Nonamplification Multiplexed Assay of Endonucleases and DNA Methyltransferases by Colocalized Particle Counting

Spherical DNA Nanomotors Enable Ultrasensitive Detection of Active Enzymes in Extracellular Vesicles for Cancer Diagnosis

Enzymes encapsulated in extracellular vesicles (EVs) hold promise as biomarkers for early cancer diagnosis. However, precise measurement of their catalytic activities within EVs remains a notable challenge. Here, we report an enzymatically triggered spherical DNA nanomotor (EDM) that enables one-pot, cascaded, and highly sensitive analysis of the activity of EV-associated or free apurinic/apyrimidinic endonuclease 1 (APE1, a key enzyme in base excision repair) across various biological samples. The EDM capitalizes on APE1-triggered activation of DNAzyme (Dz) and its autonomous cleavage of substrates to achieve nonlinear signal amplification. Using EDM, we demonstrate a strong correlation between APE1 activity in EVs and that of their parental cancer cells. Additionally, EV APE1 mirrors the fluctuation of cellular APE1 activity in response to chemotherapy-induced DNA damage. In a pilot clinical study (n=63), the EDM-based assay reveals that more than 80 % of active APE1 in serum samples is EV-encapsulated. Notably, EV APE1 can differentiate early prostate cancer (PCa) patients from healthy donors (HDs) with an overall accuracy of 92 %, outperforming free APE1 in sera. We anticipate that EDM will become a versatile tool for quantifying EV-associated enzymes.

Orientation-Guided Immobilization of Probe DNA on swCNT-FET for Enhancing Sensitivity of EcoRV Detection

We present a novel approach that integrates electrical measurements with molecular dynamics (MD) simulations to assess the activity of type-II restriction endonucleases, specifically EcoRV. Our approach employs a single-walled carbon nanotube field-effect transistor (swCNT-FET) functionalized with the EcoRV substrate DNA, enabling the detection of enzymatic cleavage events. Notably, we leveraged the methylene blue (MB) tag as an "orientation guide" to immobilize the EcoRV substrate DNA in a specific direction, thereby enhancing the proximity of the DNA cleavage reaction to the swCNT surface and consequently improving the sensitivity in EcoRV detection. We conducted computational modeling to compare the conformations and electrostatic potential (ESP) of MB-tagged DNA with its MB-free counterpart, providing strong support for our electrical measurements. Both conformational and ESP simulations exhibited robust agreement with our experimental data. The inhibitory efficacy of the EcoRV inhibitor aurintricarboxylic acid (ATA) was also evaluated, and the selectivity of the sensing device was examined.

Plasmonic scattering imaging of single Cu2-xSe nanoparticle for Hg2+ detection

The development of new efficient contrast nanoprobe has been greatly concerned in the field of scattering imaging for sensitive and accurate detection of trace analytes. In this work, the non-stoichiometric Cu_2-xSe nanoparticle with typical localized surface plasmon resonance (LSPR) properties originating from their copper deficiency as a plasmonic scattering imaging probe was developed for sensitive and selective detection of Hg²⁺ under dark-field microscopy. Hg²⁺ can compete with Cu(I)/Cu(II) which were sources of optically active holes coexisting in these Cu_2-xSe nanoparticles for its higher affinity with Se^2-. The plasmonic properties of Cu_2-xSe were adjusted effectively. Thus, the color scattering images of Cu_2-xSe nanoparticles was changed from blue to cyan, and the scattering intensity was obviously enhanced with the dark-field microscopy. There was a linear relationship between the scattering intensity enhancement and the Hg²⁺ concentration in the range of 10-300 nM with a low detection limit of 1.07 nM. The proposed method has good potential for Hg²⁺ detection in the actual water samples. This work provides a new perspective on applying new plasmonic imaging probe for the reliable determination of trace heavy metal substances in the environment at a single particle level.

Intelligent visual detection of OTC enabled by a multicolor fluorescence nanoprobe: Europium complex functionalized carbon dots

It is of great significance to realize ultra-sensitive and visual detection of oxytetracycline (OTC) residues, especially for public health and environmental safety. In this study, a multicolor fluorescence sensing platform (CDs-Cit-Eu) for OTC detection was constructed by using rare earth europium complex functionalized carbon dots (CDs). The blue-emitting CDs (λ_em = 450 nm) prepared by one-step hydrothermal method using nannochloropsis were not only the scaffold of Eu³⁺ ion coordination, but also the recognition unit of OTC. After adding OTC to the multicolor fluorescent sensor, the emission intensity of CDs decreased slowly, and the emission intensity of Eu³⁺ ions (λ_em = 617 nm) enhanced significantly, accompanying by a significant color change of the nanoprobe from blue to red. The detection limit of the probe for OTC was calculated to be 3.5 nM, manifesting ultra-high sensitivity towards OTC detection. In addition, OTC detection in real samples (honey, lake water, tap water) was successfully achieved. Moreover, a semi-hydrophobic luminescent film SA/PVA/CDs-Cit-Eu was also prepared for OTC detection. With the help of smartphone color recognition APP, real-time intelligent detection of OTC was realized.

Non-amplification on-spot identifying the sex of dioecious kiwi plants by a portable Raman device

The kiwi plant is dioecious, and its sex is generally identified from flower morphology at blossoming, which takes several years. It is quite necessary but challenging to on-spot identify the plant sex in juvenile stage. Here the target DNA was obtained by screening the Friendly boy (FrBy) gene which is sex-related for different kiwi plant species. Its complementary sequence was divided into two parts as primer DNA and further attached to different gold nanoparticles (GNPs). The connection between target DNA and primer DNA will promote the formation of plasmonic dimers. Dark field microscopy (DFM) can distinguish particles in different aggregation states. Various conditions were optimized based on the standard of increasing the proportion of dimers while reducing that of large aggregates. Furthermore, two Raman reporters (RR) are separately labeled on the nanoprobes, and the plasmonic dimers lead to a tremendous Raman enhancement of two reporters located at the dimer nanogap. Double-blind tests proved the feasibility of this method on the actual samples of kiwi plant leaves. Our SERS method is sensitive, specific, and reliable for rapid sex identification analysis at the kiwi seeding stage, with great promise for decision-making in field management.

Engineered Cancer Cells as Signal Probes for Fluorescence-Assisted Digital Counting Analysis

Fluorescence-assisted digital counting analysis allowed sensitive quantification of targets by measuring individual fluorescent labels. However, traditional fluorescent labels suffered from low brightness, small size, and sophisticated preparation procedures. Herein, engineering fluorescent dye-stained cancer cells with magnetic nanoparticles were proposed to construct single-cell probes for fluorescence-assisted digital counting analysis by quantifying the target-dependent binding or cleaving events. Various engineering strategies of cancer cells including biological recognition and chemical modification were developed for rationally designing single-cell probes. Introduction of suitable recognition elements into single-cell probes allowed digital quantification of each target-dependent event via counting the colored single-cell probes in the representative image taken using a confocal microscope. The reliability of the proposed digital counting strategy was corroborated by traditional optical microscopy- and flow cytometry-dependent counting technologies. The advantages of single-cell probes, including high brightness, big size, ease of preparation, and magnetic separation, contributed to the sensitive and selective analysis of targets of interest. As proof-to-concept assays, indirect analysis of exonuclease III (Exo III) activity, as well as direct quantitation of cancer cells, were investigated, and the potential in biological sample analysis was also assessed. This sensing strategy will open a new avenue for the development of biosensors.

Graphene-oxide-based bioassay for the fluorometric determination of agrC gene transcription in methicillin-resistant Staphylococcus aureus that uses nicking-enzyme-assisted target recycling and a hybridization chain reaction

Herein, we report the development of a graphene-oxide-based (GO-based) fluorescent bioassay for determining agrC gene transcription (mRNA) in methicillin-resistant Staphylococcus aureus (MRSA). The design is based on nicking-enzyme-assisted (Nb.BbvcI-assisted) target recycling amplification (NATR) and a hybridization chain reaction (HCR). The system consists of a helper probe (HP), a molecular beacon (MB) probe, four hairpins, and endonuclease Nb.BbvcI, which plays a role in target recycling and signal amplification. In the absence of the target, all of the carboxyfluorescein-labeled (FAM-labeled) hairpins are adsorbed through π-stacking interactions onto the surface of GO, resulting in FAM signal quenching. When the target is added, three nucleic acid chains hybridize together to form a triple complex that is recognized by Nb.BbvCI. The MB probe is then cleaved by Nb.BbvCI to generate an HP/target complex and two new DNA fragments; the former is hybridized to another MB probe and enters the next round of reaction. The two newly reproduced DNA fragments induce a HCR with the assistance of hairpins 1-4 to create double-stranded DNA (dsDNA) products. These dsDNA products are repelled by GO and generate strong fluorescence at excitation/emission wavelengths of 480/514 nm. Importantly, synergy between FAM and the dsDNA-SYBR Green I duplex structure led to significantly amplified fluorescence and enhanced sensitivity. The bioassay showed a detection limit of 7.5 fM toward the target and a good linearity in the 10 fM to 100 pM range. The developed method was applied to monitor biofilm formation and study the mechanism of drug action, with satisfactory results obtained.

Development of a single quantum dot-mediated FRET biosensor for amplification-free detection of ten-eleven translocation 2

Ten-eleven translocation (TET) family proteins play key roles in multiple cellular processes by mediating the oxidation of 5-methylcytosine to directly participate in DNA demethylation, and often aberrantly expressed in various diseases. In this research, we develop a single-quantum-dot (QD)-mediated fluorescence resonance energy transfer (FRET) biosensor for amplification-free measurement of ten-eleven translocation 2 (TET2). When TET2 is present, it catalyzes the oxidation of 5-vinylcytosine in dsDNA to 5-formylmethylcytosine, and the subsequent labeling of dsDNA with Cy5 generates a biotinylated Cy5-dsDNA complex. Biotinylated Cy5-dsDNA complexes are conjugated to the streptavidin-coated 605QDs to obtain a Cy5-dsDNA-605QD nanostructures, inducing FRET from 605QD to Cy5. FRET signal can be simply measured by single-molecule counting. This biosensor enables homogeneous detection of TET2 with a limit of detection (LOD) of 0.042 ng/μL, and it can accurately measure cellular TET2 down to 1 cell. Moreover, this biosensor can be used to screen TET2 inhibitors, offering a new platform for TET2-related medical research and clinical diagnostics.