Shijia Ding

A sensitive electrochemical DNA biosensor for specific detection of Enterobacteriaceae bacteria by Exonuclease III-assisted signal amplification

A specific and sensitive methodology was developed successfully for quantitative detection of Enterobacteriaceae bacteria by integrating Exonuclease III-assisted target recycling amplification with a simple electrochemical DNA biosensor. After target DNA hybridizes with capture DNA, Exonuclease III can selectively digest the capture DNA, which releases the target to undergo a new hybridization and cleavage cycle on sensor surface, leading to a successful target recycling. Finally, the left capture DNA is recognized by detection probe to produce the detectable signal, which decreases with the increasing target DNA concentration. Under the optimal conditions, the proposed strategy could detect target DNA down to 8.7 fM with a linear range from 0.01 pM to 1 nM, showing high sensitivity. Meanwhile, the sensing strategy was successfully used for detection of Enterobacteriaceae bacteria down to 40 CFU mL⁻¹ in milk samples. This strategy presented a simple, rapid and sensitive platform for Enterobacteriaceae bacteria detection and would become a versatile and powerful tool for food safety, biothreat detection and environmental monitoring.

Label-free and high-sensitive detection of Salmonella using a surface plasmon resonance DNA-based biosensor

A method based on surface plasmon resonance (SPR) DNA biosensor has been developed for label-free and high-sensitive detection of Salmonella. A biotinylated single-stranded oligonucleotide probe was designed to target a specific sequence in the invA gene of Salmonella and then immobilized onto a streptavidin coated dextran sensor surface. The invA gene was isolated from bacterial cultures and amplified using a modified semi-nested asymmetric polymerase chain reaction (PCR) technique. In order to investigate the hybridization detection, experiments with different concentration of synthetic target DNA sequences have been performed. The calibration curve of synthetic target DNA had good linearity from 5 nM to 1000 nM with a detection limit of 0.5 nM. The proposed method was applied successfully to the detection of single-stranded invA amplicons from three serovars of Salmonella, i.e., Typhimurium, Enterica and Derby, and the responses to PCR products were related to different S. typhimurium concentrations in the range from 10(2) to 10(10) CFU mL(-1). While with this system to detect E. coli and S. aureus, no significant signal was observed, demonstrating good selectivity of the method. In addition, the hybridization can be completed within 15 min, and the excellent sensor surface regeneration allows at least 300 assay cycles without obvious loss of performance.

A simple electrochemical biosensor for highly sensitive and specific detection of microRNA based on mismatched catalytic hairpin assembly

MicroRNAs (miRNAs) play vital regulatory roles in cancer development and a variety of diseases, which make them become promising biomarkers. Here, a simple electrochemical biosensor was developed for highly sensitive and specific detection of target miRNA using mismatched catalytic hairpin assembly (CHA). The target miRNA triggered the toehold strand displacement assembly of two hairpin substrates, which led to the cyclic reuse of the target miRNA and the CHA products. Compared with the traditional CHA, mismatched CHA could decrease the nonspecific CHA products, which reduced the background signal significantly. Under the optimal experimental conditions and using differential pulse voltammetry, the established biosensor could detect target miRNA down to 0.6 pM (S/N=3) with a linear range from 1 pM to 25 nM, and discriminate target miRNA from mismatched miRNA with a high selectivity. It was also applied to the determination of miRNA spiked into human total RNA samples. Thus, this biosensing strategy might become a potential alternative tool for detection of miRNA in biomedical research and early clinical diagnosis.

Surface plasmon resonance biosensor for highly sensitive detection of microRNA based on DNA super-sandwich assemblies and streptavidin signal amplification.

MicroRNAs (miRNAs) play an important regulatory role in cells and dysregulation of miRNA has been associated with a variety of diseases, making them a promising biomarker. In this work, a novel biosensing strategy has been developed for label-free detection of miRNA using surface plasmon resonance (SPR) coupled with DNA super-sandwich assemblies and biotin-strepavidin based amplification. The target miRNA is selectively captured by surface-bound DNA probes. After hybridization, streptavidin is employed for signal amplification via binding with biotin on the long DNA super-sandwich assemblies, resulting in a large increase of the SPR signal. The method shows very high sensitivity, capable of detecting miRNA at the concentration down to 9 pM with a wide dynamic range of 6 orders of magnitude (from 1 × 10(-11) M to 1 × 10(-6) M) in 30 min, and excellent specificity with discriminating a single base mismatched miRNA sequence. This biosensor exhibits good reproducibility and precision, and has been successfully applied to the detection of miRNA in total RNA samples extracted from human breast adenocarcinoma MCF-7 cells. It, therefore, offers a highly effective alternative approach for miRNA detection in biomedical research and clinical diagnosis.

A simple electrochemical aptasensor for ultrasensitive protein detection using cyclic target-induced primer extension

A simple electrochemical aptasensor was developed for ultrasensitive protein detection by combining a novel strategy of cyclic target-induced primer extension (CTIPE) with an aptamer-hairpin probe and enzyme-amplified electrochemical readout. In the presence of protein target, the immobilized aptamer-hairpin probe recognized the protein to trigger primer extension reaction by target-induced conformational transition, which released the protein from replicated DNA duplex. The released target could cyclically bind with other aptamer-hairpin probes and trigger new primer extension, leading to formation of numerous biotin-tagged DNA duplex, which significantly amplified the protein recognition event and facilitated the subsequent enzymatic signal enhancement, leading to an ultrasensitive electrochemical aptasensor. Using human vascular endothelial growth factor as a model protein, the designed aptasensor could detect protein down to 0.82 pg mL(-1) with a linear range from 1 pg mL(-1) to 1 ng mL(-1). The proposed aptasensor was amenable to quantification of protein in complex biological matrixes, and would become a simple and powerful tool for bioanalysis and clinic diagnostic application.

An enzyme-free surface plasmon resonance biosensor for real-time detecting microRNA based on allosteric effect of mismatched catalytic hairpin assembly.

MicroRNAs (miRNAs) play significant regulatory roles in a variety of diseases and have been emerging as a group of promising biomarkers in cancer cells. Here, a novel and simple surface plasmon resonance (SPR) biosensor was developed for specific and highly sensitive detection of target miRNA employing the mismatched catalytic hairpin assembly (CHA) amplification coupling with programmable streptavidin aptamer (SA-aptamer). The presence of target miRNA triggered the allosteric effect of CHA amplification, which brought about the recycling of the target miRNA and produced large amounts of CHA products and activated SA-aptemers. Meanwhile, the plentiful CHA products could hybridize with the capture probes on the sensor chip, and the massive activated SA-aptamers could capture the streptavidin to achieve enhancement and output of the detection signal. Benefiting from the outstanding performance of the enzyme-free CHA amplification and non-label SPR biosensor, the established biosensor exhibited simplified process, high sensitivity and good selectivity. Under the optimal conditions, this designed strategy could detect target miRNA down to 1 pM with a dynamic range from 5 pM to 100 nM, and was successfully applied to the determination of target miRNA spiked into human total RNA samples. Thus, this SPR-based biosensor might become a potential alternative tool for miRNA detection in medical research and early clinical diagnosis.

A novel electrochemical biosensor for ultrasensitive and specific detection of DNA based on molecular beacon mediated circular strand displacement and rolling circle amplification

A novel electrochemical biosensing strategy was developed for ultrasensitive and specific detection of target DNA using a cascade signal amplification based on molecular beacon (MB) mediated circular strand displacement (CSD), rolling circle amplification (RCA), biotin-strepavidin system, and enzymatic amplification. The target DNA hybridized with the loop portion of MB probe immobilized on the gold electrode and triggered the CSD, leading to multiple biotin-tagged DNA duplex. Furthermore, via biotin-streptavidin interaction, the RCA was implemented, producing long massive tandem-repeat DNA sequences for binding numerous biotinylated detection probes. This enabled an ultrasensitive electrochemical readout by further employing the streptavidin-alkaline phosphatase. The proposed biosensor showed very high sensitivity and selectivity with a dynamic response range from 1 fM to 100 pM. The proposed strategy could have the potential for applying in clinical molecular diagnostics and environmental monitoring.

A novel electrochemical sensing strategy for rapid and ultrasensitive detection of Salmonella by rolling circle amplification and DNA–AuNPs probe

A novel electrochemical sensing strategy was developed for ultrasensitive and rapid detection of Salmonella by combining the rolling circle amplification with DNA-AuNPs probe. The target DNA could be specifically captured by probe 1 on the sensing interface. Then the circularization mixture was added to form a typical sandwich structure. In the presence of dNTPs and phi29 DNA polymerase, the RCA was initiated to produce micrometer-long single-strand DNA. Finally, the detection probe (DNA-AuNPs) could recognize RCA product to produce enzymatic electrochemical signal. Under optimal conditions, the calibration curve of synthetic target DNA had good linearity from 10aM to 10pM with a detection limit of 6.76aM (S/N=3). The developed method had been successfully applied to detect Salmonella as low as 6CFUmL(-1) in real milk sample. This proposed strategy showed great potential for clinical diagnosis, food safety and environmental monitoring.

A novel surface plasmon resonance biosensor for enzyme-free and highly sensitive detection of microRNA based on multi component nucleic acid enzyme (MNAzyme)-mediated catalyzed hairpin assembly.

MicroRNAs (miRNAs) are potentially useful biomarkers for early diagnosis of human diseases. Here, a simple surface plasmon resonance (SPR) biosensor has been developed for highly sensitive detection of miRNA by designing a new enzyme-free and isothermal amplification strategy, named multi component nucleic acid enzyme-mediated mismatched catalyzed hairpin assembly (MNAzyme-CHA). The partial MNAzymes co-recognized the target to form a stable active MNAzyme, which continued to digest multiple hairpin H0 substrates, concomitantly generating a lot of fragments. The H0 fragments could initiate the mismatched CHA cycles, resulting in the generation of massive hairpin H1-H2 complexes. As a result, the H1-H2 complexes and streptavidin were attached to the sensor surface, leading to a significantly amplified SPR signal readout. The established biosensor showed high sensitivity and selectivity with a wide dynamic range from 1 pM to 100 nM. It was also successfully applied to the determination of target miRNA spiked into human total RNA samples. Thus, this developed biosensing strategy presents a simple and stable platform toward sensitive and convenient miRNA detection, and has great potential in assays of many other nucleic acids analytes for biomedical research and early clinical diagnosis.

Electrochemical immunosensor for competitive detection of neuron specific enolase using functional carbon nanotubes and gold nanoprobe.

An electrochemical immunosensor for detection of neuron specific enolase (NSE) was designed by immobilizing NSE covalently functionalized single-walled carbon nanotubes (NSE-SWNTs) on a glassy carbon electrode. The NSE-SWNTs not only enhanced electrochemical signal but also presented abundant antigen domains for competitive immunological recognition to anti-NSE primary antibody and then gold nanoprobes labeled with alkaline phosphatase conjugated secondary antibody (AP-anti-IgG/AuNPs). The AP-anti-IgG/AuNPs exhibited highly catalytic activity toward enzyme substrate and significantly amplified the amperometric signal for target molecule detection. Based on the dual signal amplification of SWNTs and gold nanoprobe, the immunosensor could response down to 0.033 ng mL(-1) NSE with a linear range from 0.1 ng mL(-1) to 2 μg mL(-1), and showed acceptable precision and reproducibility. The designed immunosensor was amenable to direct quantification of target protein with a wide range of concentration in complex clinical serum specimens. The assay results were in a good agreement with the reference values. The proposed electrochemical immunosensor provided a pragmatic platform for convenient detection of tumor markers in clinical diagnosis.