Dual catalytic DNA circuit-induced gold nanoparticle aggregation: An enzyme-free and colorimetric strategy for amplified detection of nucleic acids

Target-Responsive DNA Nanoclaw for the On-Site Identification of Chinese Medicines with Naked Eye

The identification of Chinese medicinal herbs occupies a crucial part in the development of the food and drug market. Although molecular identification based on real-time PCR offers good versatility and uniform digital standards compared with traditional methods, such as morphology, the dependence on large-scale equipment hinders spot detection and marketable applications. In this study, we developed a DNA nanoclaw for colorimetric detection and visible on-site identification of Chinese medicines. When specific miRNA is present, the DNAzyme is activated and cleaves the substrate strand, triggering the catalytic hairpin assembly (CHA) reaction and forming branched DNA junctions on AuNP-I. This can then capture AuNP-II through hybridization and facilitate their aggregation, resulting in a noticeable color change that is observable to the naked eye. By harnessing the dual amplification of DNAzyme and CHA, this highly sensitive nanoprobe successfully achieved specific identification of Chinese medicines. This offers a new perspective for on-site testing in the herbal market.

T4PPVB-COP composite-driven innovative electrochemiluminescence aptasensor for ultra-sensitive detection of chlorpyrifos

Herein, an enhanced electrochemiluminescence (ECL) aptasensor driven by a complex (T4PPVB-COP@CdS QDs) with large specific surface area and high stability was constructed for highly sensitive detection of chlorpyrifos (CPF), using electrostatic interactions and signal amplification techniques. In the presence of CPF, the specific binding between the aptamer and CPF caused partial detachment of the aptamer from the sensor, thus restoring the ECL signal. Notably, gold nanoparticles functionalized with streptavidin (SA) as signal enhancers further amplified the ECL signal in specific interactions with aptamers, thereby improving the sensitivity of the assay. Based on this, the proposed ECL aptasensor demonstrated significant detection performance for CPF with a linear range of 1-107 pg/mL and a LOD of 0.34 pg/mL. Furthermore, the feasibility of the ECL aptasensor was validated by the detection and analysis of CPF in real samples, which also provided a broad reference value for bioanalysis.

Toehold-mediated strand displacement to measure released product from self-cleaving ribozymes

This paper presents a probe comprising a fluorophore and a quencher, enabling measurement of released product from self-cleaving hammerhead ribozyme, without labeled RNA molecules, regular sampling or use of polyacrylamide gels. The probe is made of two DNA strands; one strand is labeled with a fluorophore at its 5'-end, while the other strand is labeled with a quencher at its 3'-end. These two DNA strands are perfectly complementary, but with a 3'-overhang of the fluorophore strand. These unpaired nucleotides act as a toehold, which is utilized by a detached cleaved fragment (coming from a self-cleaving hammerhead ribozyme) as the starting point for a strand displacement reaction. This reaction causes the separation of the fluorophore strand from the quencher strand, culminating in fluorescence, detectable in a plate reader. Notably, the emitted fluorescence is proportional to the amount of detached cleaved-off RNAs, displacing the DNA quencher strand. This method can replace or complement radio-hazardous unstable ³²P as a method of measurement of the product release from ribozyme cleavage reactions; it also eliminates the need for polyacrylamide gels, for the same purpose. Critically, this method allows to distinguish between the total amount of cleaved ribozymes and the amount of detached fragments, resulting from that cleavage reaction.

Colorimetric determination of DNA using an aptamer and plasmonic nanoplatform

A facile plasmonic nanoplatform was developed for rapid and sensitive determination of nucleic acid. Hg²⁺-regulated molecular beacon (MB, hairpin) containing rich thymine (T) bases at both ends is used as the probe. A hairpin structure can be formed in the MB probe due to the strong binding of Hg²⁺ to T. However, in the presence of target DNA, the hairpin structure is opened owing to target DNA-specific hybridization with the aptamer. Simultaneously, the opened MB interacts with poly(diallyldimethylammonium chloride) (PDDA) and hinders PDDA-induced aggregation of AuNPs, accompanied by a color change from blue to red and a decrease in absorption ratio (A₆₂₀/A₅₂₀). Hence, a good linear relationship was observed between the decreased absorption ratio (A₆₂₀/A₅₂₀) and DNA concentration ranging from 0.02 to 2 nmol/L with a low detection limit of 4.42 pmol/L. Moreover, this nanoplatform has been successfully utilized to discriminate between perfect target and mismatch sequences. More importantly, the bioassay is simple, versatile, rapid, and cost-effective compared with other common methods, which holds great promise for clinical diagnosis and biomedical application. Graphical abstract.