Kinetic Assay of the Michael Addition‐Like Thiol–Ene Reaction and Insight into Protein Bioconjugation

The chemical modification of proteins is a valuable technique in understanding the functions, interactions, and dynamics of proteins. Reactivity and selectivity are key issues in current chemical modification of proteins. The Michael addition‐like thiol–ene reaction is a useful tool that can be used to tag proteins with high selectivity for the solvent‐exposed thiol groups of proteins. To obtain insight into the bioconjugation of proteins with this method, a kinetic analysis was performed. New vinyl‐substituted pyridine derivatives were designed and synthesized. The reactivity of these vinyl tags with L ‐cysteine was evaluated by UV absorption and high‐resolution NMR spectroscopy. The results show that protonation of pyridine plays a key role in the overall reaction rates. The kinetic parameters were assessed in protein modification. The different reactivities of these vinyl tags with solvent‐exposed cysteine is valuable information in the selective labeling of proteins with multiple functional groups.     

Covalently bonded aptamer‐functionalised magnetic mesoporous carbon for high‐efficiency chloramphenicol detection

A novel aptamer‐modified magnetic mesoporous carbon was prepared to develop a specific and sensitive magnetic solid‐phase extraction method through combination with ultra‐high performance liquid chromatography‐tandem mass spectrometry for the analysis chloramphenicol in complex samples. More specifically, the chloramphenicol aptamer‐modified Mg/Al layered double hydroxide magnetic mesoporous carbon was employed as a novel magnetic solid‐phase extraction sorbent for analyte enrichment and sample clean‐up. The extraction solvent, extraction time, desorption solvent, and desorption time were investigated. It was found that the mesoporous structure and aptamer‐based affinity interactions resulted in acceptable selective recognition and a good chemical stability toward trace amounts of chloramphenicol. Upon combination with the ultra‐high performance liquid chromatography‐tandem mass spectrometry technique, a specific and sensitive recognition method was developed with a low limit of detection (0.94 pmol/L, S/N = 3) for chloramphenicol analysis. The developed method was successfully employed for the determination of chloramphenicol in complex serum, milk powders, fish and chicken samples, giving recoveries of 87.0‐107% with relative standard deviations of 3.1‐9.7%.     

N‐Terminal Protein Modification by Substrate‐Activated Reverse Proteolysis

Although site‐specific incorporation of artificial functionalities into proteins is an important tool in both basic and applied research, it can be a major challenge to protein chemists. Enzymatic protein modification is an attractive goal due to the inherent regio‐ and stereoselectivity of enzymes, yet their specificity remains a problem. As a result of the intrinsic reversibility of enzymatic reactions, proteinases can in principle catalyze ligation reactions. While this makes them attractive tools for site‐specific protein bioconjugation, competing hydrolysis reactions limits their general use. Here we describe the design and application of a highly specific trypsin variant for the selective modification of N‐terminal residues of diverse proteins with various reagents. The modification proceeds quantitatively under native (aqueous) conditions. We show that the variant has a disordered zymogen‐like activation domain, effectively suppressing the hydrolysis reaction, which is converted to an active conformation in the presence of appropriate substrates.     

Ultrasensitive and Signal‐on Electrochemiluminescence Aptasensor Using the Multi‐tris(bipyridine)ruthenium(II)‐β‐cyclodextrin Complexes

An ultrasensitive and signal‐on electrochemiluminescence (ECL) aptasensor to detect target protein (thrombin or lysozyme) was developed using the host‐guest recognition between a metallocyclodextrin complex and single‐stranded DNA (ss‐DNA). The aptasensor uses both the photoactive properties of the metallocyclodextrins named multi‐tris(bipyridine)ruthenium(II)‐β‐cyclodextrin complexes and their specific recognition with ss‐DNA, which amplified the ECL signal without luminophore labeling. After investigating the ECL performance of different multi‐tris(bipyridine)ruthenium(II)‐β‐cyclodextrin (multi‐Ru‐β‐CD) complexes, tris‐tris(bipyridine)‐ruthenium(II)‐β‐cyclodextrin (tris(bpyRu)‐β‐CD) was selected as a suitable host molecule to construct an atasensor. First, double‐stranded DNA (ds‐DNA) formed by hybridization of the aptamer and its target DNA was attached to a glassy carbon electrode via coupling interaction, which showed low ECL intensity with 2‐(dibutylamino) ethanol (DBAE) as coreactant, because of the weak recognition between ds‐DNA and tris(bpyRu)‐β‐CD. Upon addition of the corresponding protein, the ECL intensity increased when target ss‐DNA was released because of the higher stability of the aptamer‐protein complex than the aptamer‐DNA one. A linear relationship was observed in the range of 0.01 pmol/L to 100 pmol/L between ECL intensity and the logarithm of thrombin concentrations with a limited detection of 8.5 fmol/L (S/N=3). Meanwhile, the measured concentration of lysozyme was from 0.05 pmol/L to 500 pmol/L and the detection limit was 33 fmol/L (S/N=3). The investigations of proteins in human serum samples were also performed to demonstrate the validity of detection in real clinical samples. The simplicity, high sensitivity and specificity of this aptasensor show great promise for practical applications in protein monitoring and disease diagnosis.     

An Aptamer Intrinsically Comprising 5‐Fluoro‐2′‐deoxyuridine for Targeted Chemotherapy

An aptamer specifically binding the interleukin‐6 receptor and intrinsically comprising multiple units of the nucleoside analogue 5‐fluoro‐2′‐deoxyuridine can exert a cytostatic effect direcly on certain cells presenting the receptor. Thus the modified aptamer fulfils the requirements for active drug targeting in an unprecedented manner. It can easily be synthesized in a single enzymatic step and it binds to a cell surface receptor that is conveyed into the lysosome. Upon degradation of the aptamer by intracellular nucleases the active drug is released within the targeted cells exclusively. In this way the aptamer acts as a prodrug meeting two major prerequisites of a drug delivery system: specific cell targeting and the controlled release of the drug triggered by an endogenous stimulus.     

Aptamer‐modified magnetic metal‐organic framework MIL‐101 for highly efficient and selective enrichment of ochratoxin A

A facile and efficient strategy is developed to modify aptamers on the surface of the magnetic metal‐organic framework MIL‐101 for the rapid magnetic solid‐phase extraction of ochratoxin A. To the best of our knowledge, this is the first attempt to create a robust aptamer‐modified magnetic MIL‐101 with covalent bonding for the magnetic separation and enrichment of ochratoxin A. The saturated adsorption of ochratoxin A by aptamer‐modified magnetic MIL‐101 was 7.9 times greater than that by magnetic metal‐organic framework MIL‐101 due to the former's high selective recognition as well as good stability. It could be used for extraction more than 12 times with no significant changes in the extraction efficiency. An aptamer‐modified magnetic MIL‐101‐based method of magnetic solid‐phase extraction combined with ultra high performance liquid chromatography with tandem mass spectrometry was developed for the determination of trace ochratoxin A with limit of detection of 0.067 ng/L. Ochratoxin A of 4.53–13.7 ng/kg was determined in corn and peanut samples. The recoveries were in the range 82.8–108% with a relative standard deviation (n = 5) of 4.5–6.5%. These results show that aptamer‐modified magnetic MIL‐101 exhibits selective and effective enrichment performance and have excellent potential for the analysis of ultra‐trace targets from complex matrices.     

Proximity‐Based Sortase‐Mediated Ligation

Protein bioconjugation has been a crucial tool for studying biological processes and developing therapeutics. Sortase A (SrtA), a bacterial transpeptidase, has become widely used for its ability to site‐specifically label proteins with diverse functional moieties, but a significant limitation is its poor reaction kinetics. In this work, we address this by developing proximity‐based sortase‐mediated ligation (PBSL), which improves the ligation efficiency to over 95 % by linking the target protein to SrtA using the SpyTag–SpyCatcher peptide–protein pair. By expressing the target protein with SpyTag C‐terminal to the SrtA recognition motif, it can be covalently captured by an immobilized SpyCatcher–SrtA fusion protein during purification. Following the ligation reaction, SpyTag is cleaved off, rendering PBSL traceless, and only the labeled protein is released, simplifying target protein purification and labeling to a single step.     

Near‐Infrared‐Light‐Mediated Imaging of Latent Fingerprints based on Molecular Recognition

Photoluminescence is one of the most sensitive techniques for fingerprint detection, but it also suffers from background fluorescence and selectivity at the expense of generality. The method described herein integrates the advantages of near‐infrared‐light‐mediated imaging and molecular recognition. In principle, upconversion nanoparticles (UCNPs) functionalized with a lysozyme‐binding aptamer were used to detect fingerprints through recognizing lysozyme in the fingerprint ridges. UCNPs possess the ability to suppress background fluorescence and make it possible for fingerprint imaging on problematic surfaces. Lysozyme, a universal compound in fingerprints, was chosen as the target, thus simultaneously meeting the selectivity and generality criteria in photoluminescence approaches. Fingerprints on different surfaces and from different people were detected successfully. This strategy was used to detect fingerprints with cocaine powder by using UCNPs functionalized with a cocaine‐binding aptamer.     

One‐step preparation of magnetic imprinted nanoparticles adopting dopamine‐cupric ion as a co‐monomer for the specific recognition of bovine hemoglobin

A novel magnetic core–shell polydopamine–cupric ion complex imprinted polymer was prepared in one‐step through surface imprinting technology, which could specifically recognize bovine hemoglobin from the real blood samples. The polymerization conditions and adsorption performance of the resultant nanomaterials were investigated in detail. The results showed that the cupric ion played an important role in the recognition of template proteins. The saturating adsorption capacity of this kind of imprinted polymers was 2.23 times greater than those of imprinted polymers without cupric ion. The imprinting factor of the imprinted materials was as high as 4.23 for the template molecule. The selective separation bovine hemoglobin from the real blood sample is successfully applied. In addition, the prepared materials had excellent stability and no obvious deterioration after five adsorption–regeneration cycles. Easy preparation, rapid separation, high binding capacity and satisfactory selectivity for the template protein make this polymer attractive in the separation of high‐abundance proteins.     

Energy Landscape of Aptamer/Protein Complexes Studied by Single‐Molecule Force Spectroscopy

Aptamers are single‐stranded nucleic acid molecules selected in vitro to bind to a variety of target molecules. Aptamers bound to proteins are emerging as a new class of molecules that rival commonly used antibodies in both therapeutic and diagnostic applications. With the increasing application of aptamers as molecular probes for protein recognition, it is important to understand the molecular mechanism of aptamer–protein interaction. Recently, we developed a method of using atomic force microscopy (AFM) to study the single‐molecule rupture force of aptamer/protein complexes. In this work, we investigate further the unbinding dynamics of aptamer/protein complexes and their dissociation‐energy landscape by AFM. The dependence of single‐molecule force on the AFM loading rate was plotted for three aptamer/protein complexes and their dissociation rate constants, and other parameters characterizing their dissociation pathways were obtained. Furthermore, the single‐molecule force spectra of three aptamer/protein complexes were compared to those of the corresponding antibody/protein complexes in the same loading‐rate range. The results revealed two activation barriers and one intermediate state in the unbinding process of aptamer/protein complexes, which is different from the energy landscape of antibody/protein complexes. The results provide new information for the study of aptamer–protein interaction at the molecular level.     

An Autonomous Bio‐barcode DNA Machine for Exponential DNA Amplification and Its Application to the Electrochemical Determination of Adenosine Triphosphate

A novel autonomous bio‐barcode DNA machine that is driven by template‐dependent DNA replication is developed to exponentially amplify special DNA sequences. Combined with a DNA aptamer recognition element, the DNA machine can be further applied in the aptamer‐based, amplified analysis of small molecules. As a model analyte, adenosine triphosphate (ATP) is determined by using the DNA machine system in combination with a DNA aptamer recognition strategy and differential pulse anodic stripping voltammetry (DPASV). Under the optimum conditions, detection limits as low as 2.8×10^?17 M (3σ) for target DNA and 4.7×10^?9 M (3σ) for ATP are achieved. The satisfactory determination of ATP in K562 leukemia cell and Ramos Burkitt’s lymphoma cell reveal that this protocol possesses good selectivity and practicality. As a promising biomolecular device, this DNA machine may have an even broader application in the rapidly developing field of nanobiotechnology.     

Development of Electrochemical Impedance Spectroscopy Based Malaria Aptasensor Using HRP‐II as Target Biomarker

Current demand for a stable, low cost and sensitive malaria sensor has prompted to explore novel recognition systems that can substitute widely used protein based labile biorecognition elements to be used in point of care diagnostic devices. Here, we report a novel ssDNA aptamer of 90 mer sequence developed by SELEX process against HRP‐II, a specific biomarker for Plasmodium falciparum strains. High stability of the secondary structure of the isolated aptamer was discerned from its free energy of folding of −20.40 kcal mole⁻¹. The binding constant (K_d) of the aptamer with HRP‐II analysed by isothermal titration calorimetry was ∼1.32 μM. Circular dichroism studies indicated B form of the aptamer DNA. The aptamer was chemically immobilized on a gold electrode surface through a self‐assembled monolayer of dithio‐bis(succinimidyl) propionate to produce the aptasensor. The step wise modification of the layers over the gold electrode during fabrication of the aptasensor was confirmed by cyclic voltammetry. The aptasensor was then challenged with different concentration of HRP‐II and analysed the interaction signals through electrochemical impedance spectroscopy. The impedance signal behaved reciprocally with the increasing concentrations of the target in the sample from which a dynamic range of 1 pM–500 pM (R²=0.99) and LOD of ∼3.15 pM were discerned. The applicability of the developed aptasensor to detect HRP‐II in mimicked real sample was also validated.     

Self‐Assembled Aptamer‐Based Drug Carriers for Bispecific Cytotoxicity to Cancer Cells

Monovalent aptamers can deliver drugs to target cells by specific recognition. However, different cancer subtypes are distinguished by heterogeneous biomarkers and one single aptamer is unable to recognize all clinical samples from different patients with even the same type of cancers. To address heterogeneity among cancer subtypes for targeted drug delivery, as a model, we developed a drug carrier with a broader recognition range of cancer subtypes. This carrier, sgc8c‐sgd5a (SD), was self‐assembled from two modified monovalent aptamers. It showed bispecific recognition abilities to target cells in cell mixtures; thus broadening the recognition capabilities of its parent aptamers. The self‐assembly of SD simultaneously formed multiple drug loading sites for the anticancer drug doxorubicin (Dox). The Dox‐loaded SD (SD–Dox) also showed bispecific abilities for target cell binding and drug delivery. Most importantly, SD–Dox induced bispecific cytotoxicity in target cells in cell mixtures. Therefore, by broadening the otherwise limited recognition capabilities of monovalent aptamers, bispecific aptamer‐based drug carriers would facilitate aptamer applications for clinically heterogeneous cancer subtypes that respond to the same cancer therapy.     

Protein‐Directed Synthesis of Mn‐Doped ZnS Quantum Dots: A Dual‐Channel Biosensor for Two Proteins

Proteins typically have nanoscale dimensions and multiple binding sites with inorganic ions, which facilitates the templated synthesis of nanoparticles to yield nanoparticle–protein hybrids with tailored functionality, water solubility, and tunable frameworks with well‐defined structure. In this work, we report a protein‐templated synthesis of Mn‐doped ZnS quantum dots (QDs) by exploring bovine serum albumin (BSA) as the template. The obtained Mn‐doped ZnS QDs give phosphorescence emission centered at 590 nm, with a decay time of about 1.9 ms. A dual‐channel sensing system for two different proteins was developed through integration of the optical responses (phosphorescence emission and resonant light scattering (RLS)) of Mn‐doped ZnS QDs and recognition of them by surface BSA phosphorescent sensing of trypsin and RLS sensing of lysozyme. Trypsin can digest BSA and remove BSA from the surface of Mn‐doped ZnS QDs, thus quenching the phosphorescence of QDs, whereas lysozyme can assemble with BSA to lead to aggregation of QDs and enhanced RLS intensity. The detection limits for trypsin and lysozyme were 40 and 3 nM , respectively. The selectivity of the respective channel for trypsin and lysozyme was evaluated with a series of other proteins. Unlike other protein sensors based on nanobioconjugates, the proposed dual‐channel sensor employs only one type of QDs but can detect two different proteins. Further, we found the RLS of QDs can also be useful for studying the BSA–lysozyme binding stoichiometry, which has not been reported in the literature. These successful biosensor applications clearly demonstrate that BSA not only serves as a template for growth of Mn‐doped ZnS QDs, but also impacts the QDs for selective recognition of analyte proteins.     

Cross‐Linked Aptamer–Lipid Micelles for Excellent Stability and Specificity in Target‐Cell Recognition

The specific binding ability of DNA–lipid micelles (DLMs) can be increased by the introduction of an aptamer. However, supramolecular micellar structures based on self‐assemblies of amphiphilic DLMs are expected to demonstrate low stability when interacting with cell membranes under certain conditions, which could lead to a reduction in selectivity for targeting cancer cells. We herein report a straightforward cross‐linking strategy that relies on a methacrylamide branch to link aptamer and lipid segments. By an efficient photoinduced polymerization process, covalently linked aptamer–lipid units help stabilize the micelle structure and enhance aptamer probe stability, further improving the targeting ability of the resulting nanoassembly. Besides the development of a facile cross‐linking method, this study clarifies the relationship between aptamer–lipid concentration and the corresponding binding ability.     

Site‐Selective Cysteine–Cyclooctyne Conjugation

We report a site‐selective cysteine–cyclooctyne conjugation reaction between a seven‐residue peptide tag (DBCO‐tag, Leu‐Cys‐Tyr‐Pro‐Trp‐Val‐Tyr) at the N or C terminus of a peptide or protein and various aza‐dibenzocyclooctyne (DBCO) reagents. Compared to a cysteine peptide control, the DBCO‐tag increases the rate of the thiol–yne reaction 220‐fold, thereby enabling selective conjugation of DBCO‐tag to DBCO‐linked fluorescent probes, affinity tags, and cytotoxic drug molecules. Fusion of DBCO‐tag with the protein of interest enables regioselective cysteine modification on proteins that contain multiple endogenous cysteines; these examples include green fluorescent protein and the antibody trastuzumab. This study demonstrates that short peptide tags can aid in accelerating bond‐forming reactions that are often slow to non‐existent in water.     

Stable Pyrrole‐Linked Bioconjugates through Tetrazine‐Triggered Azanorbornadiene Fragmentation

An azanorbornadiene bromovinyl sulfone reagent for cysteine‐selective bioconjugation has been developed. Subsequent reaction with dipyridyl tetrazine leads to bond cleavage and formation of a pyrrole‐linked conjugate. The latter involves ligation of the tetrazine to the azanorbornadiene‐tagged protein through inverse electron demand Diels–Alder cycloaddition with subsequent double retro‐Diels–Alder reactions to form a stable pyrrole linkage. The sequence of site‐selective bioconjugation followed by bioorthogonal bond cleavage was efficiently employed for the labelling of three different proteins. This method benefits from easy preparation of these reagents, selectivity for cysteine, and stability after reaction with a commercial tetrazine, which has potential for the routine preparation of protein conjugates for chemical biology studies.     

Arylfluorosulfate‐Based Electrophiles for Covalent Protein Labeling: A New Addition to the Arsenal

Selective covalent modification of a targeted protein is a powerful tool in chemical biology and drug discovery, with applications ranging from identification and characterization of proteins and their functions to the development of targeted covalent inhibitors. Most covalent ligands contain an affinity motif and an electrophilic warhead that reacts with a nucleophilic residue of the targeted protein. Because the electrophilic warhead is prone to react and modify off‐target nucleophiles, its reactivity should be balanced carefully to maximize target selectivity. Arylfluorosulfates have recently emerged as latent electrophiles for selective labeling of context‐specific tyrosine and lysine residues in protein pockets. Here, we review the recent but intense introduction of arylfluorosulfates into the arsenal of available warheads for selective covalent modification of proteins. We highlight the untapped potential of this functional group for use in chemical biology and drug discovery.     

Preparation of aptamer‐bound polyamine affinity monolithic column via a facile triazine‐bridged strategy and application to on‐column specific discrimination of ochratoxin A

Developing a high‐performance modification protocol is critical for efficiently fabricating affinity monolith. Herein, by using 2,4,6‐trichloro‐1,3,5‐triazine as the linker, a simple triazine‐bridged approach was proposed for efficiently fabricating aptamer‐grafted polyhedral oligomeric silsesquioxane‐polyethyleneimine affinity monolith with high specificity toward ochratoxin A. Experimental parameters, column characteristics and specificity performances of the resultant affinity monolith were investigated in detail. Under the optimal conditions, 2,4,6‐trichloro‐1,3,5‐triazine was rapidly grafted on the polyamine matrix, and effectively applied to the subsequent bridge linkage of aptamers. It was simple and effective, which resulted in a significant decrease of modification time, excellent properties including the high coverage density of aptamer up to 1799 pmol/μL and sensitive detection of ochratoxin A as low as 10 pg/mL in beer samples. This protocol provides a facile approach for fabricating aptamer‐grafted polyamine affinity monoliths with highly selective discrimination performance.     

N‐Heterocyclic Carbene–Gold(I) Complexes Conjugated to a Leukemia‐Specific DNA Aptamer for Targeted Drug Delivery

This report describes the synthesis and characterization of novel N‐heterocyclic carbene (NHC)–gold(I) complexes and their bioconjugation to the CCRF‐CEM‐leukemia‐specific aptamer sgc8c. Successful bioconjugation was confirmed by the use of fluorescent tags on both the NHC–Au^I complex and the aptamer. Cell‐viability assays indicated that the NHC–Au^I–aptamer conjugate was more cytotoxic than the NHC–gold complex alone. A combination of flow cytometry, confocal microscopy, and cell‐viability assays provided clear evidence that the NHC–Au^I–aptamer conjugate was selective for targeted CCRF‐CEM leukemia cells.