In vitro isolation of class-specific oligonucleotide-based small-molecule receptors

Class-specific bioreceptors are highly desirable for recognizing structurally similar small molecules, but the generation of such affinity elements has proven challenging. We here develop a novel ‘parallel-and-serial’ selection strategy for isolating class-specific oligonucleotide-based receptors (aptamers) in vitro. This strategy first entails parallel selection to selectively enrich cross-reactive binding sequences, followed by serial selection that enriches aptamers binding to a designated target family. As a demonstration, we isolate a class-specific DNA aptamer against a family of designer drugs known as synthetic cathinones. The aptamer binds to 12 diverse synthetic cathinones with nanomolar affinity and does not respond to 11 structurally similar non-target compounds, some of which differ from the cathinone targets by a single atom. This is the first account of an aptamer exhibiting a combination of broad target cross-reactivity, high affinity and remarkable specificity. Leveraging the qualities of this aptamer, instantaneous colorimetric detection of synthetic cathinones at nanomolar concentrations in biological samples is achieved. Our findings significantly expand the binding capabilities of aptamers as class-specific bioreceptors and further demonstrate the power of rationally designed selection strategies for isolating customized aptamers with desired binding profiles. We believe that our aptamer isolation approach can be broadly applied to isolate class-specific aptamers for various small molecule families

Carbon based dots capped tin oxide nanosheets hybridizing with silver nanoparticles for ultra-sensitive surface enhanced raman scattering substrate

Carbon based dots capped tin oxide nanosheets (SnO₂/CDs) were synthesized by liquid exfoliation of tin oxide (SnO₂) nanoparticles in the presence of single-layer carbon based (CDs). The obtained SnO₂/CDs have lateral sizes of about 20–50 nm and heights of about 3–4 nm. A thin layer of CDs of about 1–2 nm in thickness are presence on the surface of the SnO₂ nanosheets. The SnO₂/CDs present excellent surface enhanced Raman spectroscopy (SERS) activity due to the chemical enhancement (CM) led by the charge transfer between SnO₂/CDs and the target molecules. The enhancement factor (EF) of the SnO₂/CDs is 1.42 × 10⁵, taking rhodamine 6G as a model target molecule. The SnO₂/CDs are further hybridized with silver nanoparticles (AgNPs) using an in situ synthesis method. The obtained homogeneous nano-hybrids (SnO₂/CDs@AgNPs) have a lot of nanogaps. The nanogaps among the AgNPs/CDs create strong electromagnetic enhancement (EM) due to the “hot spots” effect. The nanogaps among the SnO₂/CDs and AgNPs/CDs allow the target molecules to be embedded, and thus gained both the CM effect of SnO₂/CDs and the EM effect of AgNPs/CDs. As a result, the as-prepared SnO₂/CDs@AgNPs exhibits excellent SERS activities, with an ultrahigh enhancement factor of 3.27 × 10¹¹.Ministry of Education (MOE)This study was financially supported by National Key Research and Development Program of China (2017YFC1600500), National Natural Science Foundation of China (21675026, 21976029), Singapore Ministry of Education (MOE Tier 2 MOE2018-T2-2-072), and the Program for Changjiang Scholars and Innovative Research Team in University (No. IRT1116)

Fe₃O₄@MoS₂ Core–Shell Composites: Preparation, Characterization, and Catalytic Application

Molybdenum disulfide (MoS₂) has received tremendous attention due to the earth-abundant composition and high catalytic activity. However, the catalytic activity of MoS₂ except electro- and photocatalytic has seldom been explored. Herein, Fe₃O₄@MoS₂ core–shell composites were prepared for the first time by <i>in situ</i> growth of MoS₂ nanosheets on the surfaces of Fe₃O₄ nanoparticles under different temperature, and the catalytic performance of the resulting composites was evaluated by using the catalytic reduction of 4-nitrophenol to 4-aminophenol. FE-SEM, TEM, XRD, and XPS analyses verified the core–shell structure with MoS₂ nanosheets of defect-rich and oxygen incorporation on the surfaces of Fe₃O₄ nanoparticles. Fe₃O₄@MoS₂ composites were found to exhibit a high catalytic activity for the reduction of 4-nitrophenol with the highest activity factor <i>k</i> = 3773 min^–1 g^–1. A plausible catalytic mechanism for the reduction of 4-nitrophenol was also proposed. This study presents an inexpensive, reusable, fast, and highly efficient catalyst for the reduction of 4-nitrophenol without noble metals

Tuning the aggregation of silver nanoparticles with carbon dots for the surface-enhanced Raman scattering application

Single-layer carbon dots (CDs) are used as capping agents to synthesize silver nanoparticles (AgNPs). The obtained nanohybrids (AgNPs/CDs) can be self-assembled into nanostructures like nanochains (1D-AgNPs/CDs), nanoflats (2D-AgNPs/CDs) or nanobodys (3D-AgNPs/CDs) by simply tuning the amount of added CDs. It is found that CDs play a key role in controlling the aggregation AgNPs/CDs. The formation mechanisms of the AgNPs/CDs aggregates have been discussed. On the basis, the effects of aggregation dimension on the surface plasmon absorption and surface enhanced Raman spectroscopy (SERS) activity of AgNPs/CDs are investigated and discussed. It is found that the aggregation of AgNPs/CDs creates strong localized surface plasmon resonance. Furthermore, the aggregated AgNPs/CDs of different dimension have similar absorption intensity in the range from 500 to 800 nm, which is most commonly used in the surface enhanced Raman spectroscopy (SERS) measurement. The outstanding local electromagnetic field of the aggregated AgNPs and the enrichment effect of the CDs towards the analytes make all the obtained materials to be SERS substrates. In particular, 2D-AgNPs/CDs exhibit an ultrahigh enhancement factor of 4.02 × 1014 and a good reproducibility during the SERS test, using crystal violet as the model target molecule. The applicability of 2D-AgNPs/CDs in SERS detection is further confirmed by the measurement of trace thiram residual in apple.This study was financially supported by the National Natural Science Foundation of China (21675026, 21976029), the Natural Science Foundation of Fujian Province (2020Y0074), National Key Research and Development Program of China (2017YFC1600500), and the Program for Changjiang Scholars and Innovative Research Team in University (No. IRT1116)

Visual Monitoring of Food Spoilage Based on Hydrolysis-Induced Silver Metallization of Au Nanorods

Colorimetric detection of biogenic amines, well-known indicators of food spoilage, plays an important role for monitoring of food safety. However, common colorimetric sensors for biogenic amines suffer from low color resolution or complicated design and intricate output for the end-users. Herein, we explored a simple but effective strategy for visual monitoring of biogenic amines with multiple color change based on hydrolysis-induced silver metallization reaction to tune the localized surface plasmon resonance (LSPR) adsorption of Au nanorods (NRs). The color change and blue shift of longitudinal LSPR peak of Au NRs were closely related to the concentration of biogenic amines. This strategy provided a simple, sensitive, robust, nondestructive, cost-effective, and user-friendly platform for in situ evaluating the freshness of foodstuffs

No Structure-Switching Required: A Generalizable Exonuclease-Mediated Aptamer-Based Assay for Small-Molecule Detection

The binding of small molecules to double-stranded DNA can modulate its susceptibility to digestion by exonucleases. Here, we show that the digestion of aptamers by exonuclease III can likewise be inhibited upon binding of small-molecule targets and exploit this finding for the first time to achieve sensitive, label-free small-molecule detection. This approach does not require any sequence engineering and employs prefolded aptamers which have higher target-binding affinities than structure-switching aptamers widely used in current small-molecule detecting assays. We first use a dehydroisoandrosterone-3-sulfate-binding aptamer to show that target binding halts exonuclease III digestion four bases prior to the binding site. This leaves behind a double-stranded product that retains strong target affinity, whereas digestion of nontarget-bound aptamer produces a single-stranded product incapable of target binding. Exonuclease I efficiently eliminates these single-stranded products but is unable to digest the target-bound double-stranded product. The remaining products can be fluorescently quantified with SYBR Gold to determine target concentrations. We demonstrate that this dual-exonuclease-mediated approach can be broadly applied to other aptamers with differing secondary structures to achieve sensitive detection of various targets, even in biological matrices. Importantly, each aptamer digestion product has a unique sequence, enabling the creation of multiplex assays, and we successfully demonstrate simultaneous detection of cocaine and ATP in a single microliter volume sample in 25 min via sequence-specific molecular beacons. Due to the generality and simplicity of this assay, we believe that different DNA signal-reporting or amplification strategies can be adopted into our assay for target detection in diverse analytical contexts

Specifically and Visually Detect Methyl-Mercury and Ethyl-Mercury in Fish Sample Based on DNA-Templated Alloy Ag–Au Nanoparticles

Methyl-mercury (CH₃Hg⁺) and ethyl-mercury (C₂H₅Hg⁺) have much higher toxicity than Hg²⁺ and can be more easily accumulated by organisms to form severe bioamplification. Hence, the specific and on-site detection of CH₃Hg⁺ and C₂H₅Hg⁺ in seafood is of great significance and a hard challenge. We herein designed two T-rich aptamers (H_T5 and H_T7) for specifically recognizing CH₃Hg⁺ and the total of CH₃Hg⁺ and C₂H₅Hg⁺, respectively. In the presence of all Au³⁺, Ag⁺, and T-rich aptamer, CH₃Hg⁺ and C₂H₅Hg⁺ specifically and preferentially bind with aptamer and thus induced the formation of alloy Ag–Au nanoparticles after reduction, which led to the color change in solution. This provided a sensing platform for the instrument-free visual discrimination and detection of CH₃Hg⁺ and C₂H₅Hg⁺. By using H_T5 as probe, the method can be used to detect as low as 5.0 μM (equivalent to 1.0 μg Hg/g) of CH₃Hg⁺ by bare eye observation and 0.5 μM (equivalent to 100 ng Hg/g) of CH₃Hg⁺ by UV–visible spectrometry. By using H_T7 as probe, the method can be used to detect the total concentration of CH₃Hg⁺ and C₂H₅Hg⁺ with a visual detection limit of 5.0 μM (equivalent to 1.0 μg Hg/g) and a UV–visible spectrometry detection limit of 0.6 μM (equivalent to 120 ng Hg/g). The proposed method has been successfully used to detect CH₃Hg⁺ and C₂H₅Hg⁺ in fish muscle samples with a recovery of 101–109% and a RSD (<i>n</i> = 6) < 8%. The success of this study provided a potential method for the specific and on-site detection of CH₃Hg⁺ and C₂H₅Hg⁺ in seafood by only bare eye observation