Yurong Yan

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.

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 colorimetric biosensor for detection of attomolar microRNA with a functional nucleic acid-based amplification machine

A functional nucleic acid-based amplification machine was designed for simple and label-free ultrasensitive colorimetric biosensing of microRNA (miRNA). The amplification machine was composed of a complex of trigger template and C-rich DNA modified molecular beacon (MB) and G-rich DNA (GDNA) as the probe, polymerase and nicking enzyme, and a dumbbell-shaped amplification template. The presence of target miRNA triggered MB mediated strand displacement to cyclically release nicking triggers, which led to a toehold initiated rolling circle amplification to produce large amounts of GDNAs. The formed GDNAs could stack with hemin to form G-quadruplex/hemin DNAzyme, a well-known horseradish peroxidase (HRP) mimic, for catalyzing a colorimetric reaction. The modified MB improved the stringent target recognition and reduced background signal. The proposed sensing strategy showed very high sensitivity and selectivity with a wide dynamic range from 10 aM to 1.0 nM, and enabled successful visual analysis of trace amount of miRNA in real sample by the naked eye. This rapid and highly efficient signal amplification strategy provided a simple and sensitive platform for miRNA detection. It would be a versatile and powerful tool for clinical molecular diagnostics.

A facile and pragmatic electrochemical biosensing strategy for ultrasensitive detection of DNA in real sample based on defective T junction induced transcription amplification.

A novel and pragmatic electrochemical sensing strategy was developed for ultrasensitive and specific detection of nucleic acids by combining with defective T junction induced transcription amplification (DTITA). The homogeneous recognition and specific binding of target DNA with a pair of designed probes formed a defective T junction, further triggered primer extension reaction and in vitro transcription amplification to produce numerous single-stranded RNA. These RNA products of DTITA could hybridized with the biotinylated detection probes and immobilized capture probes for enzyme-amplified electrochemical detection on the surface of the biosensor. The proposed isothermal DTITA strategy displayed remarkable signal amplification performance and reproducibility. The electrochemical DNA biosensor showed very high sensitivity for target DNA with a low detection limit of 0.4 fM (240 molecules of the synthetic DNA), and can directly detect target pathogenic gene of Group B Streptococci (GBS) from as low as 400 copies of genomic DNA. Moreover, the established biosensor was successfully verified for directly identifying GBS in clinical samples. This proposed strategy presented a simple and pragmatic platform toward ultrasensitive and handy nucleic acids detection, and would become a potential tool for general application in point-of-care setting.

Highly sensitive surface plasmon resonance biosensor for the detection of HIV-related DNA based on dynamic and structural DNA nanodevices

Early detection, diagnosis and treatment of human immune deficiency virus (HIV) infection is the key to reduce acquired immunodeficiency syndrome (AIDS) mortality. In our research, an innovative surface plasmon resonance (SPR) biosensing strategy has been developed for highly sensitive detection of HIV-related DNA based on entropy-driven strand displacement reactions (ESDRs) and double-layer DNA tetrahedrons (DDTs). ESDRs as enzyme-free and label-free signal amplification circuit can be specifically triggered by target DNA, leading to the cyclic utilization of target DNA and the formation of plentiful double-stranded DNA (dsDNA) products. Subsequently, the dsDNA products bind to the immobilized hairpin capture probes and further combine with DDTs nanostructures. Due to the high efficiency of ESDRs and large molecular weight of DDTs, the SPR response signal was enhanced dramatically. The proposed SPR biosensor could detect target DNA sensitively and specifically in a linear range from 1pM to 150nM with a detection limit of 48fM. In addition, the whole detecting process can be accomplished in 60min with high accuracy and duplicability. In particular, the developed SPR biosensor was successfully used to analyze target DNA in complex biological sample, indicating that the developed strategy is promising for rapid and early clinical diagnosis of HIV infection.

Direct ultrasensitive electrochemical biosensing of pathogenic DNA using homogeneous target-initiated transcription amplification.

Sensitive and specific methodologies for detection of pathogenic gene at the point-of-care are still urgent demands in rapid diagnosis of infectious diseases. This work develops a simple and pragmatic electrochemical biosensing strategy for ultrasensitive and specific detection of pathogenic nucleic acids directly by integrating homogeneous target-initiated transcription amplification (HTITA) with interfacial sensing process in single analysis system. The homogeneous recognition and specific binding of target DNA with the designed hairpin probe triggered circular primer extension reaction to form DNA double-strands which contained T7 RNA polymerase promoter and served as templates for in vitro transcription amplification. The HTITA protocol resulted in numerous single-stranded RNA products which could synchronously hybridized with the detection probes and immobilized capture probes for enzyme-amplified electrochemical detection on the biosensor surface. The proposed electrochemical biosensing strategy showed very high sensitivity and selectivity for target DNA with a dynamic response range from 1 fM to 100 pM. Using salmonella as a model, the established strategy was successfully applied to directly detect invA gene from genomic DNA extract. This proposed strategy presented a simple, pragmatic platform toward ultrasensitive nucleic acids detection and would become a versatile and powerful tool for point-of-care pathogen identification.