Specific Molecular Recognition Research Articles

Electrochemical Sensing of Bisphenol A on Facet-Tailored TiO2 Single Crystals Engineered by Inorganic-Framework Molecular Imprinting Sites.

Noble metals, nanostructured carbon, and their hybrids are widely used for electrochemical detection of persistent organic pollutants. However, despite of the rapid detection process and high accuracy, these materials generally suffer from high costs, metallic impurity, heterogeneity, irreversible adsorption and poor sensitivity. Herein, the high-energy {001}-exposed TiO2 single crystals with specific inorganic-framework molecular recognition ability was prepared as the electrode material to detect bisphenol A (BPA), a typical and widely present organic pollutant in the environment. The oxidation peak current was linearly correlated to the BPA concentration from 10.0 nM to 20.0 μM ( R2 = 0.9987), with a low detection limit of 3.0 nM (S/N = 3). Furthermore, it exhibited excellent discriminating ability, high anti-interference capacity, and good long-term stability. Its good performance for BPA detection in real environmental samples, including tap water, lake and river waters, domestic wastewater, and municipal sludge, was also demonstrated. This work extends the applications of TiO2 semiconductor and suggests that this material could be used as a highly active, stable, low-cost, and environmentally benign electrode material for electrochemical sensing.

Molecularly Imprinted Polymer as an Antibody Substitution in Pseudo-immunoassays for Chemical Contaminants in Food and Environmental Samples.

The chemical contaminants in food and the environment are quite harmful to food safety and human health. Rapid, accurate, and cheap detection can effectively control the potential risks derived from these chemical contaminants. Among all detection methods, the immunoassay based on the specific interaction of antibody-analyte is one of the most widely used techniques in the field. However, biological antibodies employed in the immunoassay usually cannot tolerate extreme conditions, resulting in an unstable state in both physical and chemical profiles. Molecularly imprinted polymers (MIPs) are a class of polymers with specific molecular recognition abilities, which are highly robust, showing excellent operational stability under a wide variety of conditions. Recently, MIPs have been used in biomimetic immunoassays for chemical contaminants as an antibody substitute in food and the environment. Here, we reviewed these applications of MIPs incorporated in different analytical platforms, such as enzyme-linked immunosorbent assay, fluorescent immunoassay, chemiluminescent immunoassay, electrochemical immunoassay, microfluidic paper-based immunoassay, and homogeneous immunoassay, and discussed current challenges and future trends in the use of MIPs in biomimetic immunoassays.

Imparting Designer Biorecognition Functionality to Metal–Organic Frameworks by a DNA‐Mediated Surface Engineering Strategy

Surface functionality is an essential component for processing and application of metal-organic frameworks (MOFs). A simple and cost-effective strategy for DNA-mediated surface engineering of zirconium-based nanoscale MOFs (NMOFs) is presented, capable of endowing them with specific molecular recognition properties and thus expanding their potential for applications in nanotechnology and biotechnology. It is shown that efficient immobilization of functional DNA on NMOFs can be achieved via surface coordination chemistry. With this strategy, it is demonstrated that such porphyrin-based NMOFs can be modified with a DNA aptamer for targeting specific cancer cells. Furthermore, the DNA-NMOFs can facilitate the delivery of therapeutic DNA (e.g., CpG) into cells for efficient recognition of endosomal Toll-like receptor 9 and subsequent enhanced immunostimulatory activity in vitro and in vivo. No apparent toxicity is observed with systemic delivery of the DNA-NMOFs in vivo. Overall, these results suggest that the strategy allows for surface functionalization of MOFs with different functional DNAs, extending the use of these materials to diverse applications in biosensor, bioimaging, and nanomedicine.

Function and Regulation of Phase-Separated Biological Condensates.

Achieving functional specificity while minimizing cost to fitness is a key constraint during evolution. Formation of biological condensates by liquid-liquid phase separation (LLPS) appears to serve as an important regulatory mechanism to generate moderate specificity in molecular recognition while maintaining a reasonable cost for fitness in terms of design complexity. Formation of biological condensates serves as a unique mechanism of molecular recognition achieving some level of specificity without a huge cost to fitness. Rapid formation of biological condensates in vivo induced by specific cellular or environmental triggers has been shown to be an important mechanism for increasing cellular fitness. Here we discuss the functions and regulation of biological condensates, especially those formed by LLPS, involving interactions between proteins and nucleic acids. These condensates are spatially isolated within the cytosol or nucleus and can facilitate specific biochemical functions under conditions such as stress. The misregulation of biological condensates resulting in nondynamic aggregates has been implicated in a number of diseases. Understanding the functional importance of biological condensates and their regulation opens doors for development of therapies targeting dysfunctional biological condensates, as well as spatiotemporal engineering of functions in cells.

Studies on the Synthesis of Vitamin D Analogs with Aromatic D-Ring.

Herein, we describe our studies on the synthesis of 1α,25-dihydroxyvitamin D3 analogs possessing a benzene ring replacing the natural 5-membered D-ring by the Wittig-Horner and dienyne approaches. A key feature is the synthesis of a Cr(CO)3-complexed previtamin D derivative that enables the construction of vitamin D analogs with aromatic D-ring through a thermal [1,7]-H sigmatropic shift. This study establishes the basis for the design of new vitamin D analogs containing aromatic D-ring, complexed or uncomplexed to Cr(CO)3 type moieties for specific molecular recognition and drug research and development.

Design of Glycopolymers Carrying Sialyl Oligosaccharides for Controlling the Interaction with the Influenza Virus.

We designed glycopolymers carrying sialyl oligosaccharides by "post-click" chemistry and evaluated the interaction with the influenza virus. The glycopolymer structures were synthesized in a well-controlled manner by reversible addition-fragmentation chain transfer polymerization and the Huisgen reaction. Acrylamide-type monomers were copolymerized to give hydrophilicity to the polymer backbones, and the hydrophilicity enabled the successful introduction of the oligosaccharides into the polymer backbones. The glycopolymers with different sugar densities and polymer lengths were designed for the interaction with hemagglutinin on the virus surface. The synthesized glycopolymers showed the specific molecular recognition against different types of influenza viruses depending on the sugar units (6'- or 3'-sialyllactose). The sugar density and the polymer length of the glycopolymers affected the interaction with the influenza virus. Inhibitory activity of the glycopolymer against virus infection was demonstrated.

Separation of chiral compounds using magnetic molecularly imprinted polymer nanoparticles as stationary phase by microchip capillary electrochromatography.

In this work, a simple and rapid approach was developed for separation and detection of chiral compounds based on a magnetic molecularly imprinted polymer modified poly(dimethylsiloxane) (PDMS) microchip coupled with electrochemical detection. Molecularly imprinted polymers were prepared employing Fe3 O4 nanoparticles (NPs) as the supporting substrate and norepinephrine as the functional monomer in the presence of template molecule in a weak alkaline solution. After extracting the embedded template molecules, Fe3 O4 @polynorepinephrine NPs (MIP-Fe3 O4 @PNE NPs) showed specific molecular recognition selectivity and high affinity towards the template molecule, which were then used as stationary phase of microchip capillary electrochromatography for chiral compounds separation. Mandelic acid and histidine enantiomers were used as model compounds to test the chiral stationary phase. By using R-mandelic acid as the template molecule, mandelic acid enantiomer was effectively separated and detected on the MIP-Fe3 O4 @PNE NPs modified PDMS microchip. Moreover, the successful separation of histidine enantiomers on the MIP-Fe3 O4 @PNE NPs modified microchip using L-histidine as template molecule was also achieved.

Molecular recognition of ternary complexes: a new dimension in the structure-guided design of chemical degraders.

Molecular glues and bivalent inducers of protein degradation (also known as PROTACs) represent a fascinating new modality in pharmacotherapeutics: the potential to knockdown previously thought ‘undruggable’ targets at sub-stoichiometric concentrations in ways not possible using conventional inhibitors. Mounting evidence suggests these chemical agents, in concert with their target proteins, can be modelled as three-body binding equilibria that can exhibit significant cooperativity as a result of specific ligand-induced molecular recognition. Despite this, many existing drug design and optimization regimens still fixate on binary target engagement, in part due to limited structural data on ternary complexes. Recent crystal structures of protein complexes mediated by degrader molecules, including the first PROTAC ternary complex, underscore the importance of protein–protein interactions and intramolecular contacts to the mode of action of this class of compounds. These discoveries have opened the door to a new paradigm for structure-guided drug design: borrowing surface area and molecular recognition from nature to elicit cellular signalling.

Crystallinity of Double-Stranded RNA-Antimicrobial Peptide Complexes Modulates Toll-Like Receptor 3-Mediated Inflammation.

Double-stranded RNA (dsRNA) induces production of pro-inflammatory cytokines in normal human epidermal keratinocytes (NHEK) by specific binding to endosomal Toll-like receptor-3 (TLR3). Recently, it has been shown that hyperactivation of TLR3 in psoriatic keratinocytes by dsRNA can occur in the presence of human antimicrobial peptide (AMP) LL37. Here, we combine synchrotron X-ray scattering, microscopy, computer simulations, and measurements of NHEK cytokine production to elucidate a previously unanticipated form of specific molecular pattern recognition. LL37 and similar α-helical AMPs can form pro-inflammatory nanocrystalline complexes with dsRNA that are recognized by TLR3 differently than dsRNA alone. dsRNA complexes that activate IL-6 production in NHEK and those that do not are both able to enter cells and co-localize with TLR3. However, the crystallinity of these AMP-dsRNA complexes, specifically the geometric spacing between parallel dsRNA and the repeat number of ordered dsRNA, strongly influences the level of TLR3 activation. Crystalline complexes that present dsRNA at a spacing that matches with the steric size of TLR3 can recruit and engage multiple TLR3 receptors, driving receptor clustering and immune amplification, whereas crystalline complexes that exhibit poor steric matching do not. Reverse-transcription quantitative PCR of IL-6 during siRNA knockdown of TLR3 confirms that cytokine production is due to TLR3: High levels of IL-6 transcription are observed for sterically matched complexes without TLR3 knockdown, whereas such activity is abrogated with TLR3 knockdown.

Molecular Transformations Using Bis(iodozincio)methane–The Role of Chelation in Main Group Organometallic Chemistry

Abstract The stereoselectivity for the addition of an organometallic reagent to an aldehyde or ketone possessing a Lewis basic atom at the α-position can be predicted according to the well-known Chelation Model. Herein we discuss stereoselective reactions of bis(iodozincio)methane, which can coordinate to a heteroatom containing substrate with two zinc atoms in the reagent. Zinc atom coordination in a face-to-face manner to the substrates containing two heteroatoms enables specific molecular recognition, realizing novel molecular transformations.

Ultrasensitive Capture, Detection, and Release of Circulating Tumor Cells Using a Nanochannel-Ion Channel Hybrid Coupled with Electrochemical Detection Technique.

With the growing demands of the early, accurate, and sensitive diagnosis for cancers, the development of new diagnostic technologies becomes increasingly important. In this study, we proposed a strategy for efficient capture and sensitive detection of circulating tumor cells (CTCs) using an array nanochannel-ion channel hybrid coupled with an electrochemical detection technique. The aptamer probe was immobilized on the ion channel surface to couple with the protein overexpressed on the CTCs membrane. Through this special molecular recognition, CTCs can be selectively captured. The trapped CTCs cover the ion channel entrance efficiently, which will dramatically block the ionic flow through channels, resulting in a varied mass-transfer property of the nanochannel-ion channel hybrid. On the basis of the changed mass-transfer properties, the captured CTCs can be sensitively detected using the electrochemical linear sweep voltammetry technique. Furthermore, due to the amplified response of array channels compared to that of a single channel, the detection sensitivity can be enhanced greatly. The results showed that acute leukemia CCRF-CEM (a type of CTC) concentration as low as 100 cells mL-1 can be successfully captured and detected. The present method provides a simple, sensitive, and label-free technique for CTCs capture, detection, and release, which would hold great potential in the early clinical diagnosis and treatment of cancers.

Modulating Supramolecular Peptide Hydrogel Viscoelasticity Using Biomolecular Recognition.

Self-assembled peptide-based hydrogels are emerging materials that have been exploited for wound healing, drug delivery, tissue engineering, and other applications. In comparison to synthetic polymer hydrogels, supramolecular peptide-based gels have advantages in biocompatibility, biodegradability, and ease of synthesis and modification. Modification of the emergent viscoelasticity of peptide hydrogels in a stimulus responsive fashion is a longstanding goal in the development of next-generation materials. In an effort to selectively modulate hydrogel viscoelasticity, we report herein a method to enhance the elasticity of β-sheet peptide hydrogels using specific molecular recognition events between functionalized hydrogel fibrils and biomolecules. Two distinct biomolecular recognition strategies are demonstrated: oligonucleotide Watson-Crick duplex formation between peptide nucleic acid (PNA) modified fibrils with a bridging oligonucleotide and protein-ligand recognition between mannose modified fibrils with concanavalin A. These methods to modulate hydrogel elasticity should be broadly adaptable in the context of these materials to a wide variety of molecular recognition partners.

Molecular Recognition‐Mediated Transformation of Single‐Chain Polymer Nanoparticles into Crosslinked Polymer Films

AbstractWe describe single‐chain polymer nanoparticles (SCNPs) possessing intramolecular dynamic covalent crosslinks that can transform into polymer films through a molecular recognition‐mediated crosslinking process. The SCNPs utilise molecular recognition with surface‐immobilised proteins to concentrate upon a substrate, bringing the SCNPs into close spatial proximity with one another and allowing their dynamic covalent crosslinkers to undergo intra‐ to interpolymer chain crosslinking leading to the formation of polymeric film. SCNPs must possess both the capacity for specific molecular recognition and a dynamic nature to their intramolecular crosslinkers to form polymer films, and an investigation of the initial phase of film formation indicates it proceeds from features which form upon the surface then grow predominantly in the xy directions. This approach to polymer film formation presents a potential method to “wrap” surfaces displaying molecular recognition motifs—which could potentially include viral, cellular and bacterial surfaces or artificial surfaces displaying multivalent recognition motifs—within a layer of polymer film.

Molecular Recognition-Mediated Transformation of Single-Chain Polymer Nanoparticles into Crosslinked Polymer Films.

We describe single‐chain polymer nanoparticles (SCNPs) possessing intramolecular dynamic covalent crosslinks that can transform into polymer films through a molecular recognition‐mediated crosslinking process. The SCNPs utilise molecular recognition with surface‐immobilised proteins to concentrate upon a substrate, bringing the SCNPs into close spatial proximity with one another and allowing their dynamic covalent crosslinkers to undergo intra‐ to interpolymer chain crosslinking leading to the formation of polymeric film. SCNPs must possess both the capacity for specific molecular recognition and a dynamic nature to their intramolecular crosslinkers to form polymer films, and an investigation of the initial phase of film formation indicates it proceeds from features which form upon the surface then grow predominantly in the xy directions. This approach to polymer film formation presents a potential method to “wrap” surfaces displaying molecular recognition motifs—which could potentially include viral, cellular and bacterial surfaces or artificial surfaces displaying multivalent recognition motifs—within a layer of polymer film.

Impedimetric detection of trinitrotoluene by using a glassy carbon electrode modified with a gold nanoparticle@fullerene composite and an aptamer-imprinted polydopamine

This study introduces a method based on a combination of aptasensing and molecular imprinting for highly sensitive detection of 2,4,6-trinitrotoluene (TNT). An amino-aptamer with inherent affinity for TNT was mixed with TNT prior to covalent attachement onto a glassy carbon electrode surface which was modified with a nanocomposite of the type gold nanoparticle@fullerene (AuNP@C60). Electropolymerization of dopamine around the aptamer/TNT complex entraps the complex and retains the aptamer. After removal of TNT, it is assumed that the MIP cavity acts synergistically with the embedded aptamer to form a nanohybrid receptor (aptamer-molecular imprinting polymer). This results in recognition properties superior to that of aptamer alone. Benefiting from the double specific molecular recognition property of molecular imprinting polymers and aptamers along with the in situ generation of AuNP onto the surface of the modified GCE leads to superb sensing properties. Properties such as lower limit of detection (3.5 attomolar) and wider linear concentration range of TNT (0.01 femtomolar to 1.5 μmol L−1) are distinctly better than other reported methods. In our perception, this strategy may be extended to various diagnostically relevent proteins using not only aptamers but also other affinity molecules such as affimers, antibody and peptide fragments.

Theoretical and experimental studies of ion imprinted polymer for nitrate detection

Molecular imprinting is an approach to synthesize receptors with specific molecular recognition properties. A computational method was carried out to study interaction between template and monomer in prepolymerization mixture. The functional monomer and template complexes were optimized, at the minimum energy confirmation using Austin Model 1 semi empirical method within Restricted Hartree Fock formalism. The theoretical results showed that allylthiourea (functional monomer) has the largest interaction energy towards template (sodium nitrate) with the mole ratio of 4 : 1; functional monomer : template. The resulting polymers were characterized using Fourier Transform infrared spectroscopy, thermogravimetry analysis and field emission scanning electron microscopy. Rebinding experiments were carried out to evaluate binding capacity of the polymer. The adsorption data of ion imprinted polymer (IIP) were fitted with Langmuir-Freundlich isotherm model. Pseudo-second order kinetic model was used to describe the kinetic adsorption behavior of IIP. The experimental binding result showed good agreement with theoretical computation and the IIP was further used for nitrate ion detection. The results of membrane optimization indicated that the sensor, which composed of 30% polyvinylchloride, 60% nitrophenyl octyl ether as a plasticizer, 2% sodium tetraphenyl borate, and 10% IIP as ionophore exhibited an almost Nernstian slope with the limit of detection 3.9 × 10-6 M. The fabricated sensor had shown good potential in nitrate detection with wide linear range, low limit of detection and found to have good selectivity towards nitrate ion over other anion.

Catch and Release: Engineered Allosterically Regulated β-Roll Peptides Enable On/Off Biomolecular Recognition.

Alternative scaffolds for biomolecular recognition are being developed to overcome some of the limitations associated with immunoglobulin domains. The repeat-in-toxin (RTX) domain is a repeat protein sequence that reversibly adopts the β-roll secondary structure motif specifically upon calcium binding. This conformational change was exploited for controlled biomolecular recognition. Using ribosome display, an RTX peptide library was selected to identify binders to a model protein, lysozyme, exclusively in the folded state of the peptide. Several mutants were identified with low micromolar dissociation constants. After concatenation of the mutants, a 500-fold increase in the overall affinity for lysozyme was achieved leading to a peptide with an apparent dissociation constant of 65 nM. This mutant was immobilized for affinity chromatography experiments, and the on/off nature of the molecular recognition was demonstrated as the target is captured from a mixture in the presence of calcium and is released in the absence of calcium as the RTX peptides lose their β-roll structure. This work presents the design of a new stimulus-responsive scaffold that can be used for environmentally responsive specific molecular recognition and self-assembly.

Water-compatible micron-sized monodisperse molecularly imprinted beads for selective extraction of five iridoid glycosides from Cornus officinalis fructus

An efficient, accurate and sensitive method for the determination of five iridoid glycosides (IGs) in Cornus officinalis fructus using molecularly imprinted solid phase extraction (MISPE) coupled with high performance liquid chromatography (HPLC) has been developed. Water-compatible molecularly imprinted beads (MIBs) were synthesized by precipitation polymerization, using alkenyl glycosides glucose as the hydrophilic functional monomer. Scanning electron microscopy showed that the MIBs had a narrow particle size distribution, with diameters in the range 7.5–9.3μm. The special molecular recognition by the MIBs of IGs in aqueous media was verified by static adsorption, kinetic adsorption, and selectivity experiments. The newly prepared MIBs were used as sorbents in solid phase extraction (SPE) for the selective recognition of five IGs (loganin, morroniside, loganic acid, 7-O-ethyl-morroniside and 7-O-methyl morroniside) in Cornus officinalis fructus. When optimized, the MISPE-HPLC method had good linearity (0.02–100mgg−1), with correlation coefficient (R)≥0.994. Recoveries at three spiked levels were in the range 80.0%–94.0%. Because of its excellent specificity and hydrophilicity, SPE based on monodisperse MIBs provides a promising pretreatment strategy for the analysis of active components in natural products, especially for the quality control of traditional Chinese medicines.

Interface-induced growth of boronate-based metal-organic framework membrane on porous carbon substrate for aqueous phase molecular recognition

For metal-organic frameworks (MOFs), introduction of special functional groups and integration on porous support will endow the MOF with specific molecular affinity and tunable membrane-like surface properties. Herein, we demonstrated a facile interface-induced Zn(II)-ligand-fragment co-assembly strategy to in situ fabricate boronate-based MOF membrane on hydrophobic porous carbon substrate for specific molecular recognition and separation. Due to the phenylboronic acid groups and hydrophobic porous carbon supporting layer, a catechol-containing medicinal natural flavone Luteolin was found to be efficiently and selectively recognized on the MOF composite in water-containing solution. As compared to the separated MOF particles and carbon substrate, the MOF composite exhibited similar adsorption kinetics but significant higher adsorption capacity in static separation. Dynamic separation also revealed that the MOF composite could achieve a desirable maximum adsorption capacity under mild separation condition, implying its applicability in industrial application. As a proof of this concept, a commercially available Luteolin with 85% purity could be easily extracted and concentrated to 99.90% purity by the MOF composite in highly aqueous solution, and the products possessed the similar antibacterial performance with standard substance. These results demonstrated that, a membrane-like functionalized MOF composite with enhanced surface hydrophobicity and improved molecular specificity has great potential for separation of industrial and even biological samples under water compatible conditions.

Catch-and-Release of Target Cells Using Aptamer-Conjugated Electroactive Zwitterionic Oligopeptide SAM

Nucleic acid aptamers possess attractive features such as specific molecular recognition, high-affinity binding, and rapid acquisition and replication, which could be feasible components for separating specific cells from other cell types. This study demonstrates that aptamers conjugated to an oligopeptide self-assembled monolayer (SAM) can be used to selectively trap human hepatic cancer cells from cell mixtures containing normal human hepatocytes or human fibroblasts. Molecular dynamics calculations have been performed to understand how the configurations of the aptamers are related to the experimental results of selective cell capture. We further demonstrate that the captured hepatic cancer cells can be detached and collected along with electrochemical desorption of the oligopeptide SAM, and by repeating these catch-and-release processes, target cells can be enriched. This combination of capture with aptamers and detachment with electrochemical reactions is a promising tool in various research fields ranging from basic cancer research to tissue engineering applications.