1
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Johansson TB, Davtyan R, Valderas-Gutiérrez J, Gonzalez Rodriguez A, Agnarsson B, Munita R, Fioretos T, Lilljebjörn H, Linke H, Höök F, Prinz CN. Sub-Nanomolar Detection of Oligonucleotides Using Molecular Beacons Immobilized on Lightguiding Nanowires. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:453. [PMID: 38470783 DOI: 10.3390/nano14050453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 03/14/2024]
Abstract
The detection of oligonucleotides is a central step in many biomedical investigations. The most commonly used methods for detecting oligonucleotides often require concentration and amplification before detection. Therefore, developing detection methods with a direct read-out would be beneficial. Although commonly used for the detection of amplified oligonucleotides, fluorescent molecular beacons have been proposed for such direct detection. However, the reported limits of detection using molecular beacons are relatively high, ranging from 100 nM to a few µM, primarily limited by the beacon fluorescence background. In this study, we enhanced the relative signal contrast between hybridized and non-hybridized states of the beacons by immobilizing them on lightguiding nanowires. Upon hybridization to a complementary oligonucleotide, the fluorescence from the surface-bound beacon becomes coupled in the lightguiding nanowire core and is re-emitted at the nanowire tip in a narrower cone of light compared with the standard 4π emission. Prior knowledge of the nanowire positions allows for the continuous monitoring of fluorescence signals from each nanowire, which effectively facilitates the discrimination of signals arising from hybridization events against background signals. This resulted in improved signal-to-background and signal-to-noise ratios, which allowed for the direct detection of oligonucleotides at a concentration as low as 0.1 nM.
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Affiliation(s)
- Therese B Johansson
- Division of Solid State Physics, Lund University, 221 00 Lund, Sweden
- NanoLund, Lund University, 221 00 Lund, Sweden
| | - Rubina Davtyan
- Division of Solid State Physics, Lund University, 221 00 Lund, Sweden
- NanoLund, Lund University, 221 00 Lund, Sweden
| | - Julia Valderas-Gutiérrez
- Division of Solid State Physics, Lund University, 221 00 Lund, Sweden
- NanoLund, Lund University, 221 00 Lund, Sweden
| | | | - Björn Agnarsson
- Division of Nano and Biophysics, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Roberto Munita
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund University, 221 00 Lund, Sweden
| | - Thoas Fioretos
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, 221 00 Lund, Sweden
| | - Henrik Lilljebjörn
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, 221 00 Lund, Sweden
| | - Heiner Linke
- Division of Solid State Physics, Lund University, 221 00 Lund, Sweden
- NanoLund, Lund University, 221 00 Lund, Sweden
| | - Fredrik Höök
- NanoLund, Lund University, 221 00 Lund, Sweden
- Division of Nano and Biophysics, Chalmers University of Technology, 412 96 Gothenburg, Sweden
| | - Christelle N Prinz
- Division of Solid State Physics, Lund University, 221 00 Lund, Sweden
- NanoLund, Lund University, 221 00 Lund, Sweden
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2
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Ghasemi M, Debnath PC, Kim B, Pournoury M, Khazaeinezhad R, Hosseinzadeh Kassani S, Yeom DI, Oh K. Highly nonlinear optic nucleic acid thin-solid film to generate short pulse laser. Sci Rep 2023; 13:17494. [PMID: 37840076 PMCID: PMC10577146 DOI: 10.1038/s41598-023-44242-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 10/05/2023] [Indexed: 10/17/2023] Open
Abstract
Using aqueous precursors, we report successfully fabricating thin-solid films of two nucleic acids, ribonucleic acid (RNA) and deoxyribonucleic acid (DNA). We investigated the potential of these films deposited on a fiber optic platform as all-fiber integrated saturable absorbers (SAs) for ultrafast nonlinear optics. RNA-SA performances were comparable to those of DNA-SA in terms of its nonlinear transmission, modulation depth, and saturation intensity. Upon insertion of these devices into an Erbium-doped fiber ring-laser cavity, both RNA and DNA SAs enabled efficient passive Q-switching operation. RNA-SA application further facilitated robust mode-locking and generated a transform-limited soliton pulse, exhibiting a pulse duration of 633 femtoseconds. A detailed analysis of these pulsed laser characteristics compared RNA and DNA fiber optic SAs with other nonlinear optic materials. The findings of this research establish the feasibility of utilizing RNA as a saturable absorber in ultrafast laser systems with an equal or higher potential as DNA, which presents novel possibilities for the nonlinear photonic applications of nucleic acid thin solid films.
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Affiliation(s)
- Marjan Ghasemi
- Photonic Device Physics Laboratory, Department of Physics, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 120-749, South Korea
| | - Pulak Chandra Debnath
- Department of Physics and Energy Systems Research, Ajou University, Suwon, 443-749, South Korea
| | - Byungjoo Kim
- Department of Laser and Electron Beam Technologies, Korea Institute of Machinery and Materials (KIMM), 156, Gajeongbuk-ro, Yuseong-gu, Daejeon, 34103, Republic of Korea
| | - Marzieh Pournoury
- Department of Electrical and Electronic Engineering, Yonsei University, Seoul, 03722, South Korea
| | - Reza Khazaeinezhad
- Beckman Laser Institute, University of California, Irvine, Irvine, CA, 92697, USA
| | | | - Dong-Il Yeom
- Department of Physics and Energy Systems Research, Ajou University, Suwon, 443-749, South Korea
| | - Kyunghwan Oh
- Photonic Device Physics Laboratory, Department of Physics, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 120-749, South Korea.
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3
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Wang Z, Lou X. Recent Progress in Functional-Nucleic-Acid-Based Fluorescent Fiber-Optic Evanescent Wave Biosensors. BIOSENSORS 2023; 13:bios13040425. [PMID: 37185500 PMCID: PMC10135899 DOI: 10.3390/bios13040425] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/20/2023] [Accepted: 03/25/2023] [Indexed: 05/17/2023]
Abstract
Biosensors capable of onsite and continuous detection of environmental and food pollutants and biomarkers are highly desired, but only a few sensing platforms meet the "2-SAR" requirements (sensitivity, specificity, affordability, automation, rapidity, and reusability). A fiber optic evanescent wave (FOEW) sensor is an attractive type of portable device that has the advantages of high sensitivity, low cost, good reusability, and long-term stability. By utilizing functional nucleic acids (FNAs) such as aptamers, DNAzymes, and rational designed nucleic acid probes as specific recognition ligands, the FOEW sensor has been demonstrated to be a general sensing platform for the onsite and continuous detection of various targets ranging from small molecules and heavy metal ions to proteins, nucleic acids, and pathogens. In this review, we cover the progress of the fluorescent FNA-based FOEW biosensor since its first report in 1995. We focus on the chemical modification of the optical fiber and the sensing mechanisms for the five above-mentioned types of targets. The challenges and prospects on the isolation of high-quality aptamers, reagent-free detection, long-term stability under application conditions, and high throughput are also included in this review to highlight the future trends for the development of FOEW biosensors capable of onsite and continuous detection.
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Affiliation(s)
- Zheng Wang
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing 100048, China
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing 100048, China
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4
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Prajapati GK, Kumar A, Wany A, Pandey DM. Molecular Beacon Probe (MBP)-Based Real-Time PCR. Methods Mol Biol 2023; 2638:273-287. [PMID: 36781649 DOI: 10.1007/978-1-0716-3024-2_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
In the advancement of molecular biology techniques, several probe-based techniques, like molecular beacon probe (MBP) assay, TaqMan probe, and minor groove binder (MGB) probe assay, have been reported to identify specific sequences through real-time polymerase chain reaction (PCR). All probe-based methods are more sensitive than the conventional PCR for the detection and quantification of target genes. MBP is a hydrolysis probe that emits fluorescence when getting the specific sequences on the gene. Here, we describe the application of MBP for the identification of the motif sequences present in the promoters of differentially expressed genes.
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Affiliation(s)
- Gopal Kumar Prajapati
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.,R & D Biologics Division, Promea Therapeutics Pvt Ltd, Sultanpur, Hyderabad, India
| | - Ashutosh Kumar
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.,Department of Biotechnology, School of Sciences, PP Savani University, Kosamba, Surat, Gujarat, India
| | - Aakanksha Wany
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.,Department of Biotechnology, School of Sciences, PP Savani University, Kosamba, Surat, Gujarat, India
| | - Dev Mani Pandey
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, India.
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5
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Gao Y, Zhang S, Wu C, Li Q, Shen Z, Lu Y, Wu ZS. Self-Protected DNAzyme Walker with a Circular Bulging DNA Shield for Amplified Imaging of miRNAs in Living Cells and Mice. ACS NANO 2021; 15:19211-19224. [PMID: 34854292 DOI: 10.1021/acsnano.1c04260] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Abnormal expression of miRNAs is often detected in various human cancers. DNAzyme machines combined with gold nanoparticles (AuNPs) hold promise for detecting specific miRNAs in living cells but show short circulation time due to the fragility of catalytic core. Using miRNA-21 as the model target, by introducing a circular bulging DNA shield into the middle of the catalytic core, we report herein a self-protected DNAzyme (E) walker capable of fully stepping on the substrate (S)-modified AuNP for imaging intracellular miRNAs. The DNAzyme walker exhibits 5-fold enhanced serum resistance and more than 8-fold enhanced catalytic activity, contributing to the capability to image miRNAs much higher than commercial transfection reagent and well-known FISH technique. Diseased cells can accurately be distinguished from healthy cells. Due to its universality, DNAzyme walker can be extended for imaging other miRNAs only by changing target binding domain, indicating a promising tool for cancer diagnosis and prognosis.
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Affiliation(s)
- Yansha Gao
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Songbai Zhang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- College of Chemistry and Materials Engineering, Hunan University of Arts and Science, Changde 415000, China
| | - Chengwei Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Qian Li
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
| | - Zhifa Shen
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, and Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Yi Lu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou, 350002, China
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6
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Gao J, Liu Q, Liu W, Jin Y, Li B. Comparative evaluation and design of a G-triplex/thioflavin T-based molecular beacon. Analyst 2021; 146:2567-2573. [PMID: 33899063 DOI: 10.1039/d1an00252j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Both G-quadruplex (G4) and G-triplex (G3) can bind thioflavin T (ThT) to light up the fluorescence of ThT. G4/ThT and G3/ThT can be used as fluorescent indicators to construct a label-free molecular beacon (MB). In this work, we present a comparative perspective of G3/ThT-based MB and G4/ThT-based MB. The results showed that the G3/ThT-based MB had higher sensitivity and faster response speed than the G4/ThT-based MB. Furthermore, we systematically studied the effect of stem length and varying pairs on the response of the G3/ThT-based MB, and then proposed one rational design of the G3/ThT-based MB. This work demonstrates that the shorter G3 is more suitable for constructing the MB stem. This present work opens a promising way to develop a sensitive, simple and homogeneous biosensing method.
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Affiliation(s)
- Jingru Gao
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
| | - Qiang Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
| | - Wei Liu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
| | - Yan Jin
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
| | - Baoxin Li
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education; Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
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7
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Zhao J, Lu Z, Wang S, Wei Z, Zhou J, Ren S, Lou X. Nanoscale Affinity Double Layer Overcomes the Poor Antimatrix Interference Capability of Aptamers. Anal Chem 2021; 93:4317-4325. [PMID: 33620193 DOI: 10.1021/acs.analchem.0c05320] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Poor antimatrix interference capability of aptamers is one of the major obstacles preventing their wide applications for real-sample detections. Here, we devise a multiple-function interface, denoted as a nanoscale affinity double layer (NADL), to overcome this bottleneck via in situ simultaneous target enrichment, purification, and detection. The NADL consists of an upper aptamer layer for target purification and sensing and a lower nanoscale solid-phase microextraction (SPME) layer for sample enrichment. The targets flowing through the NADL-functionalized surface are instantly million-fold enriched and purified by the sequential extraction of aptamer and SPME. The formation of the aptamer-target complex is greatly enhanced, enabling ultrasensitive detection of targets with minimized interference from the matrix. Taking the fiber-optic evanescent wave sensor as an example, we demonstrated the feasibility and generality of the NADL. The unprecedented detection of limits of 800, 4.8, 40, and 0.14 fM were, respectively, achieved for three representative small-molecule targets with distinct hydrophobicity (kanamycin A, sulfadimethoxine, and di-(2-ethylhexyl) phthalate) and protein target (human serum albumin), corresponding to 2500 to 3 × 108-fold improvement compared to the sensors without the NADL. Our sensors also showed exceptionally high target specificity (>1000) and tunable dynamic ranges simply by manipulating the SPME layer. With these features comes the ability to directly detect targets in diluted environmental, food, and biological samples at concentrations all well below the tolerance limits.
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Affiliation(s)
- Jiaxing Zhao
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Zhangwei Lu
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Shuo Wang
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Zhenzhe Wei
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Jianshuo Zhou
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Shang Ren
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
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8
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Optical fibers in analytical electrochemistry: Recent developments in probe design and applications. Trends Analyt Chem 2021. [DOI: 10.1016/j.trac.2021.116196] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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9
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Tseng YT, Li WY, Yu YW, Chiang CY, Liu SQ, Chau LK, Lai NS, Chou CC. Fiber Optic Particle Plasmon Resonance Biosensor for Label-Free Detection of Nucleic Acids and Its Application to HLA-B27 mRNA Detection in Patients with Ankylosing Spondylitis. SENSORS 2020; 20:s20113137. [PMID: 32492975 PMCID: PMC7309088 DOI: 10.3390/s20113137] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 05/22/2020] [Accepted: 05/29/2020] [Indexed: 11/27/2022]
Abstract
We developed a label-free, real-time, and highly sensitive nucleic acid biosensor based on fiber optic particle plasmon resonance (FOPPR). The biosensor employs a single-strand deoxyoligonucleotides (ssDNA) probe, conjugated to immobilized gold nanoparticles on the core surface of an optical fiber. We explore the steric effects on hybridization affinity and limit of detection (LOD), by using different ssDNA probe designs and surface chemistries, including diluent molecules of different lengths in mixed self-assembled monolayers, ssDNA probes of different oligonucleotide lengths, ssDNA probes in different orientations to accommodate target oligonucleotides with a hybridization region located unevenly in the strand. Based on the optimized ssDNA probe design and surface chemistry, we achieved LOD at sub-nM level, which makes detection of target oligonucleotides as low as 1 fmol possible in the 10-μL sensor chip. Additionally, the FOPPR biosensor shows a good correlation in determining HLA-B27 mRNA, in extracted blood samples from patients with ankylosing spondylitis (AS), with the clinically accepted real-time reverse transcription-polymerase chain reaction (RT-PCR) method. The results from this fundamental study should guide the design of ssDNA probe for anti-sense sensing. Further results through application to HLA-B27 mRNA detection illustrate the feasibility in detecting various nucleic acids of chemical and biological relevance.
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Affiliation(s)
- Yen-Ta Tseng
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection, National Chung Cheng University, Chiayi 62102, Taiwan; (Y.-T.T.); (W.-Y.L.); (Y.-W.Y.); (C-Y.C.)
| | - Wan-Yun Li
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection, National Chung Cheng University, Chiayi 62102, Taiwan; (Y.-T.T.); (W.-Y.L.); (Y.-W.Y.); (C-Y.C.)
| | - Ya-Wen Yu
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection, National Chung Cheng University, Chiayi 62102, Taiwan; (Y.-T.T.); (W.-Y.L.); (Y.-W.Y.); (C-Y.C.)
| | - Chang-Yue Chiang
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection, National Chung Cheng University, Chiayi 62102, Taiwan; (Y.-T.T.); (W.-Y.L.); (Y.-W.Y.); (C-Y.C.)
- Graduate School of Engineering Science and Technology, National Yunlin University of Science and Technology, Yunlin 64002, Taiwan
| | - Su-Qin Liu
- Immunology and Rheumatology, Department of Medicine, Buddhist Dalin Tzu Chi General Hospital, Chiayi 62247, Taiwan;
| | - Lai-Kwan Chau
- Department of Chemistry and Biochemistry and Center for Nano Bio-Detection, National Chung Cheng University, Chiayi 62102, Taiwan; (Y.-T.T.); (W.-Y.L.); (Y.-W.Y.); (C-Y.C.)
- Correspondence: (L.-K.C.); (N.-S.L.); (C.-C.C.); Tel.: +886-5-2729377 (L.-K.C.); +886-5-264-8000 (ext. 5003) (N.-S.L.); +886-5-2720411 (ext. 66506) (C.-C.C.)
| | - Ning-Sheng Lai
- Immunology and Rheumatology, Department of Medicine, Buddhist Dalin Tzu Chi General Hospital, Chiayi 62247, Taiwan;
- Correspondence: (L.-K.C.); (N.-S.L.); (C.-C.C.); Tel.: +886-5-2729377 (L.-K.C.); +886-5-264-8000 (ext. 5003) (N.-S.L.); +886-5-2720411 (ext. 66506) (C.-C.C.)
| | - Cheng-Chung Chou
- Department of Biomedical Sciences, National Chung Cheng University, Chiayi 62102, Taiwan
- Correspondence: (L.-K.C.); (N.-S.L.); (C.-C.C.); Tel.: +886-5-2729377 (L.-K.C.); +886-5-264-8000 (ext. 5003) (N.-S.L.); +886-5-2720411 (ext. 66506) (C.-C.C.)
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10
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Han S, Liu W, Zheng M, Wang R. Label-Free and Ultrasensitive Electrochemical DNA Biosensor Based on Urchinlike Carbon Nanotube-Gold Nanoparticle Nanoclusters. Anal Chem 2020; 92:4780-4787. [PMID: 32054266 DOI: 10.1021/acs.analchem.9b03520] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nanomaterials have been extensively utilized in biosensing systems for highly sensitive and selective detection of a variety of biotargets. In this work, a facile, label-free, and ultrasensitive electrochemical DNA biosensor has been developed, based on "urchinlike" carbon nanotube-gold nanoparticle (CNT-AuNP) nanoclusters, for signal amplification. Specifically, electrochemical polymerization of dopamine (DA) was employed to modify a gold electrode for immobilization of DNA probes through the Schiff base reaction. Upon sensing the target nucleic acid, the dual-DNA (reporter and linker) functionalized AuNPs were introduced into the sensing system via DNA hybridization. Afterward, the end-modified single-wall carbon nanotubes with DNA (SWCNT-DNA) were attached to the surface of the AuNPs through linker-DNA hybridization that formed 3D radial nanoclusters, which generated a remarkable electrochemical response. Because of the larger contact surface area and super electronic conductivity of CNT-AuNP clusters, this novel designed 3D radial nanostructure exhibits an ultrasensitive detection of DNA, with a detection limit of 5.2 fM (a linear range of from 0.1 pM to 10 nM), as well as a high selectivity that discriminates single-mismatched DNA from fully matched target DNA under optimal conditions. This biosensor, which combines the synergistic properties of both CNTs and AuNPs, represents a promising signal amplification strategy for achieving a sensitive biosensor for DNA detection and diagnostic applications.
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Affiliation(s)
- Shuo Han
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Wenyan Liu
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, United States.,Center for Research in Energy and Environment, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
| | - Ming Zheng
- Materials Science and Engineering Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Risheng Wang
- Department of Chemistry, Missouri University of Science and Technology, Rolla, Missouri 65409, United States
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11
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Qi X, Xia L, Li Y, Wang T, Zhang X, Chen J, Zhang L, Fu Y. The Fabrication of 2D Cu-Based MOF Nanosheets for DNA Detection. Aust J Chem 2019. [DOI: 10.1071/ch19312] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The Cu-based metal–organic framework (MOF) analogues, copper 1,4-benzenedicarboxylate (CuBDC), copper 2,6-naphthalenedicarboxylate (Cu(2,6-NDC)), and copper 1,4-naphthalenedicarboxylate (Cu(1,4-NDC)) MOF nanosheets, are prepared as biosensor nanoplatforms for DNA detection by a spray method. With the ultrathin 2D structure, the fabricated MOF nanosheets exhibited better detection of target DNA, in particular when compared with the corresponding 3D MOF bulky crystals, when used as a DNA biosensor platform. The Cu(1,4-NDC) nanosheets display a distinct sensitivity with a detection limit of 0.3nM and linear range of 0–20nM, and selectivity for the target DNA or target DNA mixture. The feasible biosensor nanoplatform composed of 2D MOF nanosheets broadens the application scope of MOF nanosheets.
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12
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Qiu Y, Tang Y, Li B, He M. Rapid detection of cocaine using aptamer-based biosensor on an evanescent wave fibre platform. ROYAL SOCIETY OPEN SCIENCE 2018; 5:180821. [PMID: 30473831 PMCID: PMC6227954 DOI: 10.1098/rsos.180821] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 09/13/2018] [Indexed: 05/11/2023]
Abstract
The rapid detection of cocaine has received considerable attention because of the instantaneous and adverse effects of cocaine overdose on human health. Aptamer-based biosensors for cocaine detection have been well established for research and application. However, reducing the analytic duration without deteriorating the sensitivity still remains as a challenge. Here, we proposed an aptamer-based evanescent wave fibre (EWF) biosensor to rapidly detect cocaine in a wide working range. At first, the aptamers were conjugated to complementary DNA with fluorescence tag and such conjugants were then immobilized on magnetic beads. After cocaine was introduced to compete against the aptamer-DNA conjugants, the released DNA in supernatant was detected on the EWF platform. The dynamic curves of EWF signals could be interpreted by the first-order kinetics and saturation model. The semi-log calibration curve covered a working range of 10-5000 µM of cocaine, and the limit of detection was approximately 10.5 µM. The duration of the full procedure was 990 s (16.5 min), and the detection interval was 390 s (6.5 min). The specified detection of cocaine was confirmed from four typical pharmaceutic agents. The analysis was repeated for 50 cycles without significant loss of sensitivity. Therefore, the aptamer-based EWF biosensor is a feasible solution to rapidly detect cocaine.
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Affiliation(s)
- Yong Qiu
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, People's Republic of China
| | - Yunfei Tang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, People's Republic of China
- Ecological Environmental Protection Investments Company, China Communications Construction Corporation, Beijing 100013, People's Republic of China
| | - Bing Li
- School of Energy and Environmental Engineering, University of Beijing Science and Technology, Beijing 100083, People's Republic of China
| | - Miao He
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, People's Republic of China
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13
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Abstract
Aptamer biosensor that can switch its structure upon target binding offers a powerful strategy for molecular detection. However, the process of converting an aptamer into a "structure-switching" biosensor is challenging and often relies on trial-and-error without established design principles. In this Sensor Issues, we examine a variety of design approaches for incorporating structure-switching functionality into existing aptamers, and provide thermodynamic analyses to highlight the variables that most strongly influence their performance. Finally, we also describe emerging efforts for incorporating the structure-switching functionality directly into the aptamer selection process.
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Affiliation(s)
- Trevor A. Feagin
- Department of Electrical Engineering, Stanford University,350 Serra Mall, Stanford, California 94305, United States
- Department of Radiology, Stanford University School of Medicine,300 Pasteur Drive, Stanford, California 94305, United States
| | - Nicolò Maganzini
- Department of Electrical Engineering, Stanford University,350 Serra Mall, Stanford, California 94305, United States
| | - Hyongsok Tom Soh
- Department of Electrical Engineering, Stanford University,350 Serra Mall, Stanford, California 94305, United States
- Department of Radiology, Stanford University School of Medicine,300 Pasteur Drive, Stanford, California 94305, United States
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14
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Zainuddin NH, Chee HY, Ahmad MZ, Mahdi MA, Abu Bakar MH, Yaacob MH. Sensitive Leptospira DNA detection using tapered optical fiber sensor. JOURNAL OF BIOPHOTONICS 2018; 11:e201700363. [PMID: 29570957 DOI: 10.1002/jbio.201700363] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 03/16/2018] [Accepted: 03/19/2018] [Indexed: 06/08/2023]
Abstract
This paper presents the development of tapered optical fiber sensor to detect a specific Leptospira bacteria DNA. The bacteria causes Leptospirosis, a deadly disease but with common early flu-like symptoms. Optical single mode fiber (SMF) of 125 μm diameter is tapered to produce 12 μm waist diameter and 15 cm length. The novel DNA-based optical fiber sensor is functionalized by incubating the tapered region with sodium hydroxide (NaOH), (3-Aminopropyl) triethoxysilane and glutaraldehyde. Probe DNA is immobilized onto the tapered region and subsequently hybridized by its complementary DNA (cDNA). The transmission spectra of the DNA-based optical fiber sensor are measured in the 1500 to 1600 nm wavelength range. It is discovered that the shift of the wavelength in the SMF sensor is linearly proportional with the increase in the cDNA concentrations from 0.1 to 1.0 nM. The sensitivity of the sensor toward DNA is measured to be 1.2862 nm/nM and able to detect as low as 0.1 fM. The sensor indicates high specificity when only minimal shift is detected for non-cDNA testing. The developed sensor is able to distinguish between actual DNA of Leptospira serovars (Canicola and Copenhageni) against Clostridium difficile (control sample) at very low (femtomolar) target concentrations.
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Affiliation(s)
- Nurul H Zainuddin
- Department of Computer and Communication Systems, Faculty of Engineering, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Wireless and Photonic Networks Research Centre (WiPNET), Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Hui Y Chee
- Department of Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Muhammad Z Ahmad
- Biotechnology and Nanotechnology Research Center, Malaysian Agricultural Research and Development Institute (MARDI), Serdang, Selangor, Malaysia
| | - Mohd A Mahdi
- Department of Computer and Communication Systems, Faculty of Engineering, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Wireless and Photonic Networks Research Centre (WiPNET), Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Muhammad H Abu Bakar
- Department of Computer and Communication Systems, Faculty of Engineering, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Wireless and Photonic Networks Research Centre (WiPNET), Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mohd H Yaacob
- Department of Computer and Communication Systems, Faculty of Engineering, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Wireless and Photonic Networks Research Centre (WiPNET), Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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15
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Electronic Detection of DNA Hybridization by Coupling Organic Field-Effect Transistor-Based Sensors and Hairpin-Shaped Probes. SENSORS 2018; 18:s18040990. [PMID: 29584638 PMCID: PMC5948917 DOI: 10.3390/s18040990] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 03/20/2018] [Accepted: 03/23/2018] [Indexed: 11/16/2022]
Abstract
In this paper, the electronic transduction of DNA hybridization is presented by coupling organic charge-modulated field-effect transistors (OCMFETs) and hairpin-shaped probes. These probes have shown interesting properties in terms of sensitivity and selectivity in other kinds of assays, in the form of molecular beacons (MBs). Their integration with organic-transistor based sensors, never explored before, paves the way to a new class of low-cost, easy-to-use, and portable genetic sensors with enhanced performances. Thanks to the peculiar characteristics of the employed sensor, measurements can be performed at relatively high ionic strengths, thus optimizing the probes’ functionality without affecting the detection ability of the device. A complete electrical characterization of the sensor is reported, including calibration with different target concentrations in the measurement environment and selectivity evaluation. In particular, DNA hybridization detection for target concentration as low as 100 pM is demonstrated.
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16
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Meng R, Liu Q, Jin Y, Li B. Dual-Hemin-Labelled Catalytic Molecular Beacon: A Monomer-Dimer Switching Probe for Sensitive Chemiluminescence Detection of Biomolecules. ChemistrySelect 2018. [DOI: 10.1002/slct.201702963] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Rong Meng
- School of Chemistry & Chemical Engineering, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Shaanxi Normal University; Xi'an 710062 China
| | - Qiang Liu
- School of Chemistry & Chemical Engineering, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Shaanxi Normal University; Xi'an 710062 China
| | - Yan Jin
- School of Chemistry & Chemical Engineering, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Shaanxi Normal University; Xi'an 710062 China
| | - Baoxin Li
- School of Chemistry & Chemical Engineering, Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province; Shaanxi Normal University; Xi'an 710062 China
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17
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Liu J, Zhou X, Shi H. An Optical Biosensor-Based Quantification of the Microcystin Synthetase A Gene: Early Warning of Toxic Cyanobacterial Blooming. Anal Chem 2018; 90:2362-2368. [PMID: 29303555 DOI: 10.1021/acs.analchem.7b04933] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The monitoring and control of toxic cyanobacterial strains, which can produce microcystins, is critical to protect human and ecological health. We herein reported an optical-biosensor-based quantification of the microcystin synthetase A (mcyA) gene so as to discriminate microcystin-producing strains from nonproducing strains. In this assay, the mcyA-specific ssDNA probes were designed in silico with an on-line tool and then synthesized to be covalently immobilized on an optical-fiber surface. Production of fluorescently modified target DNA fragment amplicons was accomplished through the use of Cy5-tagged deoxycytidine triphosphates (dCTPs) in the polymerase chain reaction (PCR) method, which resulted in copies with internally labeled multiple sites per DNA molecule and delivered great sensitivity. With a facile surface-based hybridization process, the PCR amplicons were captured on the optical-fiber surface and were induced by an evanescent-wave field into fluorescence emission. Under the optimum conditions, the detection limit was found to be 10 pM (S/N ratio = 3) and equaled 103 gene copies/mL. The assay was triumphantly demonstrated for PCR amplicons of mcyA detection and showed satisfactory stability and reproducibility. Moreover, the sensing system exhibited excellent selectivity with quantitative spike recoveries from 87 to 102% for M. aeruginosa species in the mixed samples. There results confirmed that the method would serve as an accurate, cost-effective, and rapid technique for in-field testing of toxic Microcystis sp. in water, giving early information for water quality monitoring against microcystin-producing cyanobacteria.
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Affiliation(s)
- Jinchuan Liu
- State Key Joint Laboratory of ESPC, School of Environment and ‡Center for Sensor Technology of Environment and Health, Tsinghua University , Beijing 100084, China
| | - Xiaohong Zhou
- State Key Joint Laboratory of ESPC, School of Environment and ‡Center for Sensor Technology of Environment and Health, Tsinghua University , Beijing 100084, China
| | - Hanchang Shi
- State Key Joint Laboratory of ESPC, School of Environment and ‡Center for Sensor Technology of Environment and Health, Tsinghua University , Beijing 100084, China
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18
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Evanescent wave aptasensor for continuous and online aminoglycoside antibiotics detection based on target binding facilitated fluorescence quenching. Biosens Bioelectron 2017; 102:646-651. [PMID: 29268187 DOI: 10.1016/j.bios.2017.12.006] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Revised: 11/22/2017] [Accepted: 12/05/2017] [Indexed: 10/18/2022]
Abstract
The biosensors capable for on-site continuous and online monitoring of pollutants in environment are highly desired due to their practical importance and convenience. The group specific detection of pollutants is especially attractive due to the diversity of environmental pollutants. Here we devise an evanescent wave aptasensor based on target binding facilitated fluorescence quenching (FQ-EWA) for the online continuous and group-specific detection of aminoglycoside antibiotics (AMGAs). In FQ-EWA, a fluorophore labeled DNA aptamer selected against kanamycin was used for both the target recognition in solution and signal transduction on optical fiber of EWA. The aptamers form multiple-strand complex (M-Apt) in the absence of AMGAs. The binding between AMGA and the aptamer disrupts M-Apt and leads to the formation of AMGA -aptamer complex (AMGA-Apt). The photo-induced electron transfer between the fluorophore and AMGA partially quenches the fluorescence of AMGA-Apt. The structure-selective absorption of AMGA-Apt over M-Apt on the graphene oxide further quenches the fluorescence of AMGA-Apt. Meanwhile, the unbound aptamers in solution assemble with the unlabeled aptamers immobilized on the fiber to form M-Apt. The amount of M-Apt on the fiber is inversely proportional to the concentration of AMGAs, enabling the signal-off detection of AMGAs from 200nM to 200μM with a detection limit of 26nM. The whole detection process is carried out in an online mode without any offline operation, providing a great benefit for system automation and miniaturization. FQ-EWA also shows great surface regeneration capability and enables the continuous detection more than 60 times.
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19
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Gao S, Sun LP, Li J, Jin L, Ran Y, Huang Y, Guan BO. High-sensitivity DNA biosensor based on microfiber Sagnac interferometer. OPTICS EXPRESS 2017; 25:13305-13313. [PMID: 28788866 DOI: 10.1364/oe.25.013305] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 05/25/2017] [Indexed: 06/07/2023]
Abstract
Nucleic acid detection with label-free biosensors circumvents the need for costly fluorophore functionalization steps associated with conventional assays by utilizing optical fiber transducers. In spite of their technological prowess, however, these biosensors' sensitivity is limited by the design/configuration of their transducers. Therefore, it is imperative to integrate novel optical fiber transducers with existing label-free approaches to overcome those limitations. Herein, we present a high sensitivity label-free fiber optic biosensor that employs polarimetric interference of a high-birefringence (Hi-Bi) microfiber to specifically detect DNA molecules. A slight target DNA concentration change is converted into an optical wavelength shift of polarimetric interference generated by the microfiber Sagnac interferometer. The sensor provides a log-linear response to target ssDNA concentrations range from 100 pM to 1 μM and a minimum detectable concentration of 75 pM.
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20
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Yu L, Wang Y, Wu Q, Yuan Z, Xie X, Wang Z, Wang N, Huang X, Huang W. Surface-controlled preparation of EuWO 4(OH) nanobelts and their hybrid with Au nanoparticles as a novel enzyme-free sensing platform towards hydrogen peroxide. Chem Commun (Camb) 2017; 53:5063-5066. [PMID: 28435944 DOI: 10.1039/c7cc00734e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
EuWO4(OH) nanobelts were synthesized for the first time via a thiourea-assisted hydrothermal reaction. The nanobelts were further hybridized with Au nanoparticles (NPs) and showed excellent performance in H2O2 detection, due to both the enzyme-mimic catalytic properties of Au NPs and the radical responsive -OH groups on the EuWO4(OH) nanobelt surfaces.
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Affiliation(s)
- Linglin Yu
- Key Laboratory of Flexible Electronics (KLOFE) & Institute of Advanced Materials (IAM), Jiangsu National Synergistic Innovation Center for Advanced Materials (SICAM), Nanjing Tech University (NanjingTech), 30 South Puzhu Road, Nanjing 211816, P. R. China.
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21
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Single palindromic molecular beacon-based amplification for genetic analysis of cancers. Biosens Bioelectron 2017; 91:692-698. [DOI: 10.1016/j.bios.2017.01.035] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 01/13/2017] [Accepted: 01/17/2017] [Indexed: 12/20/2022]
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22
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A label-free colorimetric isothermal cascade amplification for the detection of disease-related nucleic acids based on double-hairpin molecular beacon. Anal Chim Acta 2017; 957:55-62. [DOI: 10.1016/j.aca.2016.12.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 12/10/2016] [Accepted: 12/16/2016] [Indexed: 11/20/2022]
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23
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Wang R, Zhou X, Zhu X, Yang C, Liu L, Shi H. Isoelectric Bovine Serum Albumin: Robust Blocking Agent for Enhanced Performance in Optical-Fiber Based DNA Sensing. ACS Sens 2017; 2:257-262. [PMID: 28723134 DOI: 10.1021/acssensors.6b00746] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Surface blocking is a well-known process for reducing unwanted nonspecific adsorption in sensor fabrication, especially important in the emerging field where DNA/RNA applied. Bovine serum albumin (BSA) is one of the most popular blocking agents with an isoelectric point at pH 4.6. Although it is widely recognized that the adsorption of a blocking agent is strongly affected by its net charge and the maximum adsorption is often observed under its isoelectric form, BSA has long been perfunctorily used for blocking merely in neutral solution, showing poor blocking performances in the optical-fiber evanescent wave (OFEW) based sensing toward DNA target. To meet this challenge, we first put forward the view that isoelectric BSA (iep-BSA) has the best blocking performance and use an OFEW sensor platform to demonstrate this concept. An optical-fiber was covalently modified with amino-DNA, and further coupled with the optical system to detect fluorophore labeled complementary DNA within the evanescent field. A dramatic improvement in the reusability of this DNA modified sensing surface was achieved with 120 stable detection cycles, which ensured accurate quantitative bioassay. As expected, the iep-BSA blocked OFEW system showed enhanced sensing performance toward target DNA with a detection limit of 125 pM. To the best of our knowledge, this is the highest number of regeneration cycles ever reported for a DNA immobilized optical-fiber surface. This study can also serve as a good reference and provide important implications for developing similar DNA-directed surface biosensors.
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Affiliation(s)
- Ruoyu Wang
- State Key Joint Laboratory
of ESPC; Research Centre of Environmental and Health Sensing Technology,
School of Environment, Tsinghua University, Beijing 100084, China
| | - Xiaohong Zhou
- State Key Joint Laboratory
of ESPC; Research Centre of Environmental and Health Sensing Technology,
School of Environment, Tsinghua University, Beijing 100084, China
| | - Xiyu Zhu
- State Key Joint Laboratory
of ESPC; Research Centre of Environmental and Health Sensing Technology,
School of Environment, Tsinghua University, Beijing 100084, China
| | - Chao Yang
- State Key Joint Laboratory
of ESPC; Research Centre of Environmental and Health Sensing Technology,
School of Environment, Tsinghua University, Beijing 100084, China
| | - Lanhua Liu
- State Key Joint Laboratory
of ESPC; Research Centre of Environmental and Health Sensing Technology,
School of Environment, Tsinghua University, Beijing 100084, China
| | - Hanchang Shi
- State Key Joint Laboratory
of ESPC; Research Centre of Environmental and Health Sensing Technology,
School of Environment, Tsinghua University, Beijing 100084, China
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24
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Rapisarda A, Giamblanco N, Marletta G. Kinetic discrimination of DNA single-base mutations by localized surface plasmon resonance. J Colloid Interface Sci 2017; 487:141-148. [DOI: 10.1016/j.jcis.2016.10.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 10/20/2022]
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25
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Xu J, Zheng T, Le J, Jia L. Long-stem shaped multifunctional molecular beacon for highly sensitive nucleic acids determination via intramolecular and intermolecular interactions based strand displacement amplification. Analyst 2017; 142:4438-4445. [DOI: 10.1039/c7an01205e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
LS-MMB based intra-SDA and inter-SDA for amplified gene signaling.
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Affiliation(s)
- Jianguo Xu
- School of Food Science and Engineering
- Hefei University of Technology
- Hefei 230009
- China
- Cancer Metastasis Alert and Prevention Center
| | - Tingting Zheng
- Cancer Metastasis Alert and Prevention Center
- and Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy
- Fuzhou University
| | - Jingqing Le
- Cancer Metastasis Alert and Prevention Center
- and Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy
- Fuzhou University
| | - Lee Jia
- Cancer Metastasis Alert and Prevention Center
- and Pharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment
- College of Chemistry
- Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy
- Fuzhou University
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26
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Khater M, de la Escosura-Muñiz A, Merkoçi A. Biosensors for plant pathogen detection. Biosens Bioelectron 2016; 93:72-86. [PMID: 27818053 DOI: 10.1016/j.bios.2016.09.091] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 09/15/2016] [Accepted: 09/26/2016] [Indexed: 10/20/2022]
Abstract
Infectious plant diseases are caused by pathogenic microorganisms such as fungi, bacteria, viruses, viroids, phytoplasma and nematodes. Worldwide, plant pathogen infections are among main factors limiting crop productivity and increasing economic losses. Plant pathogen detection is important as first step to manage a plant disease in greenhouses, field conditions and at the country boarders. Current immunological techniques used to detect pathogens in plant include enzyme-linked immunosorbent assays (ELISA) and direct tissue blot immunoassays (DTBIA). DNA-based techniques such as polymerase chain reaction (PCR), real time PCR (RT-PCR) and dot blot hybridization have also been proposed for pathogen identification and detection. However these methodologies are time-consuming and require complex instruments, being not suitable for in-situ analysis. Consequently, there is strong interest for developing new biosensing systems for early detection of plant diseases with high sensitivity and specificity at the point-of-care. In this context, we revise here the recent advancement in the development of advantageous biosensing systems for plant pathogen detection based on both antibody and DNA receptors. The use of different nanomaterials such as nanochannels and metallic nanoparticles for the development of innovative and sensitive biosensing systems for the detection of pathogens (i.e. bacteria and viruses) at the point-of-care is also shown. Plastic and paper-based platforms have been used for this purpose, offering cheap and easy-to-use really integrated sensing systems for rapid on-site detection. Beside devices developed at research and development level a brief revision of commercially available kits is also included in this review.
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Affiliation(s)
- Mohga Khater
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and Barcelona Institute of Science and Technology, Campus UAB, 08193 Barcelona, Spain; On leave from Agricultural Research Center (ARC), Ministry of Agriculture and Land Reclamation, Giza, Egypt
| | - Alfredo de la Escosura-Muñiz
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and Barcelona Institute of Science and Technology, Campus UAB, 08193 Barcelona, Spain
| | - Arben Merkoçi
- Catalan Institute of Nanoscience and Nanotechnology (ICN2), CSIC and Barcelona Institute of Science and Technology, Campus UAB, 08193 Barcelona, Spain; ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain.
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27
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Del Bonis-O'Donnell JT, Vong D, Pennathur S, Fygenson DK. A universal design for a DNA probe providing ratiometric fluorescence detection by generation of silver nanoclusters. NANOSCALE 2016; 8:14489-96. [PMID: 27406901 DOI: 10.1039/c6nr03827a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
DNA-stabilized silver nanoclusters (AgNCs), the fluorescence emission of which can rival that of typical organic fluorophores, have made possible a new class of label-free molecular beacons for the detection of single-stranded DNA. Like fluorophore-quencher molecular beacons (FQ-MBs) AgNC-based molecular beacons (AgNC-MBs) are based on a single-stranded DNA that undergoes a conformational change upon binding a target sequence. The new conformation exposes a stretch of single-stranded DNA capable of hosting a fluorescent AgNC upon reduction in the presence of Ag(+) ions. The utility of AgNC-MBs has been limited, however, because changing the target binding sequence unpredictably alters cluster fluorescence. Here we show that the original AgNC-MB design depends on bases in the target-binding (loop) domain to stabilize its AgNC. We then rationally alter the design to overcome this limitation. By separating and lengthening the AgNC-stabilizing domain, we create an AgNC-hairpin probe with consistent performance for arbitrary target sequence. This new design supports ratiometric fluorescence measurements of DNA target concentration, thereby providing a more sensitive, responsive and stable signal compared to turn-on AgNC probes. Using the new design, we demonstrate AgNC-MBs with nanomolar sensitivity and singe-nucleotide specificity, expanding the breadth of applicability of these cost-effective probes for biomolecular detection.
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28
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Xu H, Zhang R, Li F, Zhou Y, Peng T, Wang X, Shen Z. Double-hairpin molecular-beacon-based amplification detection for gene diagnosis linked to cancer. Anal Bioanal Chem 2016; 408:6181-8. [DOI: 10.1007/s00216-016-9729-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/14/2016] [Accepted: 06/20/2016] [Indexed: 01/03/2023]
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29
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Tang Y, Long F, Gu C, Wang C, Han S, He M. Reusable split-aptamer-based biosensor for rapid detection of cocaine in serum by using an all-fiber evanescent wave optical biosensing platform. Anal Chim Acta 2016; 933:182-8. [PMID: 27497011 DOI: 10.1016/j.aca.2016.05.021] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Revised: 05/11/2016] [Accepted: 05/12/2016] [Indexed: 01/28/2023]
Abstract
A rapid, facile, and sensitive assay of cocaine in biological fluids is important to prevent illegal abuse of drugs. A two-step structure-switching aptasensor has been developed for cocaine detection based on evanescent wave optical biosensing platform. In the proposed biosensing platform, two tailored aptamer probes were used to construct the molecular structure switching. In the existence of cocaine, two fragments of cocaine aptamer formed a three-way junction quickly, and the fluorophore group of one fragment was effectively quenched by the quencher group of the other one. The tail of the three-way junction hybridized with the cDNA sequences immobilized on the optical fiber biosensor. Fluorescence was excited by evanescent wave, and the fluorescence signal was proportional to cocaine concentration. Cocaine was detected in 450 s (300 s for incubation and 150 s for detection and regeneration) with a limit of detection (LOD) of 165.2 nM. The proposed aptasensor was evaluated in human serum samples, and it exhibited good recovery, precision, and accuracy without complicated sample pretreatments.
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Affiliation(s)
- Yunfei Tang
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing 100084, China
| | - Feng Long
- School of Environment and Natural Resources, Renmin University of China, Beijing 100872, China
| | - Chunmei Gu
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing 100084, China
| | - Cheng Wang
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing 100084, China
| | - Shitong Han
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing 100084, China
| | - Miao He
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing 100084, China.
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30
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Huang J, Wu J, Li Z. Molecular beacon-based enzyme-free strategy for amplified DNA detection. Biosens Bioelectron 2016; 79:758-62. [DOI: 10.1016/j.bios.2016.01.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 12/29/2015] [Accepted: 01/05/2016] [Indexed: 12/18/2022]
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31
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A Biofunctional Molecular Beacon for Detecting Single Base Mutations in Cancer Cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2016; 5:e302. [PMID: 27045206 PMCID: PMC5014519 DOI: 10.1038/mtna.2016.18] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 02/09/2016] [Indexed: 12/22/2022]
Abstract
The development of a convenient and sensitive biosensing system to detect
specific DNA sequences is an important issue in the field of genetic disease
therapy. As a classic DNA detection technique, molecular beacon (MB) is often
used in the biosensing system. However, it has intrinsic drawbacks, including
high assay cost, complicated chemical modification, and operational complexity.
In this study, we developed a simple and cost-effective label-free
multifunctional MB (LMMB) by integrating elements of polymerization primer,
template, target recognition, and G-quadruplex into one entity to detect target
DNA. The core technique was accomplished by introducing a G-hairpin that
features fragments of both G-quadruplex and target DNA recognition in the
G-hairpin stem. Hybridization between LMMB and target DNA triggered
conformational change between the G-hairpin and the common C-hairpin, resulting
in significant SYBR-green signal amplification. The hybridization continues to
the isothermal circular strand-displacement polymerization and accumulation of
the double-stranded fragments, causing the uninterrupted extension of the LMMB
without a need of chemical modification and other assistant DNA sequences. The
novel and programmable LMMB could detect target DNA with sensitivity at 250
pmol/l with a linear range from 2 to 100 nmol/l and the relative standard
deviation of 7.98%. The LMMB could sense a single base mutation from the normal
DNA, and polymerase chain reaction (PCR) amplicons of the mutant-type cell line
from the wild-type one. The total time required for preparation and assaying was
only 25 minutes. Apparently, the LMMB shows great potential for detecting DNA
and its mutations in biosamples, and therefore it opens up a new prospect for
genetic disease therapy.
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Mashhadizadeh MH, Talemi RP. Multilayer film of thiourea and gold nanoparticles as an effective platform for immobilization of activated non-labeled-DNA and construction of an ultrasensitive electrochemical DNA biosensor. RUSS J ELECTROCHEM+ 2016. [DOI: 10.1134/s1023193515080078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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33
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Li H, Wang S, Wu Z, Xu J, Shen G, Yu R. New function of exonuclease and highly sensitive label-free colorimetric DNA detection. Biosens Bioelectron 2016; 77:879-85. [DOI: 10.1016/j.bios.2015.10.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Revised: 10/09/2015] [Accepted: 10/12/2015] [Indexed: 02/03/2023]
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34
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Huang L, Aryal GH, Tam-Chang SW, Publicover NG, Hunter KW. Self-assembled biosensor with universal reporter and dual-quenchers for detection of unlabelled nucleic acids. Analyst 2016; 141:1376-82. [PMID: 26757447 DOI: 10.1039/c5an02094h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A novel biosensor with universal reporter and dual quenchers was developed for rapid, sensitive, selective, and inexpensive detection of unlabelled nucleic acids. The biosensor is based on a single-strand DNA stem-loop motif with an extended universal reporter-binding region, a G-base rich stem region, and a universal address-binding region. The self-assembly of these stem-loop probes with fluorescence labeled universal reporter and a universal address region conjugated to gold nanoparticles forms the basis of a biosensor for DNA or microRNA targets in solution. The introduction of dual quenchers (G-base quenching and gold surface plasmon resonance-induced quenching) significantly reduces the fluorescence background to as low as 12% of its original fluorescence intensity and hence enhances the detection limit to 0.01 picomoles without signal ampilication.
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Affiliation(s)
- Liming Huang
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, Reno, NV 89557, USA.
| | - Gyan H Aryal
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, Reno, NV 89557, USA.
| | - Suk-Wah Tam-Chang
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, Reno, NV 89557, USA.
| | - Nelson G Publicover
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, Reno, NV 89557, USA.
| | - Kenneth W Hunter
- Department of Microbiology and Immunology, School of Medicine, University of Nevada, Reno, NV 89557, USA.
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Xu J, Li H, Wu ZS, Qian J, Xue C, Jia L. Double-stem Hairpin Probe and Ultrasensitive Colorimetric Detection of Cancer-related Nucleic Acids. Am J Cancer Res 2016; 6:318-27. [PMID: 26909108 PMCID: PMC4737720 DOI: 10.7150/thno.13533] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Accepted: 10/01/2015] [Indexed: 12/11/2022] Open
Abstract
The development of a versatile biosensing platform to screen specific DNA sequences is still an essential issue of molecular biology research and clinic diagnosis of genetic disease. In this work, we for the first time reported a double-stem hairpin probe (DHP) that was simultaneously engineered to incorporate a DNAzyme, DNAzyme's complementary fragment and nicking enzyme recognition site. The important aspect of this hairpin probe is that, although it is designed to have a long ds DNA fragment, no intermolecular interaction occurs, circumventing the sticky-end pairing-determined disadvantages encountered by classic molecular beacon. For the DHP-based colorimetric sensing system, as a model analyte, cancer-related DNA sequence can trigger a cascade polymerization/nicking cycle on only one oligonucleotide probe. This led to the dramatic accumulation of G-quadruplexes directly responsible for colorimetric signal conversion without any loss. As a result, the target DNA is capable of being detected to 1 fM (six to eight orders of magnitude lower than that of catalytic molecular beacons) and point mutations are distinguished by the naked eye. The described DHP as a-proof-of-concept would not only promote the design of colorimetric biosensors but also open a good way to promote the diagnosis and treatment of genetic diseases.
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Ray JC, Almas MS, Tao S. Exciting fluorescence compounds on an optical fiber's side surface with a liquid core waveguide. OPTICS LETTERS 2016; 41:100-103. [PMID: 26696168 DOI: 10.1364/ol.41.000100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
A new fiber optic fluorescence spectroscopic method using a liquid core waveguide (LCW) as an excitation element has been developed for detecting a fluorescence compound absorbed on an optical fiber's surface. A laser light beam was coupled into a multimode optical fiber. The distal end of the fiber was inserted into an LCW. The diverging light emerging from the fiber's end was collected and guided within the LCW. A tapered optical fiber was inserted into the LCW from the other side. Laser light traveling in the LCW evenly illuminates the tapered fiber surface and excites fluorescence molecules absorbed on the tapered fiber's surface. Fluorescence light emitted from the tapered fiber surface was collected with the fiber itself and delivered through the fiber to an optical fiber compatible spectrometer for detection. This new technique provides an efficient way for evenly exciting fluorescence compounds absorbed on an optical fiber's surface.
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Li F, Zhou YY, Peng T, Xu H, Zhang RB, Zhao H, Wang ZY, Lv JX, Wu ZS, Shen ZF. Highly sensitive detection of cancer-related genes based on complete fluorescence restoration of a molecular beacon with a functional overhang. Analyst 2016; 141:4417-23. [DOI: 10.1039/c6an00898d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A overhang-contained molecular beacon-based sensing system was developed for cancer gene diagnosisviaexecuting cyclical nucleic acid strand-displacement polymerization and complete restoration of the quenched fluorescence.
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38
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Triple functional DNA–protein conjugates: Signal probes for Pb2+ using evanescent wave-induced emission. Biosens Bioelectron 2015; 74:78-84. [DOI: 10.1016/j.bios.2015.06.003] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 06/01/2015] [Accepted: 06/02/2015] [Indexed: 12/24/2022]
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39
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Che X, He Y, Yin H, Que L. A molecular beacon biosensor based on the nanostructured aluminum oxide surface. Biosens Bioelectron 2015; 72:255-60. [DOI: 10.1016/j.bios.2015.05.022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2015] [Revised: 05/06/2015] [Accepted: 05/08/2015] [Indexed: 01/03/2023]
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40
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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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41
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Guo Q, Bai Z, Liu Y, Sun Q. A molecular beacon microarray based on a quantum dot label for detecting single nucleotide polymorphisms. Biosens Bioelectron 2015; 77:107-10. [PMID: 26397421 DOI: 10.1016/j.bios.2015.09.031] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2015] [Revised: 09/11/2015] [Accepted: 09/12/2015] [Indexed: 11/29/2022]
Abstract
In this work, we report the application of streptavidin-coated quantum dot (strAV-QD) in molecular beacon (MB) microarray assays by using the strAV-QD to label the immobilized MB, avoiding target labeling and meanwhile obviating the use of amplification. The MBs are stem-loop structured oligodeoxynucleotides, modified with a thiol and a biotin at two terminals of the stem. With the strAV-QD labeling an "opened" MB rather than a "closed" MB via streptavidin-biotin reaction, a sensitive and specific detection of label-free target DNA sequence is demonstrated by the MB microarray, with a signal-to-background ratio of 8. The immobilized MBs can be perfectly regenerated, allowing the reuse of the microarray. The MB microarray also is able to detect single nucleotide polymorphisms, exhibiting genotype-dependent fluorescence signals. It is demonstrated that the MB microarray can perform as a 4-to-2 encoder, compressing the genotype information into two outputs.
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Affiliation(s)
- Qingsheng Guo
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Zhixiong Bai
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Yuqian Liu
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qingjiang Sun
- State Key Laboratory of Bioelectronics, School of Biological Science & Medical Engineering, Southeast University, Nanjing 210096, China.
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42
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Alonso-Cristobal P, Vilela P, El-Sagheer A, Lopez-Cabarcos E, Brown T, Muskens OL, Rubio-Retama J, Kanaras AG. Highly Sensitive DNA Sensor Based on Upconversion Nanoparticles and Graphene Oxide. ACS APPLIED MATERIALS & INTERFACES 2015; 7:12422-9. [PMID: 25622622 DOI: 10.1021/am507591u] [Citation(s) in RCA: 89] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
In this work we demonstrate a DNA biosensor based on fluorescence resonance energy transfer (FRET) between NaYF4:Yb,Er nanoparticles and graphene oxide (GO). Monodisperse NaYF4:Yb,Er nanoparticles with a mean diameter of 29.1 ± 2.2 nm were synthesized and coated with a SiO2 shell of 11 nm, which allowed the attachment of single strands of DNA. When these DNA-functionalized NaYF4:Yb,Er@SiO2 nanoparticles were in the proximity of the GO surface, the π-π stacking interaction between the nucleobases of the DNA and the sp(2) carbons of the GO induced a FRET fluorescence quenching due to the overlap of the fluorescence emission of the NaYF4:Yb,Er@SiO2 and the absorption spectrum of GO. By contrast, in the presence of the complementary DNA strands, the hybridization leads to double-stranded DNA that does not interact with the GO surface, and thus the NaYF4:Yb,Er@SiO2 nanoparticles remain unquenched and fluorescent. The high sensitivity and specificity of this sensor introduces a new method for the detection of DNA with a detection limit of 5 pM.
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Affiliation(s)
- P Alonso-Cristobal
- †Department of Physical Chemistry II, Faculty of Pharmacy, Complutense University of Madrid, 28040 Madrid, Spain
| | - P Vilela
- §Institute for Life Sciences, Physics and Astronomy, Faculty of Physical Sciences and Engineering, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - A El-Sagheer
- ‡Department of Chemistry, University of OxfordChemistry Research Laboratory, Oxford OX1 3TA, United Kingdom
| | - E Lopez-Cabarcos
- †Department of Physical Chemistry II, Faculty of Pharmacy, Complutense University of Madrid, 28040 Madrid, Spain
| | - T Brown
- ‡Department of Chemistry, University of OxfordChemistry Research Laboratory, Oxford OX1 3TA, United Kingdom
| | - O L Muskens
- §Institute for Life Sciences, Physics and Astronomy, Faculty of Physical Sciences and Engineering, University of Southampton, Southampton SO17 1BJ, United Kingdom
| | - J Rubio-Retama
- †Department of Physical Chemistry II, Faculty of Pharmacy, Complutense University of Madrid, 28040 Madrid, Spain
| | - A G Kanaras
- §Institute for Life Sciences, Physics and Astronomy, Faculty of Physical Sciences and Engineering, University of Southampton, Southampton SO17 1BJ, United Kingdom
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43
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Liu LH, Zhou XH, Shi HC. Portable optical aptasensor for rapid detection of mycotoxin with a reversible ligand-grafted biosensing surface. Biosens Bioelectron 2015; 72:300-5. [PMID: 26000463 DOI: 10.1016/j.bios.2015.05.033] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 05/11/2015] [Accepted: 05/12/2015] [Indexed: 11/17/2022]
Abstract
As food safety is gaining prominence as a global issue, the demand for developing rapid, simple, on-site, accurate and low-cost biosensor technologies will continue to grow. This study demonstrates an evanescent wave optical aptasensor with a reversible ligand-grafted biosensing surface for rapid, sensitive and highly selective detection of ochratoxin A (OTA) in food. In this system, the OTA molecules were covalently immobilized onto the surface of an optical fiber using glutaraldehyde and ethylenediamine as space linkers. An integrated evanescent wave all-fiber (EWA) biosensing platform was developed for investigating the binding kinetics between the tethered ligand and free OTA-aptamer, the performance of the aptamer-based bioassay and the reversibility of biosensing surface. The affinity constant (Ka) of aptamer with tethered OTA was measured to be 2.2 × 10(8)M(-1) based on the EWA biosensing platform. With a competitive detection mode, the quantification of OTA over concentration ranges from 0.73 μg L(-1) to 12.50 μg L(-1) with a detection limit of 0.39 μg L(-1). The performance of the aptasensor with other interfering mycotoxins and spiked real wheat samples shows high specificity and selectivity, good recovery, precision, and accuracy, indicating that it can be applied for on-site, inexpensive and easy-to-use monitoring of OTA in real samples. Moreover, since the organic ligands are grafted onto the fiber surface, this strategy may avoid the potential disadvantages caused by immobilizing the nucleic acid biomolecules, such as weak restoration to the original DNA conformation after repeated uses.
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Affiliation(s)
- Lan-hua Liu
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing 100084, China
| | - Xiao-hong Zhou
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing 100084, China.
| | - Han-chang Shi
- State Key Joint Laboratory of ESPC, School of Environment, Tsinghua University, Beijing 100084, China
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44
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Satija J, Tharion J, Mukherji S. Facile synthesis of size and wavelength tunable hollow gold nanostructures for the development of a LSPR based label-free fiber-optic biosensor. RSC Adv 2015. [DOI: 10.1039/c5ra13941d] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Hollow bimetallic nanostructures have recently emerged as attractive plasmonic materials due to the ease of optical tunability by changing their size/composition.
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Affiliation(s)
- Jitendra Satija
- Department of Biosciences and Bioengineering
- IIT Bombay
- Mumbai 400 076
- India
- School of Bio Sciences and Technology
| | - Joseph Tharion
- Department of Biosciences and Bioengineering
- IIT Bombay
- Mumbai 400 076
- India
| | - Soumyo Mukherji
- Department of Biosciences and Bioengineering
- IIT Bombay
- Mumbai 400 076
- India
- Centre of Excellence for Nanoelectronics
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45
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Xu J, Dong H, Shen W, He S, Li H, Lu Y, Wu ZS, Jia L. New molecular beacon for p53 gene point mutation and significant potential in serving as the polymerization primer. Biosens Bioelectron 2014; 66:504-11. [PMID: 25500526 DOI: 10.1016/j.bios.2014.12.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 11/20/2014] [Accepted: 12/02/2014] [Indexed: 01/10/2023]
Abstract
Molecular beacon (MB) is usually explored as a convenient probe for various bioassays. In an enzymatic polymerization-based biosensing system, primer, and MB, sometimes involving other oligonucleotides, are often required to collaboratively generate an amplified fluorescent signal to detect target molecules with high sensitivity and specificity. In the current study, a multifunctional primer-integrated MB (MP-MB) was developed to detect the p53 tumor suppressor gene. Compared with the traditional MB, our MP-MB can not only selectively identify the target of interest and signal sensitively its hybridization event, but also act as the primer during enzymatic polymerization. Specifically, hybridization of MP-MB to target p53 gene restored the fluorescence intensity and activated the pre-locked primer designed by changing the molecular configuration of MP-MB. Moreover, the p53 gene could be detected down to 1nM with a linear response range of 1×10(-9)-3×10(-7)M, and p53 gene point mutation was readily distinguished from the wild-type one. Its potential application as a primer of replication in enzymatic polymerization-based assay systems was validated by running parallel gel electrophoreses in comparison with the native counterpart of MP-MB without any chemical modification. Owning to its excellent assay characteristics, less species requirement, broad sequence diversity and preserved intrinsic bioactivity, the proof-of-concept of MP-MB exhibits a great potential in various biomedical applications.
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Affiliation(s)
- Jianguo Xu
- Cancer Metastasis Alert and Prevention Center, Pharmaceutical Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Haiyan Dong
- Cancer Metastasis Alert and Prevention Center, Pharmaceutical Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Weiyu Shen
- Cancer Metastasis Alert and Prevention Center, Pharmaceutical Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Sudan He
- Cancer Metastasis Alert and Prevention Center, Pharmaceutical Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Hongling Li
- Cancer Metastasis Alert and Prevention Center, Pharmaceutical Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Yusheng Lu
- Cancer Metastasis Alert and Prevention Center, Pharmaceutical Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Pharmaceutical Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China; State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, China.
| | - Lee Jia
- Cancer Metastasis Alert and Prevention Center, Pharmaceutical Photocatalysis, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350002, China.
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46
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Su Q, Wesner D, Schönherr H, Nöll G. Molecular beacon modified sensor chips for oligonucleotide detection with optical readout. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:14360-14367. [PMID: 25363421 DOI: 10.1021/la504105x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Three different surface bound molecular beacons (MBs) were investigated using surface plasmon fluorescence spectroscopy (SPFS) as an optical readout technique. While MB1 and MB2, both consisting of 36 bases, differed only in the length of the linker for surface attachment, the significantly longer MB3, consisting of 56 bases, comprised an entirely different sequence. For sensor chip preparation, the MBs were chemisorbed on gold via thiol anchors together with different thiol spacers. The influence of important parameters, such as the length of the MBs, the length of the linker between the MBs and the gold surface, the length and nature of the thiol spacers, and the ratio between the MBs and the thiol spacers was studied. After hybridization with the target, the fluorophore of the longer MB3 was oriented close to the surface, and the shorter MBs were standing more or less upright, leading to a larger increase in fluorescence intensity. Fluorescence microscopy revealed a homogeneous distribution of the MBs on the surface. The sensor chips could be used for simple and fast detection of target molecules with a limit of detection in the larger picomolar range. The response time was between 5 and 20 min. Furthermore, it was possible to distinguish between fully complementary and singly mismatched targets. While rinsing with buffer solution after hybridization with target did not result in any signal decrease, complete dehybridization could be carried out by intense rinsing with pure water. The MB modified sensor chips could be prepared in a repeatable manner and reused many times without significant decrease in performance.
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Affiliation(s)
- Qiang Su
- Nöll Junior Research Group, Organic Chemistry, Department of Chemistry and Biology, Faculty IV, Siegen University , Adolf-Reichwein-Strasse 2, 57068 Siegen, Germany
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47
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Wang R, Xiang Y, Zhou X, Liu LH, Shi H. A reusable aptamer-based evanescent wave all-fiber biosensor for highly sensitive detection of Ochratoxin A. Biosens Bioelectron 2014; 66:11-8. [PMID: 25460875 DOI: 10.1016/j.bios.2014.10.079] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 10/23/2014] [Accepted: 10/31/2014] [Indexed: 12/24/2022]
Abstract
Although aptamer-based biosensors have attracted ever-increasing attentions and found potential applications in a wide range of areas, they usually adopted the assay protocol of immobilizing DNA probe (e.g., aptamer, aptamer-complementary oligonucleotides) on a solid sensing surface, making it critical and challengeable to keep the integration of nucleic acid surface during the regeneration and the restoration to its original DNA probe form after repeated uses. In order to address the issue, we report a novel aptamer-based biosensing strategy based on an evanescent wave all-fiber (EWA) platform. In a simple target capturing step using aptamer-functionalized magnetic microbeads, signal probes conjugated with streptavidin are released and further detected by a EWA biosensor via a facial dethiobiotin-streptavidin recognition. Apart from the inherent advantages of aptamer-based evanescent wave biosensors (e.g. target versatility, sensitivity, selectivity and portability), the proposed strategy exhibits a high stability and remarkable reusability over other aptasensors. Under the optimized conditions, the typical calibration curve obtained for Ochratoxin A has a detection limit of 3nM with a linear response ranging from 6nM to 500nM. The dethiobiotin-streptavidin sensing surface instead of the traditional nucleic acid one can be reused for over 300 times without losing sensitivity.
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Affiliation(s)
- Ruoyu Wang
- School of environment, Tsinghua University, Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xiaohong Zhou
- School of environment, Tsinghua University, Beijing 100084, China.
| | - Lan-Hua Liu
- School of environment, Tsinghua University, Beijing 100084, China
| | - Hanchang Shi
- School of environment, Tsinghua University, Beijing 100084, China
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48
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Hairpin DNA probe-based fluorescence assay for detecting palindrome cleavage activity of HIV-1 integrase. Anal Biochem 2014; 460:36-8. [DOI: 10.1016/j.ab.2014.05.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Revised: 05/05/2014] [Accepted: 05/15/2014] [Indexed: 11/22/2022]
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49
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Genotyping single nucleotide polymorphisms using different molecular beacon multiplexed within a suspended core optical fiber. SENSORS 2014; 14:14488-99. [PMID: 25111240 PMCID: PMC4179081 DOI: 10.3390/s140814488] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Revised: 08/01/2014] [Accepted: 08/05/2014] [Indexed: 11/17/2022]
Abstract
We report a novel approach to genotyping single nucleotide polymorphisms (SNPs) using molecular beacons in conjunction with a suspended core optical fiber (SCF). Target DNA sequences corresponding to the wild- or mutant-type have been accurately recognized by immobilizing two different molecular beacons on the core of a SCF. The two molecular beacons differ by one base in the loop-probe and utilize different fluorescent indicators. Single-color fluorescence enhancement was obtained when the immobilized SCFs were filled with a solution containing either wild-type or mutant-type sequence (homozygous sample), while filling the immobilized SCF with solution containing both wild- and mutant-type sequences resulted in dual-color fluorescence enhancement, indicating a heterozygous sample. The genotyping was realized amplification-free and with ultra low-volume for the required DNA solution (nano-liter). This is, to our knowledge, the first genotyping device based on the combination of optical fiber and molecular beacons.
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50
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Satija J, Karunakaran B, Mukherji S. A dendrimer matrix for performance enhancement of evanescent wave absorption-based fiber-optic biosensors. RSC Adv 2014. [DOI: 10.1039/c4ra00198b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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