Search Results (423)

The ability to assess molecular binding kinetics in real time is critical for advancing our understanding of molecular interactions in biochemical and biotechnological systems. This work presents a novel optical tweezer (OT)-based method to monitor molecular affinity in real time, focusing on the high-affinity streptavidin–biotin system as a model. Transparent poly(methyl methacrylate) (PMMA) microparticles functionalized with streptavidin were trapped before, during, and after binding with biotinylated bovine serum albumin (biotin–BSA), enabling the analysis of forward-scattered signals to detect nanoscale changes in particle size. By applying the Power Spectral Density method, the friction coefficient of individual particles was calculated, allowing for real-time tracking of binding dynamics and the estimation of the association rate constant ($k_{\mathrm{on}}\approx {10}^6{\mathrm{M}}^{-1}{\mathrm{s}}^{-1}$). These results are consistent with literature values and demonstrate the potential of this OT-based approach for non-invasive, label-free detection of molecular interactions. Compared to existing techniques, such as atomic force microscopy and cantilever-based sensors, this method offers significant advantages, including real-time monitoring, adaptability to different bioaffinity systems, and compatibility with miniaturized setups. This work establishes a foundation for using OT-based tools to monitor high-affinity molecular interactions in real time. While demonstrated here using biotinylated BSA as a model ligand, future studies will explore the method’s applicability to smaller ligands and more subtle surface modifications. Full article

Background/Objectives: Liquid profiling of molecular and epigenetic markers in bodily fluids is an expanding field of cancer biomarker research. Recent research activity also reveals the human satellite 2 (HSAT2) repetitive element cell-free DNA (cfDNA) as a potential cancer biomarker. Based on our recent results from targeted sequencing of HSAT2 cfDNA, we tested whether a specific HSAT2 sequence (e.g., 95 bp-HSAT2) shows greater cancer enrichment than 114 bp-SAT2, from which it derives, in patients with colon cancer. Methods: By comparing the ratio of 114 bp-HSAT2 to 95 bp-HSAT2, we investigated the increased cancer enrichment of 95 bp-HSAT2 in cfDNA samples obtained from plasma DNA extraction and a hybridization capture assay, in which HSAT2 sequences were captured from plasma using a biotin-labeled probe, in samples from colon cancer patients (n = 60) and polyp-controls (n = 60), and polyp-free controls (n = 60). Results: A correlation analysis between Ct values from DNA extraction and the hybridization capture assay for both 95 bp- and 114 bp-HSAT2 showed a positive correlation in patients with colon cancer and control subjects, indicating that the hybridization capture assay provides HSAT2 levels comparable to those obtained by DNA extraction. With both approaches, we found a lower 114 bp-HSAT2 to 95 bp-HSAT2 ratio in patients with colon cancer than in the control groups. The median ratio of extracted DNA was 62, 78, and 79 in patients with colon cancer, polyp-controls (p = 0.23), and polyp-free controls (p = 0.067), respectively. Capture assay values were 49, 87, and 64 in patients with colon cancer, polyp controls (p = 0.016), and polyp-free controls (p = 0.19), respectively. Even though statistical significance was not achieved in some comparisons, these results suggest that 95 bp-HSAT2 is more abundant in the blood of patients with colon cancer than 114 bp-HSAT2 in non-malignant patients. Conclusions: To our knowledge, this is the first study to conduct a hybridization capture assay using a biotinylated probe as a feasible approach for targeted enrichment of cfDNA from plasma. Our results confirm the outcomes of our recent article based on targeted sequencing and reveal that some specific HSAT2 sequences may exhibit increased cancer abundance. Full article

Background/Objectives: The SARS-CoV-2 virus frequently undergoes mutations to evade the human immune system. Vaccines for new strains are developed each season, and an identification test confirming the specific strain is essential for vaccine quality control, as stated by the U.S. Food and Drug Administration. However, a shorter timeline of antibody discovery was required to adjust vaccine development schedules. Therefore, anti-SARS-CoV-2 strain-specific, single-domain antibodies (sdAbs) for SARS-CoV-2 vaccines were discovered using alpaca synthetic libraries without animal immunization. Methods: A synthetic sdAb library was developed based on conserved alpaca sdAb frameworks, with a degree of freedom in the three complementarity-determining regions. Specific and high-affinity sdAb clones were selected from the library by one ribosomal display round, followed by two phage display selections using a biotinylated strain-specific SARS-CoV-2 receptor-binding domain (RBD) of the spike protein as bait and non-biotinylated RBD variants to block. The sdAbs clones were applied to the identification test using Western blotting. The binding epitopes were determined by hydrogen–deuterium exchange mass spectrometry. Results: Five clones of XBB.1.5 and two clones of JN.1-specific sdAbs were discovered. Anti-JN.1 sdAb clone 1B9 detected JN.1 vaccine products but no other previously produced vaccine strains, Wuhan, BA.5 and XBB.1.5, by WB for vaccine identification test. Four binding epitopes for anti-JN.1 sdAb clone 1B9 were identified, including the L455S mutation, a critical amino acid to evade neutralizing antibodies for the JN.1 strain. Conclusions: Anti-XBB.1.5 and JN.1-specific sdAbs were discovered from a synthetic single-domain antibody library within 8–9 weeks, and these sdAbs were applied to vaccine identification testing. Full article

Aptamers are powerful tools for detecting and analyzing biomolecules that consist of proteins or nucleic acids. However, their application to aptamers against viroids—highly structured self-replicating RNAs—has not yet been explored. In this study, a magnetic bead- and high-throughput sequencing-based SELEX (MB-HTS-SELEX) protocol for selecting potential aptamers against potato spindle tuber viroid (PSTVd) is presented. Full-length biotinylated-PSTVd RNA was transcribed in vitro, immobilized on streptavidin-coated magnetic beads, and incubated with a library of ~3.32 × 10¹⁴ molecules of random single-stranded oligo-DNAs (oligo-ssDNAs) of 20, 30, or 40 nucleotides (L20, L30, or L40, respectively) flanked by primer binding sites for downstream PCR amplification. Simultaneous biotin labeling of the anti-aptamer strand of the resulting double-stranded DNA (dsDNA) amplicons facilitated strand separation using streptavidin-coated magnetic beads. After 10 selection rounds, high-throughput sequencing, followed by bioinformatics analysis of the generated sequences, allowed for the detection of several enriched sequences, representing putative PSTVd-binding aptamers. Subsequent pull-down assays showed that the most abundant oligo-ssDNA in L30 was docked on PSTVd molecules. This combination method may ameliorate the selection of high-affinity aptamers against PSTVd, reduce the number of selection cycles, time, and other costs of aptamer production, thereby promoting future massive and cost-effective viroid detection and characterization. Full article

We developed an alkaline phosphatase (AP) chemiluminescence immunoassay method by combining the superparamagnetic magnetic beads and the biotin–streptavidin signal amplification system to detect the triazolone and tebuconazole in wheat. Through optimization of the extraction solution and extraction time, acetonitrile–PBS was selected as the extraction solution with an extraction time of 5 min as the optimal pretreatment condition. Optimizing the dilution ratio of antigen antibodies, the optimal detection conditions were selected as the dilution ratios of 1:8000 and 1:20,000 for the triazolone monoclonal antibody solution and biotinylated triazolone solution, and 1:4000 and 1:20,000 for the tebuconazole monoclonal antibody solution and biotinylated tebuconazole solution, respectively. Under the optimal conditions, the method demonstrated that the limits of detection (LOD) of triazolone and tebuconazole were 0.002835 μg·mL⁻¹ and 0.00064 μg·mL⁻¹, respectively. The recovery rate was between 90.1% and 103.6%, and the relative standard deviation (RSD) was lower than 10%. The cross-reaction rates for structural analogs were all less than 0.1%, showing good specificity. In actual sample detection, this method did not detect triazolone and tebuconazole, and the results were consistent with UHPLC-MS/MS. Full article

Prostate cancer is the third-leading cause of cancer death in men. Prostate-specific membrane antigen (PSMA) is a robust biomarker that is expressed in approximately 80% of patients diagnosed with prostate cancer; several theranostic strategies have emerged based upon targeting this biomarker. This report describes a dimeric aptamer complex (DAC) which is selective for PSMA⁺ cancer cells and is amenable to derivatization with additional diagnostic and therapeutic molecules. Confocal microscopy confirmed the selective nature of the DAC for PSMA⁺ LNCAP tumor cells. In addition, the affinity of the DAC for the PSMA protein was determined to be 2.16 ± 0.15 nM using biolayer interferometry (BLI). In proof-of-principle studies, this DAC was biotinylated (BioDAC; A10), complexed with streptavidin (SA), and radiolabeled with the positron-emitting radioisotope zirconium-89 (⁸⁹Zr: t_½ = 78.4 h, β⁺: 22.8%) to form the radiopharmaceutical [⁸⁹Zr]Zr-Df-SA-BioDAC ([⁸⁹Zr]Zr-A12). Acute biodistribution studies revealed elevated levels of radioactivity in PSMA⁺ tumors when compared to PSMA⁻ tumors. Radioactivity retention in the kidney was high due to the presence of streptavidin, while radioactivity retention in the liver was comparable with that of other radiolabeled aptamer complexes. Accordingly, the data suggests that the radiopharmaceutical will need to be redesigned using a strategy that is not reliant on a biotin–streptavidin paradigm before additional preclinical assessments are made and clinical translation can be attempted. Full article

Early detection of high-risk human papillomavirus (HPV), particularly HPV16 E7, is critical for cervical cancer prevention. Here, we report a novel, portable, and instrument-free biosensing platform that integrates recombinase polymerase amplification (RPA) with CRISPR/Cas12a-mediated detection on a microfluidic paper-based analytical device (μPAD) for colorimetric, visual readout of double-stranded DNA (dsDNA). The μPAD features seven functional zones, including lyophilized RPA and CRISPR reagents, and immobilized streptavidin and anti-FAM antibodies for signal generation. Upon target recognition, Cas12a’s trans-cleavage activity releases biotinylated-FAM-labeled reporters that form a sandwich complex with gold nanoparticle (AuNP)-conjugated anti-FAM antibodies, producing a visible red signal at the test zone. The gray value of the colorimetric signal correlates linearly with target concentration, enabling the quantitative detection of HPV16 E7 dsDNA down to 100 pM within 60 min. The assay demonstrated high accuracy and reproducibility in spiked samples. By combining isothermal amplification, CRISPR specificity, and paper-based microfluidics, this platform offers a rapid, low-cost, and user-friendly solution for point-of-care HPV screening in resource-limited settings. This work advances the integration of CRISPR diagnostics with μPAD, paving the way for scalable point-of-care molecular diagnostics beyond HPV. Full article

Severe dengue virus (DENV) infections are associated with circulating non-neutralizing antibodies generated during heterotypic infections. Although antibodies are key mediators of both protection and pathogenesis, the specific dynamics of B cells (Bc) and their antibody responses remain insufficiently characterized due to limited methods of identifying DENV-specific Bc (DENV-Bc) and the absence of animal models resembling the human disease. Here, we developed a spectral flow cytometry assay employing biotinylated virus-like particles (VLPs) to detect DENV-Bc in C57BL/6 mice and children hospitalized with dengue. DENV-1 and DENV-2 VLPs were biotinylated, and the efficiency of biotin incorporation was assessed with an HABA-avidin assay and ELISA. Serotype specificity and optimal binding conditions were confirmed using hybridomas 4G2 (pan-flavivirus) and 3H5-1 (DENV-2 specific). Fluorescent agglutimers were subsequently generated by coupling biotinylated VLPs to streptavidin–fluorochrome complexes. Splenocytes from intraperitoneally DENV-infected mice and peripheral blood mononuclear cells (PBMCs) from naturally infected pediatric patients were stained with these VLPs and Bc-lineage markers. Biotinylated VLPs bound specifically to hybridomas, and this binding was competitively inhibited by unlabeled VLPs. After secondary DENV challenge, VLPs identified DENV-specific class-switched plasmablasts in mice. Circulating DENV-specific plasmablasts were also detected in children, with agglutimers enabling the discrimination of serotype-specific and cross-reactive responses in primary and secondary infections. This VLP-based approach represents a scalable platform to investigate the protective and pathogenic roles of DENV-Bc in infection and vaccination. Full article

The cell surface proteome of polarized epithelial cells plays a central role in barrier function, signaling, and vectorial transport, yet the quantitative characterization of their surface proteins remains technically challenging. We developed an optimized chemoproteomic strategy specifically tailored to studying the surface proteins of polarized cells while keeping membrane integrity intact. By applying a disulfide-linked membrane-impermeable biotin reagent, labeling was restricted to extracellular regions of transmembrane proteins (TMPs) and secreted proteins, thereby minimizing contributions from intracellular contaminants. Following biotinylated peptide-level or protein-level enrichment and mass spectrometric analysis, we systematically compared data-dependent (DDA) and data-independent acquisition (DIA) approaches, showing that while DIA increases proteome coverage, DDA more reliably identifies biotinylated peptides in our studies. To ensure robustness, we established replicate-based normalization and contaminant-aware quality control metrics that minimize biases from proteins in cell culture medium and damaged cells. The application of the workflow to Madin–Darby canine kidney (MDCK) II epithelial monolayers enabled the large-scale quantification of apical versus basolateral domains, yielding over 2100 proteins, with 235 showing significant polarized distribution, in agreement with known biology. This method offers high specificity for the extracellular labeling and quantitative resolution of cell surface protein (CSP) polarization, providing a powerful platform for studying epithelial biology and identifying extracellular epitopes relevant to diagnostics and therapeutic targeting. Full article

Ursolic acid (UA), a naturally occurring pentacyclic triterpenoid, exhibits potent anticancer properties; however, its poor solubility and bioavailability limit its therapeutic application. To overcome these challenges and facilitate molecular target identification, a set of biotin-conjugated UA derivatives (5a–d) was synthesized through selective C-28 alkylation and biotinylation. The use of microwave-assisted synthesis significantly enhanced both reaction efficiency and product purity. Among the derivatives, compound 5c exhibited increased cytotoxicity and selectivity against bladder cancer cell lines, surpassing UA in its ability to induce apoptosis, generate reactive oxygen species (ROS), and halt cell cycle progression at the G1 phase. Proteomic profiling revealed that 5c interacts with proteins involved in ER stress, RNA processing, cytoskeletal remodeling, and metabolic regulation. These findings underscore the potential of biotinylated UA derivatives as multifunctional chemical probes for mechanistic studies in the development of targeted therapies for cancer. Full article

Neutrophil gelatinase-associated lipocalin (NGAL) has emerged as a critical biomarker for the early diagnosis of acute kidney injury (AKI). The development of novel detection platforms that combine rapid analysis with high sensitivity is essential for improving clinical outcomes. In this study, we established an antibody-based detection system for NGAL using biolayer interferometry (BLI), a label-free optical biosensing technique that monitors real-time interference patterns generated by white light reflected from biomolecular binding events on a biosensor surface. A panel of six anti-NGAL monoclonal antibodies was generated and characterized for its binding properties, identifying candidates with high specificity for NGAL. For robust sensor functionalization, selected monoclonal antibodies were biotinylated and immobilized onto streptavidin-coated biosensor tips, establishing a stable and efficient detection interface. The optimized BLI platform demonstrated a limit of detection (LOD) of 46.1 ng/mL with wild dynamic range of 19 to 40,000 ng/mL. The platform’s accuracy was validated using human serum samples, with spike-and-recovery experiments yielding recovery rates of 96.6–104.6%. This demonstrates the capability to accurately quantify NGAL under physiologically relevant conditions with minimal matrix interference. Furthermore, the real-time kinetic measurements enabled rapid analysis, with the entire assay completed in less than half an hour. These findings establish a proof-of-concept for a BLI-based biosensor for NGAL detection, demonstrating sensitivity and specificity that show potential for clinical applications. Full article

We report the first analytical application of albumin nanoparticles loaded with luminescent europium complexes for immunoassay development. These nanoparticles, synthesized via a desolvation method, exhibited a uniform spherical morphology with a hydrodynamic diameter of 263 nm and strong, long-lived luminescence at 615 nm (λex = 360 nm). Surface functionalization with streptavidin enabled specific binding to biotinylated proteins. The nanoparticles were applied as labels in a sandwich time-resolved solid-phase immunoassay for human IgG detection in black 96-well plates. Unlike commercial DELFIA assays, the method eliminates the need for signal enhancement steps, as the nanoparticles intrinsically contain high concentrations of europium complexes. Optimization studies revealed that the sharp emission peaks of europium can compromise assay reproducibility; however, employing surface scanning and increasing measurement replicates per well partially mitigated this effect. Time-resolved detection reduced background by two orders of magnitude and increased signal intensity nearly tenfold in IgG-positive samples. The assay demonstrated minimal cross-reactivity with IgA and IgM (~2%) and enabled IgG detection at serum dilutions up to 1:100,000. Comparative analysis showed strong concordance with commercial immunoassays and no concentration-dependent bias. The primary limitation observed was suboptimal intra-assay reproducibility (CV > 20% in four of six tested sera). Full article

Background: Mitoxantrone (MX) is regularly used to treat several cancers. Despite its long history in the clinic, recent studies continue to unveil novel protein targets. These targets may contribute to the cytotoxic effects of the drug, as well as potential non-canonical antitumor activity. A better understanding of MX’s cellular targets is required to fully comprehend the molecular consequences of treatment and to interpret MX sensitivity in homologous recombination (HR)-deficient cancer. Methods: Here, we evaluated MX activity in HR-deficient UWB1.289 (BRCA1−) ovarian cancer cells and surveyed the binding profile of MX using TMT-labeled quantitative proteomics and chemoproteomics. Results: Mass spectrometry (MS) analysis of cellular extracts from MX-treated BRCA1−UWB1.289 cells revealed unique downregulation of pathways instrumental in maintaining genomic stability, including single-strand annealing. Moreover, the BRCA1− cells exhibited a significant upregulation of proteins involved in ribosome biogenesis and RNA processing. Additional MS analyses following affinity-purification using a biotinylated-mitoxantrone probe corroborated these findings, which showed considerable targeting of proteins involved in genome maintenance and RNA processing. Conclusions: Our results suggest that an interplay of both canonical and non-canonical MX-antitumor activity overwhelms the BRCA1− UWB1.289 cells. Furthermore, this study characterizes the target landscape of MX, providing insights into off-target effects and MX action in HR-deficient cancer. Full article

Cathepsin S (Cat S) is a cysteine protease involved in several human diseases (i.e., autoimmune, inflammatory and cardiovascular disorders, cancer, and psoriasis) and is an important target in drug development. Emerging evidence highlights the potential of inhibiting Cat S by glycosaminoglycans, particularly chondroitin sulfates (CSs), as a promising therapeutic strategy. Given the limited and heterogeneous GAG materials from animal sources, a series of synthetic biotinylated non- or sulfated chondroitin oligomers were synthesized and assessed for their ability to inhibit Cat S. The biotinylated disaccharide C4S displayed in vitro potent inhibitory activity toward Cat S with IC₅₀ value in the micromolar range and showed selectivity over cathepsins K and L. Molecular modeling studies suggested that only C4S dp2 but not C6S, C4,6S or non-sulfated chondroitin binds selectively to the active site of Cat S. In addition, a synthetic multivalent C4S dp2 glycosylated BSA was shown to be more efficient towards Cat S inhibition (nanomolar range) than the monovalent parent C4S dp2. Our findings also indicated that this new neoglycoconjugate displayed selectivity for Cat S vs. cysteine cathepsins expressed by differentiated THP-1 cells. This study reports a new approach for designing selective and potent inhibitors of Cat S using multivalent C4S derivatives as a molecular scaffold. Full article

Background/Objectives: Obesity and hyperglycemia predispose patients to respiratory infections. Although the lung is a major organ to utilize glucose, pulmonary glucose homeostasis in type 2 diabetic (T2Dx) subjects remains poorly characterized. We hypothesized that pulmonary glucose transport would be altered during T2Dx, which would be rescued with long-term metformin treatment. Methods: T2Dx was induced by feeding mice a high-fat diet for 16 weeks, with metformin treatment administered during the final 8 weeks. Results: Glucose transporter (GLUT) protein expression and trafficking was quantified by Western blotting and the biotinylated photolabeling assay, respectively. T2Dx mice exhibited obesity, and increased glucose levels in blood and bronchoalveolar lavage (BAL) fluid. T2Dx also significantly decreased protein expression of GLUTs from Class I (i.e., GLUT-2 and -4) and class III (i.e., GLUT-10 and -12) isoforms in lung. Metformin treatment restored the protein expression of GLUT-2, -4, and -10, but not GLUT-12. Pulmonary cell surface expression of GLUT-4 and -8 was also significantly reduced in T2Dx mice and rescued by metformin. Conclusions: These findings suggest that alterations in pulmonary GLUT expression and trafficking during diabetes could contribute to the elevated airway glucose levels and severity of respiratory infections. Metformin treatment restored pulmonary glucose transport during T2Dx. Full article