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Wang Z, Cao Y, Yu Z, Tian Y, Ren J, Liu W, Fan L, Zhang Q, Cao C. High-resolution nucleic acid detection using online polyacrylamide gel electrophoresis platform. J Chromatogr A 2024; 1713:464571. [PMID: 38091846 DOI: 10.1016/j.chroma.2023.464571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/19/2023] [Accepted: 12/08/2023] [Indexed: 01/08/2024]
Abstract
Polyacrylamide gel electrophoresis (PAGE) is one of the most popular techniques for the separation and detection of nucleic acids. However, it requires a complicated detection procedure and offline detection format, which inevitably leads to band broadening and thus compromises the separation resolution. To overcome this problem, we developed an online PAGE (OPAGE) platform by integrating the gel electrophoresis apparatus with the gel imaging system, so as to obviate the need for the complicated detection procedure. Notably, OPAGE enabled the real-time monitoring of the separation process and the immediate imaging of the separation results once the electrophoresis ended. Using a series of synthetic DNAs with different lengths as samples, we demonstrated that the OPAGE platform enhanced 32-64 % of the number of theoretical plates, showed a robust dynamic range of 0.1-12.5 ng/μL, and realized a limit of detection as low as 0.08 ng/μL DNA. Based on our results, we anticipate that the OPAGE platform is a promising alternative to traditional nucleic acid gel electrophoresis for simple and high-resolution detection and quantification and nucleic acid.
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Affiliation(s)
- Zihao Wang
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yiren Cao
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China; School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Zixian Yu
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Youli Tian
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China; School of Life Science and Biotechnology, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Jicun Ren
- School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Weiwen Liu
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liuyin Fan
- Student Innovation Center, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Qiang Zhang
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Chengxi Cao
- School of Sensing Science and Engineering, School of Electronic Information and Electrical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China; School of Life Science and Biotechnology, State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China.
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2
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Zhang Y, Wu H, Wang H, Yin B, Wong SHD, Zhang AP, Tam HY. Ultraminiature optical fiber-tip directly-printed plasmonic biosensors for label-free biodetection. Biosens Bioelectron 2022; 218:114761. [PMID: 36209530 PMCID: PMC9527225 DOI: 10.1016/j.bios.2022.114761] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/28/2022] [Accepted: 09/24/2022] [Indexed: 11/28/2022]
Abstract
Miniaturization of biosensors has become an imperative demand because of its great potential in in vivo biomarker detection and disease diagnostics as well as the point-of-care testing for coping with public health crisis, such as the coronavirus disease 2019 pandemic. Here, we present an ultraminiature optical fiber-tip biosensor based on the plasmonic gold nanoparticles (AuNPs) directly printed upon the end face of a standard multimode optical fiber at visible light range. An in-situ precision photoreduction technology is developed to additively print the micropatterns of size-controlled AuNPs. The AuNPs reveal distinct localized surface plasmon resonance, whose peak wavelength provides an ideal spectral signal for label-free biodetection. The fabricated optical fiber-tip plasmonic biosensor can not only detect antibody, but also test SARS-CoV-2 mimetic DNA sequence at the concentration level of 0.8 pM. Such an ultraminiature fiber-tip plasmonic biosensor offers a cost-effective biodetection technology for a myriad of applications ranging from point-of-care testing to in vivo diagnosis of stubborn diseases.
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Affiliation(s)
- Yangxi Zhang
- Photonics Research Institute, Department of Electrical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Hao Wu
- Photonics Research Institute, Department of Electrical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Han Wang
- Photonics Research Institute, Department of Electrical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Bohan Yin
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - Siu Hong Dexter Wong
- Department of Biomedical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
| | - A. Ping Zhang
- Photonics Research Institute, Department of Electrical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China,Corresponding author
| | - Hwa-Yaw Tam
- Photonics Research Institute, Department of Electrical Engineering, The Hong Kong Polytechnic University, Kowloon, Hong Kong SAR, China
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3
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Wang J, Li H, Du C, Li Y, Ma X, Yang C, Xu W, Sun C. Structure-switching aptamer triggering signal amplification strategy for tobramycin detection based on hybridization chain reaction and fluorescence synergism. Talanta 2022; 243:123318. [PMID: 35217273 DOI: 10.1016/j.talanta.2022.123318] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/18/2022] [Accepted: 02/13/2022] [Indexed: 01/13/2023]
Abstract
Based on hybridization chain reaction (HCR) and fluorescence synergism, a novel aptasensor for tobramycin was successfully constructed. Tobramycin competed with cDNA-FAM to bind aptamers immobilized on magnetic beads. After magnetic separation, the released cDNA-FAM acted as initiator to trigger HCR amplification, thus the fluorescence was significantly enhanced due to binding of SYBR Green Ⅰ (SGI) to the formed long double-stranded DNA and the synergistic fluorescence of FAM. In the absence of tobramycin, the initiator was magnetically separated and no HCR occurred, more importantly, graphene oxide can quench the fluorescence of excessive hairpins/SGI and cDNA-FAM, so almost no background signal was detected. This aptasensor can monitor tobramycin in the range of 0.3-50 μM with low detection limit of 17.37 nM. Due to the potential generality of structure-switching aptamers and effectiveness of fluorescence synergism, this enzyme-free amplification strategy can be extended to other applications by rational design of nucleic acid sequences.
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Affiliation(s)
- Junyang Wang
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Hongxia Li
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Caiyi Du
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Ying Li
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Xinyue Ma
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Chuanyu Yang
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
| | - Chunyan Sun
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China.
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4
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Zhao F, Xie S, Li B, Zhang X. Functional nucleic acids in glycobiology: A versatile tool in the analysis of disease-related carbohydrates and glycoconjugates. Int J Biol Macromol 2022; 201:592-606. [PMID: 35031315 DOI: 10.1016/j.ijbiomac.2022.01.039] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/05/2022] [Accepted: 01/07/2022] [Indexed: 12/12/2022]
Abstract
As significant components of the organism, carbohydrates and glycoconjugates play indispensable roles in energy supply, cell signaling, immune modulation, and tumor cell invasion, and function as biomarkers since aberrance of them has been proved to be associated with the emergence and development of certain diseases. Functional nucleic acids (FNAs) have properties including easy-to-synthesize, good stability, good biocompatibility, low cost, and high programmability, they have attracted significant research attention and been incorporated into biosensors for detecting disease-related carbohydrates and glycoconjugates. This review summarizes the construction strategies and biosensing applications of FNAs-based biosensors in glycobiology in terms of target recognition and signal transduction. By illustrating the mechanisms and comparing the performances, the challenges and development opportunities in this area have been critically elaborated. We believe that this review will provide a better understanding of the role of FNAs in the analysis of disease-related carbohydrates and glycoconjugates, and inspire further discovery in fields that include glycobiology, chemical biology, clinical diagnosis, and drug development.
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Affiliation(s)
- Furong Zhao
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Siying Xie
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China
| | - Bingzhi Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China.
| | - Xing Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing 210023, China.
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5
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Li L, Wang Y, Sun Y, Yang W, Yin X, Chen Y, Liu Y. Novel and green hydroxyperylene imide based fluorescent polymer for calcium sulfate scale inhibition. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117730] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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6
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Combination of bidirectional strand displacement amplification with single-molecule detection for multiplexed DNA glycosylases assay. Talanta 2021; 235:122805. [PMID: 34517663 DOI: 10.1016/j.talanta.2021.122805] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 07/30/2021] [Accepted: 08/13/2021] [Indexed: 11/21/2022]
Abstract
DNA glycosylases can initiate base excision repair pathway to repair endogenous DNA base damages for the maintenance of genome stability. Multiple DNA glycosylases exhibit abnormal in various diseases, and the simultaneous measurement of different DNA glycosylases is critical to clinical diagnosis and drug discovery. Herein, we take advantage of single-molecule detection and bidirectional strand displacement amplification (SDA) to simultaneously detect uracil DNA glycolase (UDG) and human alkyladenine DNA glycosylase (hAAG). We design a partial double-stranded DNA (dsDNA) substrate modified with specific recognition sites of UDG and hAAG. The dsDNA substrate is labeled with BHQ1 and BHQ2 at the 5'-ends and then hybridizes with the Cy3/Cy5-labeled reporter probes to obtain the BHQ1/Cy3 and BHQ2/Cy5 base pairs, resulting in the quenching of Cy3/Cy5 fluorescence by BHQ1/BHQ2 via fluorescence resonance energy transfer (FRET). When UDG and hAAG are present, they can induce the base excision repair reaction and subsequently initiate the bidirectional SDA amplification process, releasing the Cy5/Cy3-labeled reporter probes from the dsDNA substrate and consequently the recovery of Cy5 and Cy3 fluorescence, which can be measured by single-molecule detection, with Cy5 indicating UDG and Cy3 indicating hAAG. This method possesses high sensitivity and good selectivity with the capability of quantifying multiple DNA glycosylases at the single-cell level. Furthermore, it can be used to simultaneously screen DNA glycosylase inhibitors and determine enzyme kinetic parameters, with the potential of sensing various DNA/RNA enzymes by simple changing the recognition sites of DNA substrates.
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7
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Meng YR, Zhang D, Zou X, Ma F, Kang Q, Zhang CY. A trifunctional split dumbbell probe coupled with ligation-triggered isothermal rolling circle amplification for label-free and sensitive detection of nicotinamide adenine dinucleotide. Talanta 2020; 224:121962. [PMID: 33379129 DOI: 10.1016/j.talanta.2020.121962] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/17/2020] [Accepted: 11/30/2020] [Indexed: 11/15/2022]
Abstract
The nicotinamide adenine dinucleotide (NAD+) is an important small biomolecule that participates in a variety of physiological functions, and it has been regarded as a potential biomarker for disease diagnosis and a promising target for disease treatment. The conventional methods for NAD+ assay often suffer from complicated procedures, expensive labeling, poor selectivity, and unsatisfactory sensitivity. Herein, we develop a label-free and sensitive method for NAD+ assay based on the integration of a trifunctional split dumbbell probe with ligation-triggered isothermal rolling circle amplification (RCA). We design a trifunctional split dumbbell probe that can act as a probe for NAD+ recognition, a template for RCA reaction, and a substrate for SYBR Green I binding. In the presence of target NAD+, it can serve as a cofactor to active E. coli DNA ligase which subsequently catalyzes the ligation of split dumbbell probe to form a circular template for RCA reaction, generating numerous dumbbell probe amplicons which can be easily and label-free monitored by using SYBR Green I as the fluorescent indicator. Due to the high fidelity of NAD+-dependent ligation and high amplification efficiency of RCA amplification, this method exhibits high sensitivity with a detection limit of 85.6 fM and good selectivity with the capability of discriminating target NAD+ from its analogs. Moreover, this method can be applied for accurate and sensitive detection of NAD+ in complex biological samples and cancer cells, holding great potential in NAD+-related biological researches and clinical diagnosis.
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Affiliation(s)
- Ya-Ru Meng
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Dandan Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Xiaoran Zou
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Fei Ma
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China.
| | - Qi Kang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China.
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8
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Liang T, Wu X, Chen B, Liu J, Aguilar ZP, Xu H. The PCR-HCR dual signal amplification strategy for ultrasensitive detection of Escherichia coli O157:H7 in milk. Lebensm Wiss Technol 2020. [DOI: 10.1016/j.lwt.2020.109642] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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9
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Ma C, Chen M, He H, Chen L. Detection of coralyne and heparin by polymerase extension reaction using SYBR Green I. Mol Cell Probes 2019; 46:101423. [PMID: 31323319 DOI: 10.1016/j.mcp.2019.101423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2019] [Revised: 07/14/2019] [Accepted: 07/16/2019] [Indexed: 11/24/2022]
Abstract
Polydeoxyadenosine (poly (dA)) has been extensively applied for detecting many drug molecules. Herein, we developed a sensitive method for detecting coralyne and heparin using a modified DNA probe with poly (dA) at one end. In the absence of coralyne, the DNA probe was digested by the Exonuclease I (Exo I), and therefore the SYBR Green I (SG I) emitted an extremely low fluorescent signal. While coralyne specifically binding to poly (dA) with strong propensity could remarkably restrain the disintegration of the DNA probe, through which as a template the second strand of DNA sequence was formed with the introduction of DNA polymerase. Therefore, the fluorescent signal of SG I was intensified to quantify coralyne. Based on this method, heparin can be determined due to its strong affinity towards coralyne. This method showed a linear range from 2 to 500 nM for coralyne with a low detection limit of 0.98 nM, and the linear range of heparin was from 1 to 100 nM when 1.25 nm was the detection limit. The proposed method was also implemented successfully in biological samples and showed a potential application for screening potential therapeutic molecules.
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Affiliation(s)
- Changbei Ma
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 102488, China; School of Life Sciences, Central South University, Changsha, 410013, China.
| | - Miangjian Chen
- School of Life Sciences, Central South University, Changsha, 410013, China
| | - Hailun He
- School of Life Sciences, Central South University, Changsha, 410013, China
| | - Leilei Chen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University (BTBU), Beijing, 102488, China.
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10
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Tang J, Wang Z, Zhou J, Lu Q, Deng L. Enzyme-free hybridization chain reaction-based signal amplification strategy for the sensitive detection of Staphylococcus aureus. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 215:41-47. [PMID: 30818216 DOI: 10.1016/j.saa.2019.02.035] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 02/16/2019] [Accepted: 02/16/2019] [Indexed: 06/09/2023]
Abstract
In this study, based on hybridization chain reaction (HCR) amplification and graphene oxide (GO), we developed a facile enzyme-free signal amplification strategy for sensitive detection of Staphylococcus aureus (S. aureus). Two hairpin probes (HP1 and HP2) labeled by fluorophore 6-carboxyfluorescein (FAM) are designed. The HP1 and HP2 can not only trigger to the HCR but also form a long nicked double strand DNA (dsDNA) with the target (16S rRNA). In the absence of target (16 s RNA), the free FAM-labeled HP1 and HP2 are adsorbed by the GO via π-π stacking, the fluorescence signal is quenched. In the presence of target (16 s RNA), the HCR is triggered and dsDNA complexes are generated. As a result, the fluorescence signal can be strongly amplified by the synergistic effect of FAM and the dsDNA dye SYBR Green I. Based on this mechanism, a fluorescence method is designed for the detection of 16S rRNA of S. aureus. Under the optimal conditions, it has low detection limit (50 pM) and a linear response in a concentration range of 50 pM to 100 nM for 16S rRNA. Furthermore, this method has also been successfully applied to the detection of S. aureus in milk sample with the detection limit of 4 × 102 CFU·mL-1.
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Affiliation(s)
- Jie Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, People's Republic of China
| | - Zefeng Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, People's Republic of China
| | - Jiaqi Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, People's Republic of China
| | - Qiujun Lu
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, People's Republic of China
| | - Le Deng
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, Hunan, People's Republic of China.
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11
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Surface regeneration and reusability of label-free DNA biosensors based on weak polyelectrolyte-modified capacitive field-effect structures. Biosens Bioelectron 2018; 126:510-517. [PMID: 30476882 DOI: 10.1016/j.bios.2018.11.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 11/05/2018] [Accepted: 11/13/2018] [Indexed: 11/21/2022]
Abstract
The reusability of capacitive field-effect electrolyte-insulator-semiconductor (EIS) sensors modified with a cationic weak polyelectrolyte (poly(allylamine hydrochloride) (PAH)) for the label-free electrical detection of single-stranded DNA (ssDNA), in-solution- and on-chip-hybridized double-stranded DNA (dsDNA) has been studied. It has been demonstrated that via simply regeneration of the gate surface of the EIS sensor by means of an electrostatic adsorption of a new PAH layer, the same biosensor can be reused for at least five DNA-detection measurements. Because of the reversal of the charge sign of the outermost layer after each surface modification with the cationic PAH or negatively charged DNA molecules, the EIS-biosensor signal exhibits a zigzag-like behavior. The amplitude of the signal changes has a tendency to decrease with increasing number of macromolecular layers. The direction of the EIS-signal shifts can serve as an indicator for a successful DNA-immobilization or -hybridization process. In addition, we observed that the EIS-signal changes induced by each surface-modification step (PAH adsorption, immobilization of ssDNA or dsDNA molecules and on-chip hybridization of complementary target cDNA) is decreased with increasing the ionic strength of the measurement solution, due to the more efficient macromolecular charge-screening by counter ions. The results of field-effect experiments were supported by fluorescence-intensity measurements of the PAH- or DNA-modified EIS surface using various fluorescence dyes.
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12
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A novel method to detect meat adulteration by recombinase polymerase amplification and SYBR green I. Food Chem 2018; 266:73-78. [DOI: 10.1016/j.foodchem.2018.05.115] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 05/24/2018] [Accepted: 05/25/2018] [Indexed: 11/18/2022]
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13
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Xu J, Fu Y, Xiao Y. Endonuclease IV recognizes single base mismatch on the eighth base 3' to the abasic site in DNA strands for ultra-selective and sensitive mutant-type DNA detection. RSC Adv 2018; 8:27016-27020. [PMID: 35540020 PMCID: PMC9083296 DOI: 10.1039/c8ra04552f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 07/12/2018] [Indexed: 01/25/2023] Open
Abstract
Since single nucleotide polymorphism (SNP) is related with many diseases and drug metabolic polymorphous and SNP genotyping is rising rapidly in many biological and medical areas, various methods of discriminating SNPs have been developed, one of which is an enzyme-based method. We uncovered a unique property of endonuclease IV due to which it can discriminate single base mismatches in different positions of DNA strands containing an abasic site, and we also discovered a new property: a mismatch in the +8 position could inhibit the cleavage of endonuclease IV. Then, we coupled +8 mismatch with other mismatches along with the discrimination effect of melting temperature to develop a new ultra-selective and sensitive genotyping system, which showed high discrimination factors. The detection limit was as low as 0.05-0.01%. Our new discovery improves the understanding of endonuclease IV. Also, the method could be applied to clinical real samples; thus, it merits further investigation and improvement for application in clinical utilization for early screening of specific diseases.
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Affiliation(s)
- Jiaju Xu
- Department of Anesthesiology, Tongji Hospital, Huazhong University of Science and Technology Wuhan 430030 P. R. China
| | - Yanqiao Fu
- Department of Otorhinolaryngology, Taihe Hospital, Hubei University of Medicine Shiyan 442000 P. R. China
| | - Yan Xiao
- Department of Anesthesiology, Tongji Hospital, Huazhong University of Science and Technology Wuhan 430030 P. R. China
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14
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Zhang L, Cao D, Tang T, Zuo Z, Huang J, Duan L. A label-free fluorescence method for detection of ureC gene and diagnosis of Helicobacter pylori infection. LUMINESCENCE 2018; 33:941-946. [PMID: 29786166 DOI: 10.1002/bio.3493] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 03/06/2018] [Accepted: 03/16/2018] [Indexed: 12/12/2022]
Abstract
The feasibility of using a polymerase chain reaction (PCR)-based label-free DNA sensor for the detection of Helicobacter pylori is investigated. In particular, H. pylori ureC gene, a specific H. pylori nucleic acid sequence, was selected as the target sequence. In the presence of ureC gene, the target DNA could be amplified to dsDNA with much higher detectable levels. After added the SYBR green I (SGI), the sensing system could show high fluorescence. Thus, the target DNA can be detected by monitoring the change of fluorescence intensity of sensing system. The clinical performance of this method was determined by comparing it with another conventional technique urea breath test (UBT). The result also showed good distinguishing ability between negative and positive patient, which was in good agreement with that obtained by the UBT. It suggests that the label-free fluorescence-based method is more suitable for infection confirmation test of H. pylori. This approach offers great potential for simple, sensitive and cost-effective identification of H. pylori infection.
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Affiliation(s)
- Leiyi Zhang
- Department of Minimally Invasive Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China
| | - Ding Cao
- Department of Minimally Invasive Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China
| | - Tenglong Tang
- Department of Minimally Invasive Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China
| | - Zhongkun Zuo
- Department of Minimally Invasive Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China
| | - Jiangsheng Huang
- Department of Minimally Invasive Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China
| | - Lunxi Duan
- Department of Minimally Invasive Surgery, The Second Xiangya Hospital of Central South University, Changsha, Hunan, P. R. China
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15
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A simple and universal electrochemical assay for sensitive detection of DNA methylation, methyltransferase activity and screening of inhibitors. J Electroanal Chem (Lausanne) 2018. [DOI: 10.1016/j.jelechem.2018.02.060] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Godavarthi S, Mohan Kumar K, Vázquez Vélez E, Hernandez-Eligio A, Mahendhiran M, Hernandez-Como N, Aleman M, Martinez Gomez L. Nitrogen doped carbon dots derived from Sargassum fluitans as fluorophore for DNA detection. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2017; 172:36-41. [PMID: 28514712 DOI: 10.1016/j.jphotobiol.2017.05.014] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 12/22/2022]
Abstract
This work focused on the use of waste seaweed Sargassum fluitans (S. fluitans) as carbon source precursor to prepare nitrogen doped carbon dots (NCDs) by hydrothermal method. High resolution transmission electron microscopic (HR-TEM) studies revealed that the synthesized water soluble NCDs are in the size range of 2-8nm and exhibits excellent fluorescent properties with a quantum yield of 18.2%. Elemental nitrogen in NCDs was evidenced by X-ray photoelectron spectroscopy (XPS) and Fourier transformed infrared spectrum (FT-IR). The phytochemical analysis of S. fluitans using 1H NMR and 13C NMR revealed the presence of few amino acids which act as nitrogen source in the preparation of NCDs. Application of NCDs as fluorophore for double stranded DNA, single stranded DNA and RNA detection was highlighted in this study. Excellent fluorescent tagging abilities of NCDs with the biological nucleic acids were evidenced using gel electrophoresis. Significant increase in fluorescence was observed upon tagging of NCDs with nucleic acids and this particular phenomenon helps better in visualizing the nucleic acids. All three nucleic acids i.e. double stranded DNA, single stranded DNA and RNA showed similar phenomenon upon tagging with NCDs. Thus synthesized NCDs may be used as an alternate fluorophore for commercial toxic organic staining agents to visualize nucleic acids.
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Affiliation(s)
- S Godavarthi
- Universidad Nacional Autonoma de Mexico, Instituto de Ciencias Fisicas, Avenida Universidad s/n, 62210 Cuernavaca, MOR, Mexico; Conacyt - Division Academica de Ciencias Basicas, Universidad Juarez Autonoma de Tabasco, Km 1 Carretera Cunduacan, Jalpa de Mendez A.P 24 C.P 86690, Colonia Esmeralda, Cunduacan, Tabasco, Mexico
| | - K Mohan Kumar
- Universidad Nacional Autonoma de Mexico, Instituto de Ciencias Fisicas, Avenida Universidad s/n, 62210 Cuernavaca, MOR, Mexico.
| | - E Vázquez Vélez
- Universidad Nacional Autonoma de Mexico, Instituto de Ciencias Fisicas, Avenida Universidad s/n, 62210 Cuernavaca, MOR, Mexico
| | - A Hernandez-Eligio
- CONACYT - Departamento de Bioingenieria Celular y Biocatalisis, Instituto de Biotecnologia UNAM, No. 2001, Col. Chamilpa, Cuernavaca, Morelos, CP. 62210, Mexico
| | - M Mahendhiran
- Departamento de Bioingenieria Celular y Biocatalisis, Instituto de Biotecnologia UNAM, No. 2001, Col. Chamilpa, Cuernavaca, Morelos, CP. 62210, Mexico.
| | - N Hernandez-Como
- Centro de Nanociencias y Micro y Nanotecnologías, Instituto Politécnico Nacional, Mexico
| | - M Aleman
- Centro de Nanociencias y Micro y Nanotecnologías, Instituto Politécnico Nacional, Mexico
| | - L Martinez Gomez
- Universidad Nacional Autonoma de Mexico, Instituto de Ciencias Fisicas, Avenida Universidad s/n, 62210 Cuernavaca, MOR, Mexico
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Reverte M, Vasseur JJ, Smietana M. Nuclease stability of boron-modified nucleic acids: application to label-free mismatch detection. Org Biomol Chem 2016; 13:10604-8. [PMID: 26441029 DOI: 10.1039/c5ob01815c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
5'-End boronic acid-modified oligonucleotides were evaluated against various nucleases at single and double stranded levels. The results show that these modifications induce a high resistance to degradation by calf-spleen and snake venom phosphodiesterases. More importantly, this eventually led to the development of a new label-free enzyme-assisted fluorescence-based method for single mismatch detection.
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Affiliation(s)
- Maëva Reverte
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université de Montpellier-ENSCM, Place Bataillon, 34095 Montpellier, France.
| | - Jean-Jacques Vasseur
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université de Montpellier-ENSCM, Place Bataillon, 34095 Montpellier, France.
| | - Michael Smietana
- Institut des Biomolécules Max Mousseron (IBMM) UMR 5247 CNRS-Université de Montpellier-ENSCM, Place Bataillon, 34095 Montpellier, France.
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Zhu H, Lu F, Wu XC, Zhu JJ. An upconversion fluorescent resonant energy transfer biosensor for hepatitis B virus (HBV) DNA hybridization detection. Analyst 2016; 140:7622-8. [PMID: 26421323 DOI: 10.1039/c5an01634g] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A novel fluorescent resonant energy transfer (FRET) biosensor was fabricated for the detection of hepatitis B virus (HBV) DNA using poly(ethylenimine) (PEI) modified upconversion nanoparticles (NH2-UCNPs) as energy donor and gold nanoparticles (Au NPs) as acceptor. The PEI modified upconversion nanoparticles were prepared directly with a simple one-pot hydrothermal method, which provides high quality amino-group functionalized UCNPs with uniform morphology and strong upconversion luminescence. Two single-stranded DNA strands, which were partially complementary to each other, were then conjugated with NH2-UCNPs and Au NPs. When DNA conjugated NH2-UCNPs and Au NPs are mixed together, the hybridization between complementary DNA sequences on UCNPs and Au NPs will lead to the quenching of the upconversion luminescence due to the FRET process. Meanwhile, upon the addition of target DNA, Au NPs will leave the surface of the UCNPs and the upconversion luminescence can be restored because of the formation of the more stable double-stranded DNA on the UCNPs. The sensor we fabricated here for target DNA detection shows good sensitivity and high selectivity, which has the potential for clinical applications in the analysis of HBV and other DNA sequences.
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Affiliation(s)
- Hao Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, P. R. China.
| | - Feng Lu
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, P. R. China.
| | - Xing-Cai Wu
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, P. R. China.
| | - Jun-Jie Zhu
- State Key Laboratory of Analytical Chemistry for Life Science, Collaborative Innovation Center of Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210093, P. R. China.
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Liu K, Yan X, Mao B, Wang S, Deng L. Aptamer-based detection of Salmonella enteritidis using double signal amplification by Klenow fragment and dual fluorescence. Mikrochim Acta 2015. [DOI: 10.1007/s00604-015-1692-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Bae J, Jo SM, Kim HS. Comprehensive detection of diverse exon 19 deletion mutations of EGFR in lung Cancer by a single probe set. Biosens Bioelectron 2015; 74:849-55. [DOI: 10.1016/j.bios.2015.07.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 07/12/2015] [Accepted: 07/20/2015] [Indexed: 01/05/2023]
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Dong H, Wu ZS, Xu J, Ma J, Zhang H, Wang J, Shen W, Xie J, Jia L. Novel multifunction-integrated molecular beacon for the amplification detection of DNA hybridization based on primer/template-free isothermal polymerization. Biosens Bioelectron 2015; 72:182-90. [DOI: 10.1016/j.bios.2015.04.090] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/20/2015] [Accepted: 04/27/2015] [Indexed: 01/10/2023]
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