Accelerated Hybridization Chain Reaction Kinetics Using Poly DNA Tetrahedrons and Its Application in Detection of Aflatoxin B1

Single-Molecule DNA Hybridization on Tetrahedral DNA Framework-Modified Surfaces

Tetrahedral DNA frameworks (TDFs) have been extensively utilized in biosensing systems. At the macroscopic level, it has been well established that TDFs, when employed as probe scaffolds, significantly enhance the interfacial DNA hybridization efficiency between target single-stranded DNA (ssDNA) and probe ssDNA at the solid-liquid interface. However, a molecular-level understanding of how TDF scaffolds facilitate this interfacial hybridization remains elusive. In this study, we employed single-molecule total internal reflection fluorescence microscopy (SM-TIRFM) to monitor the hybridization processes between freely diffusing target ssDNA and probe ssDNA with or without TDF scaffolds. Statistical analysis of interfacial hybridization kinetics at single probe sites revealed that TDF scaffolds significantly accelerate the interfacial hybridization kinetics, reducing the target dissociation time by 0.5-fold and increasing the association constant (Ka) by nearly 4-fold. This study offers new insights for the development of DNA nanostructure-based biosensors.

Self-driven and self-catalytic tripedal DNA nanomachine for rapid and sensitive detection of miR-21 in in colorectal cancer

A self-driven and self-catalytic (SDSC) tripedal DNA nanomachine was developed for microRNA-21 (miR-21) detection. The microRNA could open one arm of tripedal DNA nanomachine to form DNAzyme with a nearby arm through the proximity effect. After DNAzyme's cleavage, the exposed DNA arm region competed with the third arm and produced a DNA segment (sequence Q). The released sequence Q initiated the next SDSC cycle of tripedal DNA nanomachine. In the special DNA nanomachines design, the components with close spatial localization were constructed on a single nanostructure, which significantly increased local reactant concentrations and reaction rates. A dynamic correlation was obtained from 10 pM to 50 nM between fluorescence signal and miR-21 concentration. The effective concentration of reactant greatly increased, compared with the free diffusible reactants. Consequently, the incubation time was significantly shorted to 35 min. This strategy showed a promising potential in miRNA detection and disease diagnosis.

Spatially Controlled DNA Frameworks for Sensitive Detection and Specific Isolation of Tumor Cells

High-affinity, specific, and sensitive probes are crucial for the specific recognition and identification of tumor cells from complex matrices. Multivalent binding is a powerful strategy, but the irrational spatial distribution of the functional moieties may reduce the probe performance. Here, we constructed a Janus DNA triangular prism nanostructure (3Zy1-JTP-3) for sensitive detection and specific isolation of tumor cells. Benefiting from spatial features of the triangular prism, the fluorescence intensity induced by 3Zy1-JTP-3 was almost 4 times that of the monovalent structure. Moreover, the DNA triangular prisms were connected to form hand-in-hand multivalent DNA triangular prism structures (Zy1-MTP), in which the fluorescence intensity and affinity were increased to 9-fold and 10-fold of 3Zy1-JTP-3, respectively. Furthermore, 3Zy1-JTP-3 and Zy1-MTP were combined with magnetic beads, and the latter showed higher capture efficiency (>90 %) in whole blood. This work provides a new strategy for the efficient capture of rare cells in complex biological samples.

Improved Catalytic Activity of Spherical Nucleic Acid Enzymes by Hybridization Chain Reaction and Its Application for Sensitive Analysis of Aflatoxin B1

Conventional spherical nucleic acid enzymes (SNAzymes), made with gold nanoparticle (AuNPs) cores and DNA shells, are widely applied in bioanalysis owing to their excellent physicochemical properties. Albeit important, the crowded catalytic units (such as G-quadruplex, G4) on the limited AuNPs surface inevitably influence their catalytic activities. Herin, a hybridization chain reaction (HCR) is employed as a means to expand the quantity and spaces of G4 enzymes for their catalytic ability enhancement. Through systematic investigations, we found that when an incomplete G4 sequence was linked at the sticky ends of the hairpins with split modes (3:1 and 2:2), this would significantly decrease the HCR hybridization capability due to increased steric hindrance. In contrast, the HCR hybridization capability was remarkably enhanced after the complete G4 sequence was directly modified at the non-sticky end of the hairpins, ascribed to the steric hindrance avoided. Accordingly, the improved SNAzymes using HCR were applied for the determination of AFB1 in food samples as a proof-of-concept, which exhibited outstanding performance (detection limit, 0.08 ng/mL). Importantly, our strategy provided a new insight for the catalytic activity improvement in SNAzymes using G4 as a signaling molecule.

Multiple Isothermal Amplification Coupled with CRISPR-Cas14a for the Naked-eye and Colorimetric Detection of Aflatoxin B1

Aflatoxin B1 (AFB1) is highly toxic and challenging to remove, posing significant risks to both human health and economic development. Therefore, there is an urgent need to develop rapid, simple, and sensitive detection technologies. In this study, we introduce a naked-eye and colorimetric method based on multiple isothermal amplifications coupled with CRISPR-Cas14a and investigate its biosensing properties. This technique utilizes composite nanoprobes (MAPs) comprising magnetic nanoparticles and gold nanoparticles. AFB1 is efficiently identified through an aptamer competition process facilitated by magnetic nanoparticles , which triggers multiple isothermal amplification. This converts trace amounts of the toxin into a large quantity of DNA signal. Upon specific activation of the CRISPR-Cas14a complex, the MAPs are cleaved, resulting in significant changes in both color and colorimetric signal. The method demonstrates acceptable sensitivity, with a detection limit of 31.90 pg mL-1 and a wide detection range from 0.05 to 10 ng mL-1. Furthermore, the assay exhibits satisfactory specificity and high accuracy when it is applied to practical samples. Our approach offers a universal sensing platform with potential applications in food safety, environmental monitoring, and clinical diagnostics.