Antibody-Bridged Beacon for Homogeneous Detection of Small Molecules

In conventional competitive immunoassays for small molecules (SM), antibodies are either immobilized to solid phases or labeled with magnetic particles or probes. The former involves laborious blocking and washing steps, whereas the latter requires complicated labeling and purification steps. To circumvent these limitations, we describe here a new type of molecular beacon, termed antibody-bridged beacon (AbB), enabling homogeneous detection of SM without any immobilization or labeling of the antibody. The AbB is formed by the binding of an antibody to a pair of SM-labeled oligonucleotide probes that each comprise a stem sequence conjugated by either a fluorophore or a quencher. Competitive binding of the SM target to the antibody destructs the stem-loop structure of AbB, restoring the quenched fluorescence. A minimum binding energy of stem sequences is required for efficient formation of the desired stem-loop structure of AbB. A systematic study of the impact of stem sequences on the fluorescence background and quenching efficiency provided useful benchmarks, e.g., binding energy of −11 kcal/mol, for the construction of AbB. The optimized AbB showed fast signal responses, as demonstrated in the analyses of two small molecule targets, biotin and digoxin. Low nanomolar limits of detection were achieved. The novel AbB strategy, along with the guidelines established for the construction and application of AbB, offers a promising approach for homogeneous detection of small molecules, obviating immobilization or labeling of antibodies as required by other competitive immunoassays

Binding-Induced Formation of DNA Three-Way Junctions and Its Application to Protein Detection and DNA Strand Displacement

DNA three-way junctions (DNA TWJs) are important building blocks to construct DNA architectures and dynamic assemblies. We describe here a binding-induced DNA TWJ strategy that is able to convert protein bindings to the formation of DNA TWJ. The binding-induced DNA TWJ makes use of two DNA motifs each conjugated to an affinity ligand. The binding of two affinity ligands to the target molecule triggers assembly of the DNA motifs and initiates the subsequent DNA strand displacement, resulting in a binding-induced TWJ. Real-time fluorescence monitoring of the binding-induced TWJ enables detection of the specific protein targets. A detection limit of 2.8 ng/mL was achieved for prostate-specific antigen. The binding-induced TWJ approach compares favorably with the toehold-mediated DNA strand-displacement, the associative (combinative) toehold-mediated DNA strand-displacement, and the binding-induced DNA strand-displacement. Importantly, the binding-induced TWJ broadens the scope of dynamic DNA assemblies and provides a new strategy to design protein-responsive DNA devices and assemblies

Binding-Induced DNA Assembly and Its Application to Yoctomole Detection of Proteins

We describe the binding-induced DNA assembly principle and strategy that enable ultrasensitive detection of molecular targets and potential construction of unique nanostructures/nanoreactors. Two DNA motifs that are conjugated to specific affinity ligands assemble preferentially only when a specific target triggers a binding event. The binding-induced assembly of the DNA motifs results in the formation of a highly stable closed-loop structure, raising the melting temperature (<i>T</i>_m) of the hybrid by >30 °C and enabling effective differentiation of the target-specific assembly from the background. The ability to detect as few as a hundred molecules (yoctomole) of streptavidin, platelet derived growth factor, and prostate specific antigen represents an improvement of detection limits by 10³–10⁵-fold over traditional immunoassays. The assay is performed in a single tube, eliminating separation, immobilization, and washing steps of conventional assays. By incorporating unique signaling and structural features into the DNA motifs, we envision diverse applications in biosensing and nanotechnology

Aptamer Capturing of Enzymes on Magnetic Beads to Enhance Assay Specificity and Sensitivity

Activity and specificity of enzyme molecules are important to enzymatic reactions and enzyme assays. We describe an aptamer capturing approach that improves the specificity and the sensitivity of enzyme detection. An aptamer recognizing the target enzyme molecule is conjugated on a magnetic bead, increasing the local concentration, and serves as an affinity probe to capture and separate minute amounts of the enzyme. The captured enzymes catalyze the subsequent conversion of fluorogenic substrate to fluorescent products, enabling a sensitive measure of the active enzyme. The feasibility of this technique is demonstrated through assays for human alpha thrombin and human neutrophil elastase (HNE), two important enzymes. Thrombin (2 fM) and 100 fM HNE can be detected. The incorporation of two binding events, substrate recognition and aptamer binding, greatly improves assay specificity. With its simplicity, this approach is applicable to biosensing and detection of disease biomarkers

Accumulation and Transport of Roxarsone, Arsenobetaine, and Inorganic Arsenic Using the Human Immortalized Caco‑2 Cell Line

Roxarsone (Rox), an organoarsenic compound, served as a feed additive in the poultry industry for more than 60 years. Residual amounts of Rox present in chicken meat could give rise to potential human exposure to Rox. However, studies on the bioavailability of Rox in humans are scarce. We report here the accumulation and transepithelial transport of Rox using the human colon-derived adenocarcinoma cell line (Caco-2) model. The cellular accumulation and transepithelial passage of Rox in Caco-2 cells were evaluated and compared to those of arsenobetaine (AsB), arsenite (As^III), and arsenate (As^V). When Caco-2 cells were exposed to 3 μM Rox, AsB, and As^III separately for 24 h, the maximum accumulation was reached at 12 h. After 24-h exposure, the accumulated Rox was 6–20 times less than AsB and As^III. The permeability of Rox from the apical to basolateral side of Caco-2 monolayers was similar to As^V but less than As^III and AsB. The results of lower bioavailability of Rox are consistent with previous observations of relatively lower amounts of Rox retained in the breast meat of Rox-fed chickens. These data provide useful information for assessing human exposure to and intestinal bioavailability of Roxarsone

Thermal Stability of DNA Functionalized Gold Nanoparticles

Therapeutic uses of DNA functionalized gold nanoparticles (DNA-AuNPs) have shown great potential and exciting opportunities for disease diagnostics and treatment. Maintaining stable conjugation between DNA oligonucleotides and gold nanoparticles under thermally stressed conditions is one of the critical aspects for any of the practical applications. We systematically studied the thermal stability of DNA-AuNPs as affected by organosulfur anchor groups and packing densities. Using a fluorescence assay to determine the kinetics of releasing DNA molecules from DNA-AuNPs, we observed an opposite trend between the temperature-induced and chemical-induced release of DNA from DNA-AuNPs when comparing the DNA-AuNPs that were constructed with different anchor groups. Specifically, the bidentate Au–S bond formed with cyclic disulfide was thermally less stable than those formed with thiol or acyclic disulfide. However, the same bidentate Au–S bond was chemically more stable under the treatment of competing thiols (mercaptohexanol or dithiothreitol). DNA packing density on AuNPs influenced the thermal stability of DNA-AuNPs at 37 °C, but this effect was minimum as temperature increased to 85 °C. With the improved understanding from these results, we were able to design a strategy to enhance the stability of DNA-AuNPs by conjugating double-stranded DNA to AuNPs through multiple thiol anchors

Binding-Induced Fluorescence Turn-On Assay Using Aptamer-Functionalized Silver Nanocluster DNA Probes

We present here a binding-induced fluorescence turn-on assay for protein detection. Key features of this assay include affinity binding-induced DNA hybridization and fluorescence enhancement of silver nanoclusters (Ag NCs) using guanine-rich DNA sequences. In an example of an assay for human α-thrombin, two aptamers (Apt15 and Apt29) were used and were modified by including additional sequence elements. A 12-nucleotide (nt) sequence was used to link the first aptamer with a nanocluster nucleation sequence at the 5′-end. The second aptamer was linked through a complementary sequence (12-nt) to a G-rich overhang at the 3′-end. Binding of the two aptamer probes to the target protein initiates hybridization between the complementary linker sequences attached to each aptamer and thereby bring the end of the G-rich overhang to close proximity to Ag NCs, resulting in a significant fluorescence enhancement. With this approach, a detection limit of 1 nM and a linear dynamic range of 5 nM–2 μM were achieved for human α-thrombin. This fluorescence assay is performed in a single tube, and it does not require washing or separation steps. The principle of the binding-induced DNA hybridization and fluorescence enhancement of Ag NCs can be extended to other homogeneous assay applications provided that two appropriate probes are available to bind with the same target molecule

Identification of Methylated Dithioarsenicals in the Urine of Rats Fed with Sodium Arsenite

Biotransformation of inorganic arsenic results in the formation of methylarsenicals of both oxygen and sulfur analogues. Aiming to improve our understanding of metabolism of inorganic arsenic in animals, we conducted an animal feeding study with an emphasis on identifying new arsenic metabolites. Female F344 rats were given 0, 1, 10, 25, 50, and 100 μg/g of arsenite (iAs^III) in the diet. Arsenic species in rat urine were determined using high performance liquid chromatography (HPLC) separation and inductive coupled plasma mass spectrometry (ICPMS) and electrospray ionization tandem mass spectrometry (ESI MS/MS) detection. Nine arsenic species were detected in the urine of the iAs^III-dosed rats. Seven of these arsenic species were consistent with previous reports, including iAs^III, arsenate, monomethyarsonic acid, dimethylarsinic acid, trimethylarsine oxide, monomethylmonothioarsonic acid, and dimethylmonothioarsinic acid. Two new methyldithioarsencals, monomethyldithioarsonic acid (MMDTA^V) and dimethyldithioarsinic acid (DMDTA^V), were identified for the first time in the urine of rats treated with iAs^III. The concentrations of both MMDTA^V and DMDTA^V in rat urine were dependent on the dosage of iAs^III in diet. The concentration of DMDTA^V was approximately 5 times higher than that of MMDTA^V. MMDTA^V has not been identified in any biological samples of animals, and DMDTA^V has not been reported as a metabolite of inorganic arsenic in the rats. The identification of novel methylated dithioarsenicals as metabolites of inorganic arsenic in the rat urine provided further insights into the understanding of the metabolism of arsenic

Arsenic Binding to Proteins

Arsenic Binding to Protein

Kinetics of Proximity-Induced Intramolecular DNA Strand Displacement

Proximity-induced intramolecular DNA strand displacement (PiDSD) is one of the key mechanisms involved in many DNA-mediated proximity assays and protein-responsive DNA devices. However, the kinetic profile of PiDSD has never been systematically examined before. Herein, we report a systematic study to explore the kinetics of PiDSD by combining the uses of three DNA strand displacement techniques, including a binding-induced DNA strand displacement to generate PiDSD, an intermolecular DNA strand-exchange strategy to measure a set of key kinetic parameters for PiDSD, and a toehold-mediated DNA strand displacement to generate fluorescence signals for the real-time monitoring of PiDSD. By using this approach, we have successfully revealed the kinetic profiles of PiDSD, determined the enhanced local effective concentrations of DNA probes that are involved in PiDSD, and identified a number of key factors that influence the kinetics of PiDSD. Our study on PiDSD establishes knowledge and strategies that can be used to guide the design and operation of various DNA-mediated proximity assays and protein-triggered DNA devices