate, and with no dependence on pH in the physiological pH range. These features suggest that the new ligand 2-APB is a potential candidate for the development of glucose-selective sensors.

Cp*Rh-Based Indicator-Displacement Assays for the Identification of Amino Sugars and Aminoglycosides

Indicator-displacement assays based on the organometallic complex [{Cp*RhCl2}2] (Cp*=pentamethylcyclopentadienyl) and the dye gallocyanine were used to sense amino sugars and aminoglycosides in buffered aqueous solution by conducting UV-visible spectroscopy. The data of three assays at pH 7.0, 8.0, and 9.0 were sufficient to distinguish between the amino sugars galactosamine, glucosamine, mannosamine and the aminoglycosides kanamycin A, kanamycin B, amikacin, apramycin, paromomycin, and streptomycin. Furthermore, the assays were used to characterize mixtures of aminoglycosides and obtain quantitative information about the respective analytes.

Self-Assembled Fluorescent Chemosensors

Self-assembling and self-organizing methodologies are powerful tools for the "bottom-up" approach for the realization of complex structure with functional properties. Recently, this concept has been extended to the design of fluorescent chemosensors providing new exciting potentialities for the development of innovative sensing systems. This Concept Article deals mainly with this new approach and discusses its evolution, applications, and limitations.