Specific Recognition Events Research Articles

Overview of the Design and Application of Photothermal Immunoassays.

Developing powerful immunoassays for sensitive and real-time detection of targets has always been a challenging task. Due to their advantages of direct readout, controllable sensing, and low background interference, photothermal immunoassays have become a type of new technology that can be used for various applications such as disease diagnosis, environmental monitoring, and food safety. By modification with antibodies, photothermal materials can induce temperature changes by converting light energy into heat, thereby reporting specific target recognition events. This article reviews the design and application of photothermal immunoassays based on different photothermal materials, including noble metal nanomaterials, carbon-based nanomaterials, two-dimensional nanomaterials, metal oxide and sulfide nanomaterials, Prussian blue nanoparticles, small organic molecules, polymers, etc. It pays special attention to the role of photothermal materials and the working principle of various immunoassays. Additionally, the challenges and prospects for future development of photothermal immunoassays are briefly discussed.

From Gene-for-Gene to Resistosomes: Flor's Enduring Legacy.

The gene-for-gene model proposed by H. H. Flor has been one of the fundamental precepts of plant-pathogen interactions that has underpinned decades of research towards our current concepts of plant immunity. The broad validity of this model as an elegant and accurate genetic description of specific recognition events between the products of plant resistance (R) and pathogen avirulence (Avr) genes has been demonstrated many times over in a wide variety of plant disease systems. In recent years detailed molecular and structural analyses have provided a deep understanding of the principles by which plant immune receptors recognize pathogen effectors, including providing molecular descriptions of many of the genetic loci in flax and flax rust characterized by Flor. Recent advances in molecular and structural understanding of immune receptor recognition and activation mechanisms have brought the field to a new level, where rational design of novel receptors through engineering approaches is becoming a realizable goal. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

MOF-derived magnetic trimetallic oxide-carbon nanocomposites for modification-free and dual molecular events-dependent ratiometric electrochemical analysis of intracellular glutathione

The response of ratiometric electrochemical signals toward the targets of interest generally depends on specific molecules-mediated single molecular recognition event, which limits the application in analyzing the targets without specific recognition molecules. In this work, novel dual molecular recognition events were proposed for rapid and reliable electrochemical analysis of glutathione (GSH) using MOF-derived trimetallic oxide-carbon (Fe3O4/CuO/NiO-C) nanocomposites. The binding of GSH to CuO caused a decrease in the oxidation signal of Cu(Ⅱ) due to the formation of nonelectroactive complex, while NiO could electrocatalyze the oxidation of GSH. These GSH-involved dual molecular recognition events guaranteed the readout of ratiometric electrochemical signals with a complementary response range, allowing sensitive and wide-range analysis of GSH. Besides, the difference in spatial conformation gave rise to a different oxidation potential for different biothiols, which guaranteed selective analysis of GSH. The presence of Fe3O4 allowed modification-free detection within 5 min using a magnetic working electrode. Taking advantage of these merits, the developed electrochemical sensor could rapidly and reliably monitor the intracellular GSH.

Exploring Zr-based Metal-Organic Frameworks as Smart Electrochromic Sensors by Coordination-Driven Surface Engineering.

As emerging stimuli-responsive materials, electrochromic metal-organic frameworks (MOFs) are still not utilized in sensing applications due to difficulties in water stability, facile synthesis and functionalization, and efficient translation of specific recognition events. Here, we firstly find that a Zr-based MOF furnished with postsynthetically created viologen-like electron-deficient moiety was electrochromic active. With a coordination-driven surface engineering strategy where phosphate-containing biomolecules are tethered to Zr nodes of the MOF, fine tuning the interface electron transfer was readily achieved, thus benefitting for constructing smart electrochromic sensors through the combination of the sensitivity of electrochemistry with the visuality of colorimetry. Particularly, MOF-coated conductive films enabled label-free detection of phosphoproteins, and aptamer-functionalized ones responded specifically to the target. In two cases distinct color changes allow for visual quantification. This study represents the first example of MOF-based electrochromic sensors developed by an efficient strategy, indicating the generality to electrochromic counterparts for various sensing applications.

Analyte Sensing with Catalytic Micromotors

Catalytic micromotors can be used to detect molecules of interest in several ways. The straightforward approach is to use such motors as sensors of their "fuel" (i.e., of the species consumed for self-propulsion). Another way is in the detection of species which are not fuel but still modulate the catalytic processes facilitating self-propulsion. Both of these require analysis of the motion of the micromotors because the speed (or the diffusion coefficient) of the micromotors is the analytical signal. Alternatively, catalytic micromotors can be used as the means to enhance mass transport, and thus increase the probability of specific recognition events in the sample. This latter approach is based on "classic" (e.g., electrochemical) analytical signals and does not require an analysis of the motion of the micromotors. Together with a discussion of the current limitations faced by sensing concepts based on the speed (or diffusion coefficient) of catalytic micromotors, we review the findings of the studies devoted to the analytical performances of catalytic micromotor sensors. We conclude that the qualitative (rather than quantitative) analysis of small samples, in resource poor environments, is the most promising niche for the catalytic micromotors in analytical chemistry.

Protein-activated and FRET enhanced excited-state intermolecular proton transfer fluorescent probes for high-resolution imaging of cilia and tunneling nanotubes in live cells

Excited-state intermolecular proton transfer (inter-ESPT) fluorescent probes responsive to specific bioactive molecules should be greatly promising for protein sensing, DNA mutation simulating and cellular process regulating. However, the inter-ESPT molecules are recessive ESPT fluorophores, which need the assistance of other molecules with both hydrogen-bond accepting and donating abilities to turn on the tautomeric fluorescence. Valid design strategies to create powerful inter-ESPT fluorescent probes are poorly developed, particularly for proteins as targets. We recently reported a unique supramolecular strategy to trigger the inter-ESPT process based on the probe-protein recognition by H-bonding and to image protein-based subcellular structures in live cells. Herein, we found that our inter-ESPT probes (inter-ESPT-01) bearing a 2-amino-3-cyanopyridine scaffold can anchor proteins and light up the “invisible” ESPT state, so as to image the proteins or the protein-based subcellular organelles. More importantly, the inter-ESPT emission of inter-ESPT-01 can be significantly enhanced by the FRET process between amino and imino tautomers, endowing the inter-ESPT-01 probes with super-bright tautomeric fluorescence. The expressed proteins Ecallantide and MarTX were selected as the models to light up the inter-ESPT fluorescence of the probes and revealed that the inter-ESPT process can be triggered by the specific probe-protein recognition events. In the use of the super-bright inter-ESPT fluorescence, not only the proteins, but also the protein-based cilia and tunneling nanotubes (TNTs) can be specifically visualized in living cancer cells. Furthermore, such recognition-driven strategy allows us to construct a unique inter-ESPT probe to track and image specific endogenous proteins in live cells, highlighting the potential of inter-ESPT fluorogens as novel intelligent biomaterials.

Amplifying the Sensitivity of Polydiacetylene Sensors: The Dummy Molecule Approach.

There is an increasing need for fast and accurate assessment of various health conditions, where polydiacetylenes (PDA), having unique stress-sensitive optical properties, have great potential. When the conjugated backbone of PDA is disturbed by steric repulsion between the receptor-target complexes formed at the PDA surface via specific recognition events, the bandgap of PDA increases and produces color change and fluorescent emission as a dual sensory signal. However, this detection mechanism suggests an intrinsic sensitivity limit of PDA platform because unless adjacent receptors are occupied by target molecules no signal is anticipated. A novel approach to improve the sensitivity and limit of detection of PDA sensors has been developed by preoccupying the surface of PDA liposomes with an optimized amount of artificial target molecules named as dummy molecules. The sensitivity and limit of detection (LOD) showed large improvement by the surface-bound dummy molecules. In addition, the dummy strategy was synergically integrated with another sensitivity enhancing method with a different working mechanism in a PDA sensor for Neomycin detection. When optimized, the LOD of the PDA sensor was improved to 7 nM from 80 nM of the control and the signal intensity increased consistently throughout the entire tested concentration range of the target Neomycin. Finally, the general applicability of the dummy strategy to other target molecules was successfully confirmed by implementing the dummy strategy in a PDA sensor for Surfactin detection.

Nanophysical Mapping of Inflammasome Activation by Nanoparticles via Specific Cell Surface Recognition Events.

Silica nanoparticles (SiNP) trigger a range of innate immune responses in relevant essential organs, such as the liver and the lungs. Inflammatory reactions, including NLRP3 inflammasome activation, have been linked to particulate materials; however, the molecular mechanisms and key actors remain elusive. Although many receptors, including several scavenger receptors, were suggested to participate in SiNP cellular uptake, mechanistic evidence of their role on innate immunity is lacking. Here we present an atomic force microscopy-based approach to physico-mechanically map the specific interaction occurring between nanoparticles and scavenger receptor A1 (SRA1) in vitro on living lung epithelial cells. We find that SiNP recognition by SRA1 on human macrophages plays a key role in mediating NLRP3 inflammasome activation, and we identify cellular mechanical changes as clear indicators of inflammasome activation in human macrophages, greatly advancing our knowledge on the interplay among nanomaterials and innate immunity.

Adamantane Containing Peptidoglycan Fragments Enhance RANTES and IL-6 Production in Lipopolysaccharide-Induced Macrophages.

We report the enhancement of the lipopolysaccharide-induced immune response by adamantane containing peptidoglycan fragments in vitro. The immune stimulation was detected by Il-6 (interleukine 6) and RANTES (regulated on activation, normal T cell expressed and secreted) chemokine expression using cell assays on immortalized mouse bone-marrow derived macrophages. The most active compound was a α-D-mannosyl derivative of an adamantylated tripeptide with L-chirality at the adamantyl group attachment, whereby the mannose moiety assumed to target mannose receptors expressed on macrophage cell surfaces. The immune co-stimulatory effect was also influenced by the configuration of the adamantyl center, revealing the importance of specific molecular recognition event taking place with its receptor. The immunostimulating activities of these compounds were further enhanced upon their incorporation into lipid bilayers, which is likely related to the presence of the adamantyl group that helps anchor the peptidoglycan fragment into lipid nanoparticles. We concluded that the proposed adamantane containing peptidoglycan fragments act as co-stimulatory agents and are also suitable for the preparation of lipid nanoparticle-based delivery of peptidoglycan fragments.

Cell Surface Receptor Identification Using Genome-Scale CRISPR/Cas9 Genetic Screens.

Intercellular communication mediated by direct interactions between membrane-embedded cell surface receptors is crucial for the normal development and functioning of multicellular organisms. Detecting these interactions remains technically challenging, however. This manuscript describes a systematic genome-scale CRISPR/Cas9 knockout genetic screening approach that reveals cellular pathways required for specific cell surface recognition events. This assay utilizes recombinant proteins produced in a mammalian protein expression system as avid binding probes to identify interaction partners in a cell-based genetic screen. This method can be used to identify the genes necessary for cell surface interactions detected by recombinant binding probes corresponding to the ectodomains of membrane-embedded receptors. Importantly, given the genome-scale nature of this approach, it also has the advantage of not only identifying the direct receptor but also the cellular components that are required for the presentation of the receptor at the cell surface, thereby providing valuable insights into the biology of the receptor.

Signal amplification based on tannic acid-assisted cyclic conversion of Fe(III)/Fe(II) for ultrasensitive electrochemical immunoassay of CA 12-5

A signal amplification protocol based on tannic acid (TA)-assisted cyclic conversion of Fe(III)/Fe(II) was designed for highly sensitive immunoassay of carbohydrate antigen 12-5 (CA12-5). Initially, graphene oxide-methylene blue (GO-MB) and ionic liquid functionalized reduced graphene oxide-Au (IL-rGO-Au) composite were sequentially covered on the surface of electrode as stable signal substrate. The labeling antibody/Au-reduced graphene oxide/zeolitic imidazolate framework-metal polyphenol network (Ab2/Au-rGO/ZIF-MPN) as novel probe was prepared by firstly coating TA on ZIF-8 to form ZIF-TA, then adsorbing a certain amount of Fe(III) to form intense metal polyphenol network (MPN) as the coating of probe on account of combination of TA and Fe(III), finally adsorbing Au-rGO composite on ZIF-MPN for immobilization of Ab2. In the existence of target CA12-5, a sandwiched electrochemical immunosensor was successfully constructed via specific recognition events between antigen and antibody. With acidic H2O2 stimulation, the coating of probe was cracked into TA and Fe(III), then TA reduced Fe(III) into Fe(II) with significant catalytic capacity, which reacted with H2O2 to activate Fenton reaction and meanwhile produced Fe(III) and hydroxyl radicals (·OH). Subsequently, the gained Fe(III) was reduced to Fe(II) again by TA, forming the cyclic conversion of Fe(III)/Fe(II) to produce adequate ·OH for degradation of MB. The tactic averted the employment of vulnerable enzymes and noble metal materials, meanwhile achieving conspicuous assay performance with a linear range from 0.00005–500 U mL−1 and ultralow detection limit of 2.3 × 10−3 mU mL−1 under optimal conditions.

Highly Sensitive Colorimetric Detection of a Variety of Analytes via the Tyndall Effect

This work initially reports the use of a quite familiar optical phenomenon of colloidal solutions, namely, the Tyndall Effect (TE) as signal readout for highly sensitive colorimetric chemical and biological analysis. Taking gold nanoparticles (GNPs) as a model colloid, the TE-inspired assay (TEA) is developed based on the conversion of a specific recognition event (e.g., the aptamer-analyte binding) into the aggregation of GNPs, leading to a significant TE enhancement. In the TEA, a cheap laser pointer pen is used as a hand-held light source, while a smartphone serves as a portable quantitative reader. The results show that the TE signaling strategy achieves a ∼1000-fold sensitivity improvement compared with the most common surface plasmon resonance signaling method using GNPs. The utility of the TEA is well demonstrated with the inexpensive, rapid, and portable detection of trace levels of analytes ranging from an important small-molecule drug (cocaine, ∼1.5 pM detection limit) to a protein biomarker (interferon-γ, ∼2.2 fM detection limit) and a toxic metal ion (Ag+, ∼1.4 nM detection limit). In addition, as the TE enhancement simply stems from the aggregation of either bare (unmodified) or modified GNPs, the TEA is universally applicable to almost all of the existing GNP-based liquid-phase colorimetric assays. The TEA method developed herein lights a new way for equipment-free point-of-care analysis in various fields including medical diagnosis, food safety evaluation, and environmental monitoring, especially in the resource-poor areas of the world.

Construction of Cell–Extracellular Matrix Microenvironments by Conjugating ECM Proteins on Supported Lipid Bilayers

The cell membrane is an organized and fluid structure that modulates cellular activities in response to specific extracellular signals, and maintains the critical communication, integration and homeostasis between the cytosol and the extracellular matrix (ECM). In recent years, tissue engineering and cell biology research has been rapidly progressed by a remarkable understanding of cell and ECM interfaces. In this review, the design of new biomimetic platforms based on the conjugation of ECM proteins on solid supported lipid bilayers (SLBs) will be summarized. The platforms provide a better system to evaluate cellular responses to specific recognition events, gradient, mechanical property, nanostructures, and inter- and intra-molecular interactions of ECM proteins on a nonfouling and fluid membrane. Moreover, the findings from the molecular interactions and cellular activities will be highlighted to look into the cell-materials mechanisms.

Organization of motor pools depends on the combined function of N-cadherin and type II cadherins.

Type I and type II classical cadherins constitute a family of cell adhesion molecules expressed in complex combinatorial profiles in the nervous system, suggesting that a cadherin code implements specific adhesive recognition events that control the development of neural circuits. In the spinal cord, classical cadherins define at a molecular level the positional organization of motor neuron subtypes into discrete nuclear structures termed motor pools. However, the roles and contributions of different members of the family in defining motor neuron spatial organization are not yet clear. By combining mouse genetics with quantitative positional analysis, we found that motor neuron organization into pools depends on type II cadherins. Type II cadherin function, however, does not strictly reflect the predictions arising from binding specificities at a molecular level, but instead relies on N-cadherin, a type I cadherin whose elimination is required to reveal type II contributions.

A colorimetric aptasensor for the antibiotics oxytetracycline and kanamycin based on the use of magnetic beads and gold nanoparticles.

An aptamer based assay is presented for the determination of the antibiotics oxytetracycline (OTC) and kanamycin (KAN). Magnetic beads were applied for separation, and gold nanoparticles (AuNPs) for signal amplification. DNA aptamers against OTC and KAN were firstly designed. After specific recognition events, the aptamer sequences were released from the surface of magnetic beads and the remaining DNA probes captured horseradish peroxidase (HRP) modified AuNPs. Subsequently, 3,3',5,5'-tetramethylbenzidine and o-phenylenediamine are catalytically oxidized by HRP, and the generated colorimetric responses can reflect the concentrations of OTC (at 370nm) and KAN (at 450nm), respectively. Experimental results demonstrate that the method is highly sensitive with the detection limit as low as 1 ag mL-1 for OTC and KAN. An extremely wide linear range (over 11 orders of magnitude) is achieved. The high selectivity is attributed to the high affinity between aptamer and the substrate. The results of real sample tests also verify that the method is promising for antibiotics analysis in the applications of food monitoring and clinical diagnosis. Graphical abstract Schematic presentation of a colorimetric assay for antibiotics based on aptamer-modified magnetic beads and horseradish peroxidase modified gold nanoparticles. Colorimetric responses result from the enzymatic oxidation of 3,3',5,5'-tetramethylbenzidine (TMB) and o-phenylenediamine (OPD), respectively.

Glycans as Modulators of Plant Defense Against Filamentous Pathogens.

Plants and microbes utilize glycoconjugates as structural entities, energy reserves for cellular processes, and components of cellular recognition or binding events. The structural heterogeneity of carbohydrates in such systems is a result of the ability of the carbohydrate biosynthetic enzymes to reorient sugar monomers in a variety of forms, generating highly complex, linear, branched, or hierarchical structures. During the interaction between plants and their microbial pathogens, the microbial cell surface glycans, cell wall derived glycans, and glycoproteins stimulate the signaling cascades of plant immune responses, through a series of specific or broad spectrum recognition events. The microbial glycan-induced plant immune responses and the downstream modifications observed in host-plant glycan structures that combat the microbial attack have garnered immense interest among scientists in recent times. This has been enabled by technological advancements in the field of glycobiology, making it possible to study the ongoing co-evolution of the microbial and the corresponding host glycan structures, in greater detail. The new glycan analogs emerging in this evolutionary arms race brings about a fresh perspective to our understanding of plant–pathogen interactions. This review discusses the role of diverse classes of glycans and their derivatives including simple sugars, oligosaccharides, glycoproteins, and glycolipids in relation to the activation of classical Pattern-Triggered Immunity (PTI) and Effector-Triggered Immunity (ETI) defense responses in plants. While primarily encompassing the biological roles of glycans in modulating plant defense responses, this review categorizes glycans based on their structure, thereby enabling parallels to be drawn to other areas of glycobiology. Further, we examine how these molecules are currently being used to develop new bio-active molecules, potent as priming agents to stimulate plant defense response and as templates for designing environmentally friendly foliar sprays for plant protection.

Genome-scale identification of cellular pathways required for cell surface recognition

Interactions mediated by cell surface receptors initiate important instructive signaling cues but can be difficult to detect in biochemical assays because they are often highly transient and membrane-embedded receptors are difficult to solubilize in their native conformation. Here, we address these biochemical challenges by using a genome-scale, cell-based genetic screening approach using CRISPR gene knockout technology to identify cellular pathways required for specific cell surface recognition events. By using high-affinity monoclonal antibodies and low-affinity ligands, we determined the necessary screening parameters, including the importance of establishing binding contributions from the glycocalyx, that permitted the unequivocal identification of genes encoding directly interacting membrane-embedded receptors with high statistical confidence. Importantly, we show that this genome-wide screening approach additionally identified receptor-specific pathways that are required for functional display of receptors on the cell surface that included chaperones, enzymes that add post-translational modifications, trafficking proteins, and transcription factors. Finally, we demonstrate the utility of the approach by identifying IGF2R (insulin like growth factor 2 receptor) as a binding partner for the R2 subunit of GABAB receptors. We show that this interaction is direct and is critically dependent on mannose-6-phosphate, providing a mechanism for the internalization and regulation of GABAB receptor signaling. We conclude that this single approach can reveal both the molecular nature and the genetic pathways required for functional cell surface display of receptors recognized by antibodies, secreted proteins, and membrane-embedded ligands without the need to make any prior assumptions regarding their biochemical properties.

Synergy of Two Highly Specific Biomolecular Recognition Events: Aligning an AT-Hook Peptide in DNA Minor Grooves via Covalent Conjugation to 2'-Amino-LNA.

Two highly specific biomolecular recognition events, nucleic acid duplex hybridization and DNA-peptide recognition in the minor groove, were coalesced in a miniature ensemble for the first time by covalently attaching a natural AT-hook peptide motif to nucleic acid duplexes via a 2'-amino-LNA scaffold. A combination of molecular dynamics simulations and ultraviolet thermal denaturation studies revealed high sequence-specific affinity of the peptide-oligonucleotide conjugates (POCs) when binding to complementary DNA strands, leveraging the bioinformation encrypted in the minor groove of DNA duplexes. The significant cooperative DNA duplex stabilization may pave the way toward further development of POCs with enhanced affinity and selectivity toward target sequences carrying peptide-binding genetic islands.

Bifunctional polydopamine thin film coated zinc oxide nanorods for label-free photoelectrochemical immunoassay

Photoelectrochemical (PEC) detection is a promising method for label-free immunoassay by reporting the specific biological recognition events with electrical signals. However, it is challenging to rationally incorporate immunosensing components with a photocurrent conversion interface, which generally necessitates multistep fabrication and careful tailoring of various components such as photoactive material and biological probe. For high detection reliability and reproducibility, it is highly desirable to rationally construct an efficient PEC interface with architecture as simple as possible. In this work, a novel yet simple PEC immunosensor based on bio-inspired polydopamine (PDA) thin film-coated zinc oxide (ZnO) nanorods was reported. In this PEC immunosensor, the PDA thin film serves simultaneously as a unique sensitizer for charge separation as well as a functional layer for probe antibody attachment. The photocurrent on this electrode under illumination decreases upon the immunoreaction on the surface, possibly due to the blocking effect of formed immunocomplexes on the access of reducing reagent to the photoelectrode, thus offering a simple and reliable platform for PEC label-free immunoassay. By using an antibody-antigen pair as a model, successful label-free immunoassay was achieved with a detection limit of 10pgmL−1 and a dynamic range from 100pgmL−1 to 500ngmL−1. This work demonstrates intriguing electro-optical property and bioconjugation activity of PDA film and may pave the way toward advanced PEC immunoassays.

Multi-target pharmacology: possibilities and limitations of the "skeleton key approach" from a medicinal chemist perspective.

Multi-target drugs have raised considerable interest in the last decade owing to their advantages in the treatment of complex diseases and health conditions linked to drug resistance issues. Prospective drug repositioning to treat comorbid conditions is an additional, overlooked application of multi-target ligands. While medicinal chemists usually rely on some version of the lock and key paradigm to design novel therapeutics, modern pharmacology recognizes that the mid- and long-term effects of a given drug on a biological system may depend not only on the specific ligand-target recognition events but also on the influence of the repeated administration of a drug on the cell gene signature. The design of multi-target agents usually imposes challenging restrictions on the topology or flexibility of the candidate drugs, which are briefly discussed in the present article. Finally, computational strategies to approach the identification of novel multi-target agents are overviewed.