Targeted Protein Surface Sensors as a Tool for Analyzing Small Populations of Proteins in Biological Mixtures

A dynamic Eu(III)-macrocycle served as the turn-on fluorescent probe for distinguishing H2O from D2O

H2O and D2O are an important pair of analogues, and their high-efficient detections are closely related to fields of chemical industry, food processing, semiconductor, environmental monitoring, etc. Because of their extremely similar physical and chemical properties, H2O and D2O can be mutually soluble in any ratios, and it is generally thought that the discrimination of H2O and D2O is an enormous challenge. Herein, upon the fact that vibrational frequency of O-H is greater than O-D, we design a dynamic Eu(III)-macrocycle Eu-2a with two emitters which exhibits the imine bond breakage of macrocycle emitter H2L2a in H2O or D2O, resulting in the turn-on fluorescence of Eu(III) emitter. For their differential fluorescence sensing signals of Eu-2a on three emission bands (433, 500 and 615 nm), the statistical analysis method is employed to produce fully separated fingerprints and thus high-throughput discrimination of 13 common solvents, especially the H2O and D2O. Fluorescent titration experiments by instrumental or smartphone-based analysis method also prove the successful determination of proportional H2O/D2O mixtures together with the good sensitivity and wide linear response range. Moreover, this H2O-triggered fluorescent complex Eu-2a used as the fluorescence ink also shows its potential in information encryption application. This article must be a valuable reference for the areas of lanthanide-based luminescent material, multianalyte detection and information encryption.

Fluorescent Investigation of Proteins Using DNA-Synthetic Ligand Conjugates

The unfathomable role that fluorescence detection plays in the life sciences has prompted the development of countless fluorescent labels, sensors, and analytical techniques that can be used to detect and image proteins or investigate their properties. Motivated by the demand for simple-to-produce, modular, and versatile fluorescent tools to study proteins, many research groups have harnessed the advantages of oligodeoxynucleotides (ODNs) for scaffolding such probes. Tight control over the valency and position of protein binders and fluorescent dyes decorating the polynucleotide chain and the ability to predict molecular architectures through self-assembly, inherent solubility, and stability are, in a nutshell, the important properties of DNA probes. This paper reviews the progress in developing DNA-based, fluorescent sensors or labels that navigate toward their protein targets through small-molecule (SM) or peptide ligands. By describing the design, operating principles, and applications of such systems, we aim to highlight the versatility and modularity of this approach and the ability to use ODN-SM or ODN-peptide conjugates for various applications such as protein modification, labeling, and imaging, as well as for biomarker detection, protein surface characterization, and the investigation of multivalency.

Molecules that Generate Fingerprints: A New Class of Fluorescent Sensors for Chemical Biology, Medical Diagnosis, and Cryptography

ConspectusFluorescent molecular sensors, often referred to as "turn-on" or "turn-off" fluorescent probes, are synthetic agents that change their fluorescence signal in response to analyte binding. Although these sensors have become powerful analytical tools in a wide range of research fields, they are generally limited to detecting only one or a few analytes. Pattern-generating fluorescent probes, which can generate unique identification (ID) fingerprints for different analytes, have recently emerged as a new class of luminescent sensors that can address this limitation. A unique characteristic of these probes, termed ID-probes, is that they integrate the qualities of conventional small-molecule-based fluorescent sensors and cross-reactive sensor arrays (often referred to as chemical, optical, or electronic noses/tongues). On the one hand, ID-probes can discriminate between various analytes and their combinations, akin to array-based analytical devices. On the other hand, their minute size enables them to analyze small-volume samples, track dynamic changes in a single solution, and operate in the microscopic world, which the macroscopic arrays cannot access.Here, we describe the principles underlying the ID-probe technology, as well as provide an overview of different ID-probes that have been developed to date and the ways they can be applied to a wide range of research fields. We describe, for example, ID-probes that can identify combinations of protein biomarkers in biofluids and in living cells, screen for several protein inhibitors simultaneously, analyze the content of Aβ aggregates, as well as ensure the quality of small-molecule and biological drugs. These examples highlight the relevance of this technology to medical diagnosis, bioassay development, cell and chemical biology, and pharmaceutical quality assurance, among others. ID-probes that can authorize users and protect secret data are also presented and the mechanisms that enable them to hide (steganography), encrypt (cryptography), and prevent access to (password protection) information are discussed.The versatility of this technology is further demonstrated by describing two types of probes: unimolecular ID-probes and self-assembled ID-probes. Probes from the first type can operate inside living cells, be recycled, and their initial patterns can be more easily obtained in a reproducible manner. The second type of probes can be readily modified and optimized, allowing one to prepare various different probes from a much wider range of fluorescent reporters and supramolecular recognition elements. Taken together, these developments indicate that the ID-probe sensing methodology is generally applicable, and that such probes can better characterize analyte mixtures or process chemically encoded information than can the conventional fluorescent molecular sensors. We therefore hope that this review will inspire the development of new types of pattern-generating probes, which would extend the fluorescence molecular toolbox currently used in the analytical sciences.

Chemically programmable bacterial probes for the recognition of cell surface proteins

Common methods to label cell surface proteins (CSPs) involve the use of fluorescently modified antibodies (Abs) or small-molecule-based ligands. However, optimizing the labeling efficiency of such systems, for example, by modifying them with additional fluorophores or recognition elements, is challenging. Herein we show that effective labeling of CSPs overexpressed in cancer cells and tissues can be obtained with fluorescent probes based on chemically modified bacteria. The bacterial probes (B-probes) are generated by non-covalently linking a bacterial membrane protein to DNA duplexes appended with fluorophores and small-molecule binders of CSPs overexpressed in cancer cells. We show that B-probes are exceptionally simple to prepare and modify because they are generated from self-assembled and easily synthesized components, such as self-replicating bacterial scaffolds and DNA constructs that can be readily appended, at well-defined positions, with various types of dyes and CSP binders. This structural programmability enabled us to create B-probes that can label different types of cancer cells with distinct colors, as well as generate very bright B-probes in which the multiple dyes are spatially separated along the DNA scaffold to avoid self-quenching. This enhancement in the emission signal enabled us to label the cancer cells with greater sensitivity and follow the internalization of the B-probes into these cells. The potential to apply the design principles underlying B-probes in therapy or inhibitor screening is also discussed here.

General Method for Pesticide Recognition Using Albumin-Based Host-Guest Ensembles

The massive use of pesticides nowadays has led to serious consequences for the environment and public health. Fluorescence analytical methods for pesticides are particularly advantageous with respect to simplicity and portability; however, currently available fluorescence methods (enzyme-based assays and indicator displacement assays) with poor universality are only able to detect few specific pesticides (e.g., organophosphorus). Making use of the multiple flexible and asymmetrical binding sites in albumin, we herein report a set of multicolor albumin-based host-guest ensembles. These ensembles exhibit a universal but distinctive fluorescent response to most of the common pesticides and allow array-based identification of pesticides with high accuracy. Furthermore, the simplicity, portability, and visualization of this method enable on-site determination of pesticides in a practical setting. This albumin host strategy largely expands the toolbox of traditional indicator displacement assays (synthetic macrocycles as hosts), and we expect it to inspire a series of sensor designs for pesticide detection.

Carbon Quantum Dots Based Chemosensor Array for Monitoring Multiple Metal Ions

The simultaneous identification of multiple metal ions in water has attracted enormous research interest in the past few decades. We herein describe a novel method for multiple metal ion detection using a carbon quantum dots (CQDs)-based chemosensor array and the CQDs are functionalized with different amino acids (glutamine, histidine, arginine, lysine and proline), which act as sensing elements in the sensor array. Eleven metal ions are successfully identified by the designed chemosensor array, with 100% classification accuracy. Importantly, the proposed method allowed the quantitative prediction of the concentration of individual metal ions in the mixture with the aid of a support vector machine (SVM). The sensor array also enables the qualitative detection of unknown metal ions under the interference of tap water and local river water. Thus, the strategy provides a novel high-throughput approach for the identification of various analytes in complex systems.

Assessing changes in the expression levels of cell surface proteins with a turn-on fluorescent molecular probe

Tri-nitrilotriacetic acid (NTA)-based fluorescent probes were developed and used to image His-tagged-labelled outer membrane protein C (His-OmpC) in live Escherichia coli. One of these probes was designed to light up upon binding, which provided the means to assess changes in the His-OmpC expression levels by taking a simple fluorescence spectrum.

Visual sensing of multiple proteins based on three kinds of metal nanoparticles as sensor receptors

We propose a colorimetric sensing array consisting of 4-aminothiophenol (p-ATP)-modified gold nanoparticles (Au NPs), silver nanoparticles (Ag NPs), and core-shell Au@Ag nanocubes (Au@Ag NCs) as sensing elements to identify multiple proteins according to the diverse colorimetric response patterns. In the absence of proteins, the sensor element solution itself did not agglomerate. After interacting with six proteins (lysozyme (LZM), hemoglobin (HGB), peroxidase from horseradish (HRP), bovine liver from peroxidase (CAT), trypsin from bovin pancreas (TRY), and pepsin (PEP)), due to the different binding ability between the sensing elements and various proteins, the sensing array exhibits a unique pattern of colorimetric variations, linear discrimination analysis (LDA) was applied to analyze the pattern and produced a clustering map for a clearer differentiation of these proteins.

Glycoform Differentiation by a Targeted, Self-Assembled, Pattern-Generating Protein Surface Sensor

A method for generating targeted, pattern-generating, protein surface sensors via the self-assembly of modified oligodeoxynucleotides (ODNs) is described. The simplicity by which these systems can be created enabled the development of a sensor that can straightforwardly discriminate between distinct glycoform populations. By using this sensor to identify glycosylation states of a therapeutic protein, we demonstrate the diagnostic potential of this approach as well as the feasibility of integrating a wealth of supramolecular receptors and sensors into higher-order molecular analytical devices with advanced properties. For example, the facile device integration was used to attach the well-known anthracene-boronic acid (An-BA) probe to a biomimetic DNA scaffold and consequently, to use the unique photophysical properties of An-BA to improve glycoform differentiation. In addition, the noncovalent assembly enabled us to modify the sensor with a trinitrilotriacetic acid (tri-NTA)-Ni²⁺ complex, which endows it with selectivity toward a hexa-histidine tag (His-tag). The selective responses of the system to diverse His-tag-labeled proteins further demonstrate the potential applicability of such sensors and validate the mechanism underlying their function.

Application of Chemometrics in Biosensing: A Review

The field of biosensing is rapidly developing, and the number of novel sensor architectures and different sensing elements is growing fast. One of the most important features of all biosensors is their very high selectivity stemming from the use of bioreceptor recognition elements. The typical calibration of a biosensor requires simple univariate regression to relate a response value with an analyte concentration. Nevertheless, dealing with complex real-world sample matrices may sometimes lead to undesired interference effects from various components. This is where chemometric tools can do a good job in extracting relevant information, improving selectivity, circumventing a non-linearity in a response. This brief review aims to discuss the motivation for the application of chemometric tools in biosensing and provide some examples of such applications from the recent literature.

High-content and high-throughput identification of macrophage polarization phenotypes

Macrophages are plastic cells of the innate immune system that perform a wide range of immune- and homeostasis-related functions. Due to their plasticity, macrophages can polarize into a spectrum of activated phenotypes. Rapid identification of macrophage polarization states provides valuable information for drug discovery, toxicological screening, and immunotherapy evaluation. The complexity associated with macrophage activation limits the ability of current biomarker-based methods to rapidly identify unique activation states. In this study, we demonstrate the ability of a 2-element sensor array that provides an information-rich 5-channel output to successfully determine macrophage polarization phenotypes in a matter of minutes. The simple and robust sensor generates a high dimensional data array which enables accurate macrophage evaluations in standard cell lines and primary cells after cytokine treatment, as well as following exposure to a model disease environment.

Decorating bacteria with self-assembled synthetic receptors

The responses of cells to their surroundings are mediated by the binding of cell surface proteins (CSPs) to extracellular signals. Such processes are regulated via dynamic changes in the structure, composition, and expression levels of CSPs. In this study, we demonstrate the possibility of decorating bacteria with artificial, self-assembled receptors that imitate the dynamic features of CSPs. We show that the local concentration of these receptors on the bacterial membrane and their structure can be reversibly controlled using suitable chemical signals, in a way that resembles changes that occur with CSP expression levels or posttranslational modifications (PTMs), respectively. We also show that these modifications can endow the bacteria with programmable properties, akin to the way CSP responses can induce cellular functions. By programming the bacteria to glow, adhere to surfaces, or interact with proteins or mammalian cells, we demonstrate the potential to tailor such biomimetic systems for specific applications.

Cell surface proteins mediate the interactions between cells and their extracellular environment. Here the authors design synthetic biomemetic receptor-like sensors that facilitate programmable interactions between bacteria and their target.

Quantification of ERK Kinase Activity in Biological Samples Using Differential Sensing

The understanding of complex biological systems requires an ability to evaluate interacting networks of genes, proteins, and cellular reactions. Enabling technologies that support the rapid quantification of these networks will facilitate the development of biological models and help to identify treatment targets and to assess treatment plans. The biochemical process of protein phosphorylation, which underlies almost all aspects of cell signaling, is typically evaluated by immunoblotting procedures (Western blot) or more recently proteomics procedures, which provide qualitative estimates of the concentration of proteins and their modifications in cells. However, protein modifications are difficult to correlate with activity, and while immunoblotting and proteomics approaches have the potential to be quantitative, they require a complex series of steps that diminish reproducibility. Here, a complementary approach is presented that allows for the rapid quantification of a protein kinase activity in cell lysates and tumor samples. Using the activity of cellular ERK (extracellular signal-regulated kinase) as a test case, an array sensing approach that utilizes a library of differential peptide-based biosensors and chemometric tools was used to rapidly quantify nanograms of active ERK in micrograms of unfractionated cell lysates and tumor extracts. This approach has the potential both for high-throughput and for quantifying the activities of multiple protein kinases in a single biological sample. The critical advantages of this differential sensing approach over others are that it removes the need for the addition of exogenous inhibitors to suppress the activities of major off-target kinases and allows us to quantitate the amount of active kinase in tested samples rather than measuring the changes in its activity upon induction or inhibition.

Aggregation-induced emission based one-step “lighting up” sensor array for rapid protein identification

Based on the distinct fingerprint-like fluorescence responses generated by different electrostatic and hydrophobic interactions, a “lighting up” aggregation-induced emission (AIE) sensor array was developed for rapid protein discrimination.

A colorimetric sensor array for detection and discrimination of antioxidants based on Ag nanoshell deposition on gold nanoparticle surfaces

There is growing interest in developing a high-performance sensor array for detection and discrimination of antioxidants owing to their widespread use and essential role in the human body. The present work unveils a novel colorimetric sensor array for colorimetric discrimination of antioxidants based on the red, green, and blue alteration (ΔRGB) pattern recognition. In this sensor array, three concentrations of AgNO3 were used as sensing elements, and gold nanoparticles (AuNPs) were employed as a colorimetric probe. In the presence of antioxidants, the sensor array produces unique colorimetric response patterns for the discrimination of these antioxidants due to different reactivities between three different concentrations of AgNO3 and each antioxidant, leading to deposition of different quantities of Ag nanoshells on the surface of AuNPs, enabling an excellent discrimination of six antioxidants (catechin, epigallocatechin 3-gallate, epicatechin, epigallocatechin, epicatechin 3-gallate, and gallocatechin) at a 20 nM level, when linear discriminant analysis (LDA), hierarchical cluster analysis (HCA), centroid diagram, spidergram, and color contour profiles were smartly combined. Furthermore, different concentrations of antioxidants and binary antioxidant mixtures, even ternary mixtures, could also be discriminated with this sensor array. Finally, the sensor array was successfully used for the discrimination of antioxidants in serum samples, demonstrating its potential applications in the diagnosis of antioxidant-related diseases.

Simultaneous dual-colour tracking lipid droplets and lysosomes dynamics using a fluorescent probe

After entering a cell, most small molecule fluorescent probes are dispersed in the cytoplasm before they then accumulate in a specific organelle or subcellular zone. Molecules that can enter two or more organelles with high selectivity are all but unknown. In this work, we report a naphthalimide-based fluorescent probe, NIM-7, that allows lipid droplets and lysosomes to be labelled simultaneously and with high specificity. These subcellular entities can then be visualized readily through yellow and red fluorescence, using different excitation and detection channels. NIM-7 allows 3D imaging and quantitative visualizing of lipid droplets and lysosomes. It is also able to track simultaneously the movement of lipid droplets and lysosomes in real-time. We also report here that NIM-7 can be used to image both different cell lines and zebrafish embryos.

Nanozyme Sensor Arrays for Detecting Versatile Analytes from Small Molecules to Proteins and Cells

Nanozymes have emerged as promising alternatives to overcome the high cost and low stability of natural enzymes. Nanozymes with peroxidase-like activities have been studied to construct versatile biosensors by using specific biorecognition ligands (such as enzymes, antibodies, and aptamers) or molecularly imprinted polymers (MIPs). However, the use of bioligands compromises the high stability and low cost promise of nanozymes, while the MIPs may not be applicable to multiplex detection. To address these limitations, here we constructed the nanozyme sensor arrays based on peroxidase-like Pt, Ru, and Ir nanozymes. The cross-reactive nanozyme sensor arrays were successfully used for the detection of biothiols and proteins as well as the discrimination of cancer cells because of the differential nonspecific interactions between the components of the sensor arrays and the analytes. The usefulness of the nanozyme sensor arrays was further validated by the detection of blind unknown samples, where 28 of 30 biothiols and 42 of 45 proteins were correctly identified. Moreover, the practical application of the nanozyme sensor arrays was demonstrated by the successful discrimination of biothiols in serum and proteins in human urine.

Microarray Analysis of Oligosaccharide-Mediated Multivalent Carbohydrate-Protein Interactions and Their Heterogeneity

Carbohydrate-protein interactions (CPIs) are involved in a wide range of biological phenomena. Hence, the characterization and presentation of carbohydrate epitopes that closely mimic the natural environment is one of the long-term goals of glycosciences. Inspired by the multivalency, heterogeneity and nature of carbohydrate ligand-mediated interactions, we constructed a combinatorial library of mannose and galactose homo- and hetero-glycodendrons to study CPIs. Microarray analysis of these glycodendrons with a wide range of biologically important plant and animal lectins revealed that oligosaccharide structures and heterogeneity interact with each other to alter binding preferences.

Protein sensing and discrimination using highly functionalised ruthenium(ii) tris(bipyridyl) protein surface mimetics in an array format

Ruthenium(ii) tris(bipyridyl) protein surface mimetics are used in an array format to sense and discriminate proteins including therapeutically relevant targets, hDM2 and MCL-1, using linear discriminant analysis (LDA).

Protein recognition by a pattern-generating fluorescent molecular probe

Fluorescent molecular probes have become valuable tools in protein research; however, the current methods for using these probes are less suitable for analysing specific populations of proteins in their native environment. In this study, we address this gap by developing a unimolecular fluorescent probe that combines the properties of small-molecule-based probes and cross-reactive sensor arrays (the so-called chemical 'noses/tongues'). On the one hand, the probe can detect different proteins by generating unique identification (ID) patterns, akin to cross-reactive arrays. On the other hand, its unimolecular scaffold and selective binding enable this ID-generating probe to identify combinations of specific protein families within complex mixtures and to discriminate among isoforms in living cells, where macroscopic arrays cannot access. The ability to recycle the molecular device and use it to track several binding interactions simultaneously further demonstrates how this approach could expand the fluorescent toolbox currently used to detect and image proteins.

Specific Targeting of Melanotic Cells with Peptide Ligated Photosensitizers for Photodynamic Therapy

A strategy combining covalent conjugation of photosensitizers to a peptide ligand directed to the melanocortin 1 (MC1) receptor with the application of sequential LED light dosage at near-IR wavelengths was developed to achieve specific cytotoxicity to melanocytes and melanoma (MEL) with minimal collateral damage to surrounding cells such as keratinocytes (KER). The specific killing of melanotic cells by targeted photodynamic therapy (PDT) described in this study holds promise as a potentially effective adjuvant therapeutic method to control benign skin hyperpigmentation or superficial melanotic malignancy such as Lentigo Maligna Melanoma (LMM).

A Multi-Fluorescent DNA/Graphene Oxide Conjugate Sensor for Signature-Based Protein Discrimination

Signature-based protein sensing has recently emerged as a promising prospective alternative to conventional lock-and-key methods. However, most of the current examples require the measurement of optical signals from spatially-separated materials for the generation of signatures. Herein, we present a new approach for the construction of multi-fluorescent sensing systems with high accessibility and tunability, which allows generating protein fluorescent signatures from a single microplate well. This approach is based on conjugates between nano-graphene oxide (nGO) and three single-stranded DNAs (ssDNAs) that exhibit different sequences and fluorophores. Initially, the three fluorophore-modified ssDNAs were quenched simultaneously by binding to nGO. Subsequent addition of analyte proteins caused a partial recovery in fluorescent intensity of the individual ssDNAs. Based on this scheme, we have succeeded in acquiring fluorescence signatures unique to (i) ten proteins that differ with respect to pI and molecular weight and (ii) biochemical marker proteins in the presence of interferent human serum. Pattern-recognition methods demonstrated high levels of discrimination for this system. The high discriminatory power and simple format of this sensor system should enable an easy and fast evaluation of proteins and protein mixtures.

Near infrared fluorescent dual ligand functionalized Au NCs based multidimensional sensor array for pattern recognition of multiple proteins and serum discrimination

Here, a multidimensional sensor array capable of analyzing various proteins and discriminating between serums from different stages of breast cancer patients were developed based on six kinds of near infrared fluorescent dual ligand functionalized Au NCs (functionalized with different amino acids) as sensing receptors. These six kinds of different amino acids functionalized Au NCs were synthesized for the first time within 2h due to the direct donation of delocalized electrons of electron-rich atoms or groups of the ligands to the Au core. Based on this, ten proteins could be simultaneously and effectively discriminated by this "chemical nose/tongue" sensor array. Linear discrimination analysis (LDA) of the response patterns showed successful differentiation of the analytes at concentrations as low as 10nM with high identification accuracy. Isothermal titration calorimetry (ITC) experiment illustrates that Au NCs interacted with proteins mainly by hydrogen bonding and van der Waals forces. Furthermore, the greatest highlight of this sensor array is demonstrated by successfully discriminating between serums from different stages of breast cancer patients (early, middle and late) and healthy people, suggesting great potential for auxiliary diagnosis.

A multicoloured Au NCs based cross-reactive sensor array for discrimination of multiple proteins

An easily accessible and potentially powerful effective cross-reactive sensor array based on six kinds of fluorescent Au NCs for discriminating multiple proteins according to the diverse fluorescence intensity response patterns was developed.

Acquiring multiple signals along with the reaction time: improving recognition capability of a multidimensional colorimetric sensor array for sensitive protein detection

Signal changes along with catalytic reaction time improve the protein discrimination ability of the sensor array based on AuNP–DNA conjugates.

Rapid synthesis of nitrogen doped carbon dots and their application as a label free sensor array for simultaneous discrimination of multiple proteins

A label free sensor array for discriminating various proteins and distinguishing serums from rectal cancer patients, Alzheimer's disease patients and healthy people was developed by utilizing novel nitrogen doped carbon dots.

Discrimination of Metalloproteins by a Mini Sensor Array Based on Bispyrene Fluorophore/Surfactant Aggregate Ensembles

Fluorescent sensor arrays with pattern recognition ability have been widely used to detect and identify multiple chemically similar analytes. In the present work, two particular bispyrene fluorophores containing hydrophilic oligo(oxyethylene) spacer, 6 and 4, were synthesized, but one is with and the other is without cholesterol unit. Their ensembles with cationic surfactant (CTAB) assemblies realize multiple fluorescence responses to different metalloproteins, including hemoglobin, myoglobin, ferritin, cytochrome c, and alcohol dehydrogenase. The combination of fluorescence variation at monomer and excimer emission of the two binary sensor ensembles enables the mini sensor array to provide a specific fingerprint pattern to each metalloprotein. Linear discriminant analysis shows that the two-ensemble-sensor-based array could well discriminate the five tested metalloproteins. The present work realizes using a mini sensor array to accomplish discrimination of complex analytes like proteins. They also display a very high sensitivity to the tested metalloproteins with detection limits in the range of picomolar concentration.

Mimicking the Function of Signaling Proteins: Toward Artificial Signal Transduction Therapy

Signal transduction pathways, which control the response of cells to various environmental signals, are mediated by the function of signaling proteins that interact with each other and activate one other with high specificity. Synthetic agents that mimic the function of these proteins might therefore be used to generate unnatural signal transduction steps and consequently, alter the cell's function. We present guidelines for designing 'chemical transducers' that can induce artificial communication between native proteins. In addition, we present detailed protocols for synthesizing and testing a specific 'transducer', which can induce communication between two unrelated proteins: platelet-derived growth-factor (PDGF) and glutathione-S-transferase (GST). The way by which this unnatural PDGF-GST communication could be used to control the cleavage of an anticancer prodrug is also presented, indicating the potential for using such systems in 'artificial signal transduction therapy'. This work is intended to facilitate developing additional 'transducers' of this class, which may be used to mediate intracellular protein-protein communication and consequently, to induce artificial cell signaling pathways.

Protein-directed synthesis of highly monodispersed, spherical gold nanoparticles and their applications in multidimensional sensing

An in-situ reduction method has been reported to prepare gold nanoparticles (GNPs) of 40–110 nm by using the green reducing agents of proteins, which are activated by H₂O₂ and the superoxide anion (). The protein of collagen turns HAuCl₄ to the aqueous Au(I) ainions, which are further reduced by other proteins to be highly monodispersed and spherical GNPs of different sizes. The GNPs reduced by different proteins are found to be with the exposed {100} facets, the distinctive UV-vis absorption spectra and various colors (See Fig. 1). By means of extracting the color responses, such as red, green and blue (RGB) alterations, an in-situ reduction method-based multidimensional sensing platform is fabricated in the process of GNPs synthesis. Without further modification of GNPs, nine common proteins are found to be well detected and discriminated at different concentrations. Moreover, this sensing platform also demonstrates great potentials in qualitative and semiquantitative analysis on the individuals of these proteins with high sensitivity. Furthermore, the validation of this multidimensional sensing platform has been carried out by analysis on the spiked proteins in human urine and the target proteins in complex matrix (e.g. lysozyme in human tear).

A Miniaturized Therapeutic Chromophore for Multiple Metal Pollutant Sensing, Pathological Metal Diagnosis and Logical Computing

The efficacy of a miniaturized unimolecular analytic system is illustrated. The easily accessible therapeutic chromophore "temoporfin", which responds differentially to bound metals at multiple wavelengths of Q-band absorption using chemometric analysis, expeditiously detects and discriminates a wide range of metals regarded as priority pollutants in water and hence may also be used for diagnosis of medically relevant metals in human urine. The molecule was further investigated as an electronic logic device, e.g. keypad lock device, to authorize multiple highly secure chemical passwords for information protection.

Multicolor Quantum Dot-Based Chemical Nose for Rapid and Array-Free Differentiation of Multiple Proteins

Nanomaterial-based differential sensors (e.g., chemical nose) have shown great potential for identification of multiple proteins because of their modulatable recognition and transduction capability but with the limitation of array separation, single-channel read-out, and long incubation time. Here, we develop a multicolor quantum dot (QD)-based multichannel sensing platform for rapid identification of multiple proteins in an array-free format within 1 min. A protein-binding dye of bromophenol blue (BPB) is explored as an efficient reversible quencher of QDs, and the mixture of BPB with multicolor QDs may generate the quenched QD-BPB complexes. The addition of proteins will disrupt the QD-BPB complexes as a result of the competitive protein-BPB binding, inducing the separation of BPB from the QDs and the generation of distinct fluorescence patterns. The multicolor patterns may be collected at a single-wavelength excitation and differentiated by a linear discriminant analysis (LDA). This multichannel sensing platform allows for the discrimination of ten proteins and seven cell lines with the fastest response rate reported to date, holding great promise for rapid and high-throughput medical diagnostics.

Ratiometric fluorescence sensor arrays based on quantum dots for detection of proteins

Optical cross-reactive sensor arrays have recently been demonstrated as a powerful tool for high-throughput protein analysis.

Oligonucleotide-Based Mimetics of Hepatocyte Growth Factor

Oligonucleotide-based hepatocyte growth factor (HGF) mimetics are described. A DNA aptamer to Met, a cognate receptor for HGF, was shown to induce Met activation when used in dimer form. The most potent aptamer dimer, ss-0, which was composed solely of 100-mer single-stranded DNA, exhibited nanomolar potency. Aptamer ss-0 reproduced HGF-induced cellular behaviors, including migration and proliferation. The present work sheds light on oligonucleotides as a novel chemical entity for the design of growth factor mimetics.

A polyion complex sensor array for markerless and noninvasive identification of differentiated mesenchymal stem cells from human adipose tissue

Currently available methods for stem cell evaluation require both prior knowledge of specific markers and invasive cell lysis or staining, hampering the development of stem cell products with assured safety and quality. Here, we present a strategy using optical cross-reactive sensor arrays for markerless and noninvasive identification of differentiated stem cell lineages with common laboratory equipment. The sensor array consists of a library of polyion complexes (PICs) between anionic enzymes and synthetic poly(ethylene glycol)-modified polyamines, which can recognize "secretomic signatures" in cell culture supernatants. Due to the reversible nature of PIC formation, the incubation of diluted culture supernatants with PICs caused enzyme release through competitive interactions between the secreted molecules and the PICs, generating unique patterns of recovery in enzyme activity for individual cell types or lineages. Linear discriminant analysis of the patterns allowed not only normal/cancer cell discrimination but also lineage identification of osteogenic and adipogenic differentiation of human mesenchymal stem cells, therefore providing an effective way to characterize cultured cells in the fields of regenerative medicine, tissue engineering and cell biology.

Protein-Protein Communication and Enzyme Activation Mediated by a Synthetic Chemical Transducer

The design and function of a synthetic "chemical transducer" that can generate an unnatural communication channel between two proteins is described. Specifically, we show how this transducer enables platelet-derived growth factor to trigger (in vitro) the catalytic activity of glutathione-s-transferase (GST), which is not its natural enzyme partner. GST activity can be further controlled by adding specific oligonucleotides that switch the enzymatic reaction on and off. We also demonstrate that a molecular machine, which can regulate the function of an enzyme, could be used to change the way a prodrug is activated in a "programmable" manner.