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Li P, Zhang H, Yang Z, Li Y, Huang M, Yang L, Zhang X. Rapid fluorescent nucleic acid sensing with ultra-thin gold nanosheets. Anal Chim Acta 2024; 1317:342872. [PMID: 39030016 DOI: 10.1016/j.aca.2024.342872] [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: 01/20/2024] [Revised: 05/31/2024] [Accepted: 06/13/2024] [Indexed: 07/21/2024]
Abstract
Fluorescently labeled DNA oligonucleotides and gold nanospheres have been frequently utilized in biosensors, providing efficient nucleic acid detection. Nevertheless, the restricted loading capacity of gold nanospheres undermines overall sensitivity. In this study, we employed four-atom-thick ultrathin gold nanosheets (AuNSs), utilizing a "pre-mix model" for rapid target nucleic acid detection. In this approach, fluorescently labeled DNA probes were pre-incubated with the target nucleic acid, followed by the addition of AuNSs for probe adsorption and fluorescence quenching. With the developed method, we efficiently and rapidly detected the SARS-CoV-2 N gene sequence within 30 min, involving a brief 15-min target pre-incubation and a subsequent 15-min adsorption of free probes and fluorescence quenching by AuNSs. This method exhibited heightened sensitivity compared to gold nanospheres, boasting a limit of detection (LOD) of 0.808 nM. Furthermore, exceptional recovery was achieved in simulated biological samples. The study introduces an effective strategy for nucleic acid sensing characterized by rapidity, heightened sensitivity, ease of operation, and robustness. These findings encourage further development of rapid biomarker sensing methods employing 2D nanomaterials.
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Affiliation(s)
- Peiyin Li
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
| | - Huiyang Zhang
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
| | - Zhenyu Yang
- School of Biomedical Engineering, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Guangdong, 518055, China
| | - Yiling Li
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
| | - Manli Huang
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China
| | - Lingzhi Yang
- School of Pharmacy, Shenzhen University Medical School, Shenzhen University, Shenzhen, 518055, China.
| | - Xueji Zhang
- School of Biomedical Engineering, Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, Shenzhen University, Guangdong, 518055, China
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2
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Li Y, Zhao S, Xu Z, Qiao X, Li M, Li Y, Luo X. Peptide nucleic acid and antifouling peptide based biosensor for the non-fouling detection of COVID-19 nucleic acid in saliva. Biosens Bioelectron 2023; 225:115101. [PMID: 36708624 DOI: 10.1016/j.bios.2023.115101] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/24/2022] [Accepted: 01/23/2023] [Indexed: 01/26/2023]
Abstract
The electrochemical biosensor with outstanding sensitivity and low cost is regarded as a viable alternative to current clinical diagnostic techniques for various disease biomarkers. However, their actual analytical use in complex biological samples is severely hampered due to the biofouling, as they are also highly sensitive to nonspecific adsorption on the sensing interfaces. Herein, we have constructed a non-fouling electrochemical biosensor based on antifouling peptides and the electroneutral peptide nucleic acid (PNA), which was used as the recognizing probe for the specific binding of the viral RNA of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Different from the negatively charged DNA probes that will normally weaken the biosensors' antifouling capabilities owing to the charge attraction of positively charged biomolecules, the neutral PNA probe will generate no side-effects on the biosensor. The biosensor demonstrated remarkable sensitivity in detecting SARS-CoV-2 viral RNA, possessing a broad linear range (1.0 fM - 1.0 nM) and a detection limit down to 0.38 fM. Furthermore, the sensing performance of the constructed electrochemical biosensor in human saliva was nearly similar to that in pure buffer, indicating satisfying antifouling capability. The combination of PNA probes with antifouling peptides offered a new strategy for the development of non-fouling sensing systems capable of assaying trace disease biomarkers in complicated biological media.
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Affiliation(s)
- Yanxin Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China
| | - Shuju Zhao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China
| | - Zhenying Xu
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China
| | - Xiujuan Qiao
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China
| | - Mingxuan Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China
| | - Youke Li
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China
| | - Xiliang Luo
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, MOE, Shandong Key Laboratory of Biochemical Analysis, College of Chemistry and Molecular Engineering, Qingdao University of Science & Technology, Qingdao, 266042, China.
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Colorimetric Assaying of Exosomal Metabolic Biomarkers. Molecules 2023; 28:molecules28041909. [PMID: 36838895 PMCID: PMC9962048 DOI: 10.3390/molecules28041909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 02/19/2023] Open
Abstract
Exosomes released into the extracellular matrix have been reported to contain metabolic biomarkers of various diseases. These intraluminal vesicles are typically found in blood, urine, saliva, breast milk, cerebrospinal fluid, semen, amniotic fluid, and ascites. Analysis of exosomal content with specific profiles of DNA, microRNA, proteins, and lipids can mirror their cellular origin and physiological state. Therefore, exosomal cargos may reflect the physiological processes at cellular level and can potentially be used as biomarkers. Herein, we report an optical detection method for assaying exosomal biomarkers that supersedes the state-of-the-art time consuming and laborious assays such as ELISA and NTA. The proposed assay monitors the changes in optical properties of poly(3-(4-methyl-3'-thienyloxy) propyltriethylammonium bromide) upon interacting with aptamers/peptide nucleic acids in the presence or absence of target biomarkers. As a proof of concept, this study demonstrates facile assaying of microRNA, DNA, and advanced glycation end products in exosomes isolated from human plasma with detection levels of ~1.2, 0.04, and 0.35 fM/exosome, respectively. Thus, the obtained results illustrate that the proposed methodology is applicable for rapid and facile detection of generic exosomal biomarkers for facilitating diseases diagnosis.
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Wang Y, Yan T, Mei K, Rao D, Wu W, Chen Y, Peng Y, Wang J, Wu S, Zhang Q. Nanomechanical assay for ultrasensitive and rapid detection of SARS-CoV-2 based on peptide nucleic acid. NANO RESEARCH 2023; 16:1183-1195. [PMID: 35610981 PMCID: PMC9118818 DOI: 10.1007/s12274-022-4333-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/14/2022] [Accepted: 03/16/2022] [Indexed: 05/14/2023]
Abstract
UNLABELLED The massive global spread of the COVID-19 pandemic makes the development of more effective and easily popularized assays critical. Here, we developed an ultrasensitive nanomechanical method based on microcantilever array and peptide nucleic acid (PNA) for the detection of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) RNA. The method has an extremely low detection limit of 0.1 fM (105 copies/mL) for N-gene specific sequence (20 bp). Interestingly, it was further found that the detection limit of N gene (pharyngeal swab sample) was even lower, reaching 50 copies/mL. The large size of the N gene dramatically enhances the sensitivity of the nanomechanical sensor by up to three orders of magnitude. The detection limit of this amplification-free assay method is an order of magnitude lower than RT-PCR (500 copies/mL) that requires amplification. The non-specific signal in the assay is eliminated by the in-situ comparison of the array, reducing the false-positive misdiagnosis rate. The method is amplification-free and label-free, allowing for accurate diagnosis within 1 h. The strong specificity and ultra-sensitivity allow single base mutations in viruses to be distinguished even at very low concentrations. Also, the method remains sensitive to fM magnitude lung cancer marker (miRNA-155). Therefore, this ultrasensitive, amplification-free and inexpensive assay is expected to be used for the early diagnosis of COVID-19 patients and to be extended as a broad detection tool. ELECTRONIC SUPPLEMENTARY MATERIAL Supplementary material (experimental section, N gene sequences and all nucleic acid sequences used in the study, Figs. S1-S6, and Tables S1-S3) is available in the online version of this article at 10.1007/s12274-022-4333-3.
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Affiliation(s)
- Yu Wang
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Tianhao Yan
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Kainan Mei
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Depeng Rao
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Wenjie Wu
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Ye Chen
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Yongpei Peng
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Jianye Wang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, First Affiliated Hospital of Anhui Medical University, Hefei, 230022 China
| | - Shangquan Wu
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
| | - Qingchuan Zhang
- CAS Key Laboratory of Mechanical Behavior and Design of Material, Department of Modern Mechanics, University of Science and Technology of China, Hefei, 230027 China
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Ren L, Ming Z, Zhang W, Liao Y, Tang X, Yan B, Lv H, Xiao X. Shared-probe system: An accurate, low-cost and general enzyme-assisted DNA probe system for detection of genetic mutation. CHINESE CHEM LETT 2022. [DOI: 10.1016/j.cclet.2021.09.038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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6
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Goyal G, Sharma A, Tok AIY, Palaniappan A, Liedberg B. Affimer sandwich probes for stable and robust lateral flow assaying. Anal Bioanal Chem 2022; 414:4245-4254. [DOI: 10.1007/s00216-022-04078-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/28/2022] [Accepted: 04/07/2022] [Indexed: 11/01/2022]
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Faikhruea K, Choopara I, Somboonna N, Assavalapsakul W, Kim BH, Vilaivan T. Enhancing Peptide Nucleic Acid-Nanomaterial Interaction and Performance Improvement of Peptide Nucleic Acid-Based Nucleic Acid Detection by Using Electrostatic Effects. ACS APPLIED BIO MATERIALS 2022; 5:789-800. [PMID: 35119822 DOI: 10.1021/acsabm.1c01177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Single-stranded peptide nucleic acid (PNA) probes interact strongly with several nanomaterials, and the interaction was diminished in the presence of complementary nucleic acid targets which forms the basis of many nucleic acid sensing platforms. As opposed to the negatively charged DNA probes, the charges on the PNA probes may be fine-tuned by incorporating amino acids with charged side chains. The contribution of electrostatic effects to the interaction between PNA probes and nanomaterials has been largely overlooked. This work reveals that electrostatic effects substantially enhanced the quenching of dye-labeled conformationally constrained pyrrolidinyl PNA probes by several nanomaterials including graphene oxide (GO), reduced graphene oxide, gold nanoparticles (AuNPs), and silver nanoparticles. The fluorescence quenching and the color change from red to purple in the case of AuNPs because of aggregation were inhibited in the presence of complementary nucleic acid targets. Thus, fluorescence and colorimetric assays for DNA and RNA that can distinguish even single-base-mismatched nucleic acids with improved sensitivity over conventional DNA probes were established. Both the GO- and AuNP-based sensing platforms have been successfully applied for the detection of real DNA and RNA samples in vitro and in living cells. This study emphasizes the active roles of electrostatic effects in the PNA-nanomaterial interactions, which paves the way toward improving the performance of PNA-nanomaterial based assays of nucleic acids.
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Affiliation(s)
- Kriangsak Faikhruea
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Ilada Choopara
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Naraporn Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Wanchai Assavalapsakul
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
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Liu BW, Huang P, Wu FY. Rapid visual detection for nitroreductase based on the copper ions-induced and NADH-mediated aggregation of gold-silver alloy nanoparticles. Talanta 2021; 234:122681. [PMID: 34364481 DOI: 10.1016/j.talanta.2021.122681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/27/2021] [Accepted: 06/30/2021] [Indexed: 12/25/2022]
Abstract
Hypoxia refers to the lack of oxygen supply to cells or tissues. The overexpression of nitroreductase has been shown to be closely related to the degree of hypoxia, which leads to the level of nitroreductase (NTR) being used as an indicator of hypoxia. We reported a facile visual detection of NTR based on the aggregation of gold and silver alloy nanoparticles. Compared with gold nanoparticles (AuNPs), the aggregation behavior of Au80Ag20 NPs caused a more prominent color change. Copper ions (Cu2+) can be rapidly reduced by nicotinamide adenine dinucleotide (NADH) under the catalysis of Au80Ag20 NPs. But NADH is consumed as an electron donor during the catalytic reduction reaction of p-nitrophenol (pNP) by NTR. A decrease of NADH amount results in the aggregation of Au80Ag20 NPs by the excess Cu2+ and different aggregation degrees of Au80Ag20 NPs lead to observable color change. A linear correlation of A600/A505 = 0.0285 [NTR]+0.361 (R2 = 0.980) was obtained with a limit of detection (LOD) of 0.23 μg/mL for UV-vis spectrophotometer. For visual detection, the values of R/B against the concentration of NTR obtains a calibration curve of R/B = -0.031 [NTR]+ 1.54 (R2 = 0.985) with a LOD of 0.76 μg/mL, which is of the same order of magnitude as the UV-vis spectrophotometer analysis. As a comparison, Au80Ag20 NPs was replaced by several different composition nanoparticles (Au NPs, Au70Ag30 NPs, Au50Ag50 NPs) to be a chromogenic substrate, and the results suggest the Au80Ag20 NPs is the most sensitive substrate in our assay. Selectivity tests showed that the detection system did not respond to other common substances, and the reaction mechanism was verified by inhibitor research. Finally, the assay was used on the human serum samples with spiking NTR, and the recovery rates of this assay with UV-vis spectrophotometer were basically consistent with RGB analysis.
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Affiliation(s)
- Bo-Wen Liu
- College of Chemistry, Nanchang University, Nanchang, 330031, China
| | - Pengcheng Huang
- College of Chemistry, Nanchang University, Nanchang, 330031, China.
| | - Fang-Ying Wu
- College of Chemistry, Nanchang University, Nanchang, 330031, China.
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Liang X, Liu M, Komiyama M. Recognition of Target Site in Various Forms of DNA and RNA by Peptide Nucleic Acid (PNA): From Fundamentals to Practical Applications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2021. [DOI: 10.1246/bcsj.20210086] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Xingguo Liang
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
- Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao 266235, P. R. China
| | - Mengqin Liu
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
| | - Makoto Komiyama
- College of Food Science and Engineering, Ocean University of China, Qingdao 266003, P. R. China
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Development of a colorimetric sensor array based on monometallic and bimetallic nanoparticles for discrimination of triazole fungicides. Anal Bioanal Chem 2021; 414:5297-5308. [PMID: 33855603 DOI: 10.1007/s00216-021-03272-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/26/2021] [Accepted: 03/04/2021] [Indexed: 10/21/2022]
Abstract
Due to the widespread use of pesticides and their harmful effects on humans and wildlife, monitoring their residual amounts in crops is critically essential but still challenging regarding the development of high-throughput approaches. Herein, a colorimetric sensor array has been proposed for discrimination and identification of triazole fungicides using monometallic and bimetallic silver and gold nanoparticles. Aggregation-induced behavior of AgNPs, AuNPs, and Au-AgNPs in the presence of four triazole fungicides produced a fingerprint response pattern for each analyte. Innovative changes to the metal composition of nanoparticles leads to the production of entirely distinct response patterns that can be used for the detection and discrimination of triazoles. Pattern recognition methods, including linear discriminant analysis (LDA) and hierarchical cluster analysis, have been employed for the differentiation of triazoles in the concentration range of 0.1-0.55 μg mL-1. Besides, the sensor array demonstrates promising practicability to satisfactorily distinguished triazole in mixtures and complex media of wheat flour and cucumber samples. The proposed colorimetric sensor array might pave the way towards a cost-effective and rapid, yet sensitive platform for high-throughput monitoring of residual amounts of pesticides for on-site applications.
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