Multichannel-Structured Three-Dimensional Chip for Highly Sensitive Pathogenic Bacteria Detection Based on Fast DNA-Programmed Signal Polymerization.

An enzyme-free and ratiometric biosensor for single nucleotide polymorphism with portable electrochemical system

Three kinds of porphyrin dots as near-infrared electrochemiluminescence luminophores: Facile synthesis and biosensing

Sensitive detection of vascular endothelial growth factor (VEGF165) is important for early cancer disease diagnosis in the clinic. A sensitive fluorescent sensing platform for VEGF165 detection is developed in this work. It is based on a target-triggered hybridization chain reaction (HCR) and graphene oxide (GO) selective fluorescence quenching. In this assay, in the presence of the VEGF165, the hairpin structure of Hp opens up and the initiation sequence will be exposed to Hp1 to open its hairpin structure. Then the opened Hp1 hybridizes with Hp2 to expose the complementary sequence of Hp1 which hybridizes with Hp1 again by HCR. Thus HCR would be initiated, generating super-long dsDNA. After the HCR, the double strands of the HCR product cannot be adsorbed on the GO surface. As a result, the HCR product gives a strong fluorescence signal which is dependent on the concentration of VEGF165. By using VEGF165 as a model analyte, the assay provides a highly sensitive fluorescence detection method for VEGF165 with a detection limit down to 20 pg mL−1. The proposed aptasensing strategy based on target-triggered HCR amplification can thus be realized. It was successfully applied to the determination of VEGF165 in spiked human serum, urine and saliva. Therefore, it can easily have wide applications in the diagnosis of vital diseases.

In this study, we developed a novel method for the detection of Vibrio alginolyticus, utilizing the specific recognition of an aptamer for V. alginolyticus and signal amplification via hybridization chain reaction (HCR) and horseradish-peroxidase-conjugated streptavidin. The proposed HCR-based multivalent aptamer (multi-Apt) amplifier allows for sensitive detection of V. alginolyticus in a linear range from 10 to 107 CFU/mL. The linear equation is y = 747.5x + 126.2, R2 = 0.986, and the limit of detection (LOD) is 3 CFU/mL. Seawater and freshwater samples were utilized in the spike recovery experiment, yieldng a recovery rates ranging from 94.3% to 108.8%. The relative standard deviation (RSD) for all samples is below 6.73%. Taken together, the proposed method has great potential for application in monitoring of V. alginolyticus in aquaculture environments.

The convenient and sensitive assay of antibiotic residuals is important for monitoring food safety and human health. Here, with a new self-constrained metal ion-dependent DNAzyme and hybridization chain reaction (HCR) signal amplifications, a simple label-free and highly sensitive aptamer-based fluorescent sensing assay for sarafloxacin is established. The target sarafloxacin molecules bind the aptamers in the duplex DNA probes to release the complementary strands, which cyclically activate the catalytic activity of the self-constrained DNAzymes to cut the substrate sequences to liberate many ssDNA strands. Subsequent HCR of two hairpins is initiated by these ssDNA strands for yielding long dsDNAs with lots of G-quadruplexes, which intercalate thioflavin T dye to generate drastically magnified fluorescence for non-label and sensitive sarafloxacin detection at the detection limit of 29 pM. Also, a highly selective assay of low levels of sarafloxacin in diluted milk samples has been demonstrated, showing the great potential of our approach for the development of versatile sensitive and convenient aptasensors for monitoring different antibiotics.

A zeolitic imidazolate framework-90 enhanced ultrasensitive ATP sensing platform with HCR and CRISPR-Cas12a dual signal amplification for live bacteria detection.

DNA walker-assisted aptasensor for highly sensitive determination of Ochratoxin A

Navigable DNA walker coupled with exonucleases-assisted signal amplification for sensitive fluorescent detection of Staphylococcus aureus

An electrochemical aptasensor for exosomes based on strand displacement amplification and hybridization chain reaction amplification

For the thermal management of three-dimensional (3D) chip stack, its thermal resistance needs to be clearly understood. In this study, 3D stacked test chips are fabricated, which are implemented with PN junction diodes for temperature sensors and diffused resistors for heating. At SemiTherm2011, the equivalent thermal conductivity of the interconnection, including BEOL (Back-End-Of-the-Line, wiring layer) is experimentally obtained to be 1.6W/mC and this time, we measure the thermal effect of Cu TSVs and it is experimentally supported that as the Cu TSV area ratio increases, the thermal conductivity of chip with TSVs in the vertical direction increases, on the contrary, that in the horizontal direction decreases. Also, the transient thermal measurement is performed and its result is compared with steady state measurement result. Further, the thermal capacitance measurement of 3D stacked test chip with hot spot heating is performed, which is essential to determine the transient thermal performance of 3D chip stack.

Magnetic separation coupled with gold nanoparticle-assisted hybridization chain reaction for simultaneous detection of exomiR-21 and exomiR-155.

Efficient approaches for intracellular delivery of nucleic acid reagents to achieve sensitive detection and regulation of gene and protein expressions are essential for chemistry and biology. We develop a novel electrostatic DNA nanoassembly that, for the first time, realizes hybridization chain reaction (HCR), a target-initiated alternating hybridization reaction between two hairpin probes, for signal amplification in living cells. The DNA nanoassembly has a designed structure with a core gold nanoparticle, a cationic peptide interlayer, and an electrostatically assembled outer layer of fluorophore-labeled hairpin DNA probes. It is shown to have high efficiency for cellular delivery of DNA probes via a unique endocytosis-independent mechanism that confers a significant advantage of overcoming endosomal entrapment. Moreover, electrostatic assembly of DNA probes enables target-initialized release of the probes from the nanoassembly via HCR. This intracellular HCR offers efficient signal amplification and enables ultrasensitive fluorescence activation imaging of mRNA expression with a picomolar detection limit. The results imply that the developed nanoassembly may provide an invaluable platform in low-abundance biomarker discovery and regulation for cell biology and theranostics.

The Hybridization Chain Reaction (HCR) is an isothermal amplification technique widely used for sensing nucleic acids and small molecules. Despite its effectiveness, conventional linear HCR exhibits relatively slow kinetics and insufficient sensitivity. To address this challenge, we have innovatively combined HCR with DNAzyme technology to enhance nucleic acid detection. In this novel approach, the presence of a target molecule triggers the formation of DNAzyme, leading to the cleavage of substrate S, the initiation of HCR, and the production of DNA nanowires and labeled DNAzyme. The newly generated DNAzyme continuously cleaves substrate S, promoting sequential HCR amplification and significantly enhancing the fluorescence signal. This system offers a simple, sensitive, selective, and versatile method for nucleic acid detection, with a detection limit as low as 5 pM. When tested on classical swine fever virus (CSFV) samples, the system demonstrated detection accuracy comparable to RT-qPCR and exhibited superior repeatability.

Detection of methyltransferase (MTase) activity is of great significance in methylation-related disease diagnosis and drug screening. Herein, we present a dual-amplification sensing strategy that is assisted by plasmonically enhanced Raman intensity at engineered nanoholes array, along with signal amplification by the hybridization chain reaction (HCR) for the ultrasensitive detection of M.SssI MTase activity and inhibitor screening. An engineered surface-enhanced Raman scattering (SERS) substrate, namely, a structured nanoholes array (NHA) with wavelength-matched surface plasmon resonance (SPR) at the wavelength of laser excitation (785 nm), was rationally designed through finite-difference time-domain (FDTD) simulations, precisely fabricated through master-assisted replication, and then used as a sensing platform. Uniform and intense SERS signals were achieved by turning on the plasmonic enhancement under the excitation of SPR. Probe DNA was designed to hybridize with target DNA (a BRCA1 gene fragment), and the formed dsDNA with the recognition site of M.SssI was assembled on the NHA. In the presence of M.SssI, the HCR process was triggered upon adding DNAs labeled with the Raman reporter Cy5, leading to an amplified SERS signal of Cy5. The intensity of Cy5 increases with increasing M.SssI activity, which establishes the basis of the assay for M.SssI. The developed assay displays an ultrasensitivity that has a broad linear range (0.002-200 U/mL) and a low detection limit (2 × 10-4 U/mL), which is superior to that of the reported SERS-based detection methods. Moreover, it can selectively detect M.SssI in human serum samples and evaluate the efficiency of M.SssI inhibitors.

Hybridization chain reaction amplification for highly sensitive fluorescence detection of DNA with dextran coated microarrays