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Sharma P, Hasan MR, Naikoo UM, Khatoon S, Pilloton R, Narang J. Aptamer Based on Silver Nanoparticle-Modified Flexible Carbon Ink Printed Electrode for the Electrochemical Detection of Chikungunya Virus. BIOSENSORS 2024; 14:344. [PMID: 39056620 PMCID: PMC11274990 DOI: 10.3390/bios14070344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 07/10/2024] [Accepted: 07/11/2024] [Indexed: 07/28/2024]
Abstract
Medical devices have progressed from their initial bulky forms to smart devices. However, their rigidity hampers their seamless integration into everyday life. The fields of stretchable, textile, and flexible electronics are emerging research areas with the potential to drive significant technological progress. This research presents a laboratory-based technique to produce highly sensitive and flexible biosensors for detecting the chikungunya virus. These biosensors are based on 0D nanomaterials and demonstrate significant advancements in voltammetry. The electrochemical platform was created utilizing the stencil printing (StPE) technique. Adapting the biosensor setup involved the selection of aptamer as the biorecognition element bound with silver nanoparticles (AgNPs). This biosensor was employed in the voltammetric identification of the Chikungunya virus antigen (CHIKV-Ag) within a solution containing 0.5 mM potassium ferro/ferri cyanide, a redox pair. The biosensor was employed to evaluate CHIKV-Ag within a human serum sample. It demonstrated a linear detection span ranging from 0.1 ng/mL to 1 μg/mL, with a detection limit of 0.1 ng/mL for CHIKV-Ag. The proposed approach, due to its flexibility in production and the electrocatalytic attributes displayed by the zero-dimensional nanostructure, presents innovative opportunities for cost-effective and tailored aptamer-based bioelectronics, thereby broadening the scope of this domain.
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Affiliation(s)
- Pradakshina Sharma
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India; (P.S.); (M.R.H.); (U.M.N.); (S.K.)
| | - Mohd. Rahil Hasan
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India; (P.S.); (M.R.H.); (U.M.N.); (S.K.)
| | - Ubaid Mushtaq Naikoo
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India; (P.S.); (M.R.H.); (U.M.N.); (S.K.)
| | - Shaheen Khatoon
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India; (P.S.); (M.R.H.); (U.M.N.); (S.K.)
| | - Roberto Pilloton
- Institute of Crystallography, National Research Council, 00143 Rome, Italy
| | - Jagriti Narang
- Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, Hamdard Nagar, New Delhi 110062, India; (P.S.); (M.R.H.); (U.M.N.); (S.K.)
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Dou S, Zhou S, Wang H, Liu M, Wang Y, Sun X, Guo Y. UIO66 low background signal and fluorescence synergism strategy for highly sensitive detection of Salmonella typhimurium. Talanta 2024; 274:126013. [PMID: 38569373 DOI: 10.1016/j.talanta.2024.126013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/24/2024] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
Successful construction of a detection method for Salmonella typhimurium (S. typhimurium) based on the synergy of hybridization chain reaction (HCR) and fluorescence was realized in this paper. First, the aptamer modified with the quenching group Black Hole Quencher-1 acid (BHQ1) was immobilized on the magnetic beads in combination with the complementary chain of the aptamer modified with 6-carboxyfluorescein (6-FAM). Second, S. typhimurium and cDNA-6-FAM immobilized on magnetic beads competitively bound to the aptamer. Finally, the cDNA-6-FAM was released after magnetic separation acted as a promoter to trigger HCR amplification when the target presented. The fluorescence signal could be significantly improved by the combination of green SYBR Green I (SGI) and HCR long double-stranded DNA and the fluorescent synergy of 6-FAM and SGI. Because of the separation of target and its aptamer, the trigger strand was abstracted by magnetic separation. There was no HCR to generate long double-stranded DNA, and the fluorescence of excess hairpin/SGI could be adsorbed through UIO66 so that only a very low background signal was detected. This fluorescent sensor was capable of monitoring S. typhimurium in the range of 10-3.2 × 107 CFU mL-1 with a limit of detection as low as 1.5 CFU mL-1. Because of the excellent properties of the aptasensor and the validity of SGI fluorescence synergy, this HCR enzyme-free amplification strategy could be generalized to other areas.
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Affiliation(s)
- Shouyi Dou
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Shuxian Zhou
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Haifang Wang
- Dongzhimen Hospital, Beijing University of Chinese Medicine, Beijing, 100700, China
| | - Mengyue Liu
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Yinghui Wang
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China
| | - Xia Sun
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China.
| | - Yemin Guo
- College of Agricultural Engineering and Food Science, Shandong University of Technology, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China; Zibo City Key Laboratory of Agricultural Product Safety Traceability, No. 266 Xincun Xilu, Zibo, Shandong, 255049, China.
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Wang B, Liu Z, Li Z, Xu N, Zhang X, Su R, Wang J, Jin R, Sun C. Facile and sensitive detection of mercury ions based on fluorescent structure-switching aptamer probe and exonuclease Ⅲ-assisted signal amplification. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2023; 303:123223. [PMID: 37562208 DOI: 10.1016/j.saa.2023.123223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023]
Abstract
Hg2+ is highly toxic to human health and ecosystem. In this work, based on the unique fluorescent property of 2-Aminopurine (2-AP), the formation of T-Hg2+-T mismatch structure and the signal amplification of exonuclease III (Exo III) assisted target cycle, a fluorescent probe for facile and sensitive detection of Hg2+ is constructed. The hairpin-looped DNA probe is rationally designed with 2-AP embedded in the stem and thymine-rich recognition overhangs extended at the termini. The cleavage of the double stranded DNA stem with stable T-Hg2+-T pairs catalyzed by Exo III is prompted to happen upon recognition of trace Hg2+. Under the optimal reaction conditions, there is an excellent linear relationship between Hg2+ concentration and fluorescence intensity in the range of 7.5-200 nM with a detection limit of 0.38 nM. In addition, the detection results of Hg2+ in Songhua River water and fish samples are satisfactory. The fluorescent probe avoids labeling additional quenchers or quenching materials and has strong anti-interference ability. Thus, the fluorescent probe has a broad prospect in practical application.
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Affiliation(s)
- Boxu Wang
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Zheng Liu
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Zhihong Li
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Ningyi Xu
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Xuejiao Zhang
- Changchun Coordinated Administrative Law Enforcement Detachment of Market Regulation, Changchun 130102, China
| | - Ruifang Su
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Junyang Wang
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Rui Jin
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China.
| | - Chunyan Sun
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China.
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Patterson AT, Styczynski MP. Rapid and Finely-Tuned Expression for Deployable Sensing Applications. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 186:141-161. [PMID: 37316621 DOI: 10.1007/10_2023_223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Organisms from across the tree of life have evolved highly efficient mechanisms for sensing molecules of interest using biomolecular machinery that can in turn be quite valuable for the development of biosensors. However, purification of such machinery for use in in vitro biosensors is costly, while the use of whole cells as in vivo biosensors often leads to long sensor response times and unacceptable sensitivity to the chemical makeup of the sample. Cell-free expression systems overcome these weaknesses by removing the requirements associated with maintaining living sensor cells, allowing for increased function in toxic environments and rapid sensor readout at a production cost that is often more reasonable than purification. Here, we focus on the challenge of implementing cell-free protein expression systems that meet the stringent criteria required for them to serve as the basis for field-deployable biosensors. Fine-tuning expression to meet these requirements can be achieved through careful selection of the sensing and output elements, as well as through optimization of reaction conditions via tuning of DNA/RNA concentrations, lysate preparation methods, and buffer conditions. Through careful sensor engineering, cell-free systems can continue to be successfully used for the production of tightly regulated, rapidly expressing genetic circuits for biosensors.
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Affiliation(s)
- Alexandra T Patterson
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mark P Styczynski
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
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Aptamer-based enzyme-linked oligonucleotide assay for specific detection of clinical bacterial strains isolated from cerebrospinal fluid samples. J Biosci Bioeng 2022; 134:441-449. [PMID: 36109302 DOI: 10.1016/j.jbiosc.2022.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 07/07/2022] [Accepted: 07/13/2022] [Indexed: 11/23/2022]
Abstract
Meningitis, acute infection of the meninges, is the 10th leading cause of mortality among infectious diseases. Although many different causes for meningitis (viruses and bacteria) have been diagnosed, the most common ones are Neisseria meningitidis, Haemophilus influenzae, and Streptococcus pneumoniae. The effort to find a new method for detection of bacterial meningitis is an urgent need for clinical treatment. DNA aptamers generated by cell-systematic evolution of ligands by exponential enrichment (SELEX) against bacterial cells provide a novel cell labeling and biosensing technique. Here, we isolated single-stranded DNA aptamers during the SELEX method with a high affinity for different bacterial genera. This approach was demonstrated on H. influenzae type B, N. meningitidis serogroups A, B, C, and Y, and Streptococcus pneumoniae serotypes 18, 14, 19A, 6A, and 6B which served as targets in 20 rounds of cell-SELEX. After 20 rounds of SELEX, a total of 93 aptamers were identified. Among these, aptamers C65 and C50 showed the highest affinity toward targets with a dissociation constant of 6.98 and 15.79, respectively. Selected aptamers were able to successfully detect clinical bacterial strains isolated from cerebrospinal fluid samples of meningitis patients by double-aptamer sandwich enzyme-linked oligonucleotide assay (ELONA). Our findings demonstrated that aptamers with broad affinity to bacterial taxa in different genera can be isolated for the development of diagnostic tools for multiple targets. We further showed that sandwich ELONA based on single-stranded DNA aptamer is sensitive and specific enough for detection of the superior cause of bacterial meningitis.
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Wang J, Li H, Du C, Li Y, Ma X, Yang C, Xu W, Sun C. Structure-switching aptamer triggering signal amplification strategy for tobramycin detection based on hybridization chain reaction and fluorescence synergism. Talanta 2022; 243:123318. [PMID: 35217273 DOI: 10.1016/j.talanta.2022.123318] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/18/2022] [Accepted: 02/13/2022] [Indexed: 01/13/2023]
Abstract
Based on hybridization chain reaction (HCR) and fluorescence synergism, a novel aptasensor for tobramycin was successfully constructed. Tobramycin competed with cDNA-FAM to bind aptamers immobilized on magnetic beads. After magnetic separation, the released cDNA-FAM acted as initiator to trigger HCR amplification, thus the fluorescence was significantly enhanced due to binding of SYBR Green Ⅰ (SGI) to the formed long double-stranded DNA and the synergistic fluorescence of FAM. In the absence of tobramycin, the initiator was magnetically separated and no HCR occurred, more importantly, graphene oxide can quench the fluorescence of excessive hairpins/SGI and cDNA-FAM, so almost no background signal was detected. This aptasensor can monitor tobramycin in the range of 0.3-50 μM with low detection limit of 17.37 nM. Due to the potential generality of structure-switching aptamers and effectiveness of fluorescence synergism, this enzyme-free amplification strategy can be extended to other applications by rational design of nucleic acid sequences.
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Affiliation(s)
- Junyang Wang
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Hongxia Li
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Caiyi Du
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Ying Li
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Xinyue Ma
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Chuanyu Yang
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
| | - Chunyan Sun
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun, 130062, China.
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Joe C, Lee BH, Kim SH, Ko Y, Gu MB. Aptamer duo-based portable electrochemical biosensors for early diagnosis of periodontal disease. Biosens Bioelectron 2021; 199:113884. [PMID: 34942544 DOI: 10.1016/j.bios.2021.113884] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 01/25/2023]
Abstract
Recently, point-of-care tests (POCT) have gained much attention due to their convenient, fast, simple, and easy characteristics. For POCT, portability is an essential feature. In this study, we have successfully fabricated a portable mini-potentiostat. Using chronoamperometry, electrical signals of this portable mini-potentiostat were measured, and the analytical performance of electrochemical aptasensors was compared with a benchtop potentiostat. The electrochemical signals measured by mini-potentiostat can be displayed on the screen of a smartphone. To verify the analytical performance of this portable electrochemical aptasensor platform with a mini-potentiostat, two well-known model protein biomarkers, vaspin, a type 2 diabetes biomarker, and thrombin, a biomarker for pulmonary metastasis and cardiovascular disease, were confirmed to be detected by using corresponding aptamer duo. After solid verification of this portable electrochemical aptasensor platform, we have successfully implemented this portable mini-potentiostat system to develop a portable sandwich-type binding pair of aptamers-based electrochemical biosensor, which can diagnose periodontal disease by measuring ODAM biomarker. The linear range of this ODAM biosensor was 0 to 15 nM with a detection limit of 0.02 nM and 1 nM in buffer and saliva, respectively. The sensitivity of this biosensor has been greatly enhanced, compared to previously developed surface plasmon resonance (SPR) or lateral flow assay (LFA) based aptasensors. This study showed that this new portable aptamer duo-based biosensor is expected to diagnose the early stage of periodontal diseases from real samples, such as saliva or gingival crevicular fluid in a short time as a point-of-care (POC) testing.
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Affiliation(s)
- Cheulmin Joe
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong, Seongbuk-gu, Seoul, 02841, Republic of Korea
| | - Bang Hyun Lee
- Department of Electrical & Computer Engineering, North Carolina State University, 890 Oval Dr, Raleigh, NC, 27695, USA
| | - Sang Hoon Kim
- University of North Carolina -- Chapel Hill, Department of Applied Physical Sciences, 1112 Murray Hall, CB#3050, Chapel Hill, NC, 27599-2100, USA
| | - Youngkyung Ko
- Department of Periodontics, Seoul St Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Man Bock Gu
- Department of Biotechnology, College of Life Sciences and Biotechnology, Korea University, Anam-dong, Seongbuk-gu, Seoul, 02841, Republic of Korea.
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Sen RK, Prabhakar P, Bisht N, Patel M, Mishra S, Yadav AK, Venu DV, Gupta GK, Solanki PR, Ramakrishnan S, Mondal D, Srivastava AK, Dwivedi N, Dhand C. 2D Materials-Based Aptamer Biosensors: Present Status and Way Forward. Curr Med Chem 2021; 29:5815-5849. [PMID: 34961455 DOI: 10.2174/0929867328666211213115723] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/13/2021] [Accepted: 10/26/2021] [Indexed: 11/22/2022]
Abstract
Current advances in constructing functional nanomaterials and elegantly designed nanostructures have opened up new possibilities for the fabrication of viable field biosensors. Two-dimensional materials (2DMs) have fascinated much attention due to their chemical, optical, physicochemical, and electronic properties. They are ultrathin nanomaterials with unique properties such as high surface-to-volume ratio, surface charge, shape, high anisotropy, and adjustable chemical functionality. 2DMs such as graphene-based 2D materials, Silicate clays, layered double hydroxides (LDHs), MXenes, transition metal dichalcogenides (TMDs), and transition metal oxides (TMOs) offer intensified physicochemical and biological functionality and have proven to be very promising candidates for biological applications and technologies. 2DMs have a multivalent structure that can easily bind to single-stranded DNA/RNA (aptamers) through covalent, non-covalent, hydrogen bond, and π-stacking interactions, whereas aptamers have a small size, excellent chemical stability, and low immunogenicity with high affinity and specificity. This review discussed the potential of various 2D material-based aptasensor for diagnostic applications, e.g., protein detection, environmental monitoring, pathogens detection, etc.
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Affiliation(s)
- Raj Kumar Sen
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
| | - Priyanka Prabhakar
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
| | - Neha Bisht
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
| | - Monika Patel
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
| | - Shruti Mishra
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
| | - Amit Kumar Yadav
- Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067. India
| | - Divya Vadakkumana Venu
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
| | - Gaurav Kumar Gupta
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
| | - Pratima R Solanki
- Special Centre for Nanoscience, Jawaharlal Nehru University, New Delhi 110067. India
| | - Seeram Ramakrishnan
- Center for Nanofibers and Nanotechnology, Department of Mechanical Engineering, Faculty of Engineering, 2 Engineering Drive 3, National University of Singapore, Singapore, 117576. Singapore
| | - Dehipada Mondal
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
| | | | - Neeraj Dwivedi
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
| | - Chetna Dhand
- CSIR-Advanced Materials and Processes Research Institute, Hoshangabad Road, Bhopal. India
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Zara L, Achilli S, Chovelon B, Fiore E, Toulmé JJ, Peyrin E, Ravelet C. Anti-pesticide DNA aptamers fail to recognize their targets with asserted micromolar dissociation constants. Anal Chim Acta 2021; 1159:338382. [PMID: 33867041 DOI: 10.1016/j.aca.2021.338382] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Revised: 03/07/2021] [Accepted: 03/08/2021] [Indexed: 01/28/2023]
Abstract
Herein, we originally aimed at developing fluorescence anisotropy biosensor platforms devoted to the homogeneous-phase detection of isocarbophos and phorate pesticides by using previously isolated DNA aptamers. To achieve this, two reporting approaches displaying very high generalizability features were implemented, based on either the complementary strand or the SYBR green intercalator displacement strategies. Unfortunately, none of the transduction methods led to phorate-dependent signals. Only the SYBR green displacement method provided a small output in the presence of isocarbophos, but at an analyte concentration greater than 100 μM. In order to identify the origin of such data, isothermal titration calorimetry (ITC) experiments were subsequently performed. It was shown that aptamers bind neither isocarbophos nor phorate in free solution with the claimed micromolar dissociation constants. This work puts forward some doubts about the previously described aptasensors that rely on the use of these functional DNA molecules. It also highlights the need to carefully investigate the binding capabilities of aptamers after their isolation and to include appropriate control experiments with scrambled or mutated oligonucleotides.
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Affiliation(s)
- Lorena Zara
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France; Novaptech, 2 Allée Du Doyen Georges Brus, 33600, Pessac, France
| | - Silvia Achilli
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France
| | - Benoît Chovelon
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France; Service de Biochimie, Biologie Moléculaire, Toxicologie Environnementale, CHU de Grenoble-Alpes Site Nord- Institut de Biologie et de Pathologie, La Tronche, France
| | | | | | - Eric Peyrin
- Univ. Grenoble Alpes, CNRS, DPM, 38000, Grenoble, France.
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Wang J, Guo X, Liu R, Guo J, Zhang Y, Zhang W, Sang S. Detection of carcinoembryonic antigen using a magnetoelastic nano-biosensor amplified with DNA-templated silver nanoclusters. NANOTECHNOLOGY 2020; 31:015501. [PMID: 31530749 DOI: 10.1088/1361-6528/ab4506] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Here we develop a magnetoelastic (ME) nano-biosensor based on the competitive strategy for the detection of a carcinoembryonic antigen (CEA). Specifically, the gold-coated ME material provided a platform and the thiolated single-stranded DNA (HS-DNA) containing a half-complementary sequence towards the CEA aptamer was modified on the surface via Au-S bonding. DNA-templated silver nanoclusters (DNA-AgNCs) containing another half-complementary sequence towards the aptamer were used to amplify the signals by about 2.1 times, compared to those obtained using just the aptamer. CEA aptamers as a bio-recognition element were employed to link HS-DNA and DNA-AgNCs through DNA hybridization. The CEA aptamer preferentially combined with CEA rather than hybridized with DNA. Due to the magnetostrictive nature of the ME materials, the resonant frequency of the nano-biosensor would increase along with the release of DNA-AgNCs and CEA aptamers. The modification process was demonstrated by UV-vis spectra, x-ray photoelectron spectroscopy (XPS), Raman spectroscopy, transmission electron microscope (TEM) and an atomic force microscope (AFM). The nano-biosensor has a linear response to the logarithmic CEA concentrations ranging from 2 pg ml-1 to 6.25 ng ml-1, with a limit of detection (LOD) of 1 pg ml-1 and a sensitivity of 105.05 Hz/ng · ml-1. This study provides a low-cost, highly sensitive and wireless method for selective detection of CEA.
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Affiliation(s)
- Jingzhe Wang
- MicroNano System Research Center, Key Lab of Advanced Transducers and Intelligent Control System of the Ministry of Education & College of Information and Computer, Taiyuan University of Technology, Jinzhong 030600, People's Republic of China
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11
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Wang H, Wang H, Zhang M, Jia Y, Li Z. A label-free aptamer-based biosensor for microRNA detection by the RNA-regulated fluorescence of malachite green. RSC Adv 2019; 9:32906-32910. [PMID: 35529731 PMCID: PMC9073149 DOI: 10.1039/c9ra07552f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 10/02/2019] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) have been considered as promising molecular biomarkers for disease diagnosis, prognosis, as well as drug development. Herein, we wish to report a low background and label-free aptamer-based biosensor for miRNA assay by RNA-regulated fluorescence of malachite green (MG). In this biosensor-based strategy, target miRNA can specifically hybridize with the DNA extension template to form the T7 in vitro transcription system. Then the following transcription amplification produces a large number of MG RNA aptamers (MGAs) which light up the fluorescence of the MG, achieving significant fluorescence enhancement for miRNA quantitative analysis. The aptamer-based biosensor exhibits high sensitivity with a quite low detection limit of 10 amol target miRNA and high specificity to clearly discriminate very similar miRNA family members, even only one base difference. Furthermore, we have demonstrated that the biosensor is practical and reliable for the quantitative detection of miRNA in complex real samples.
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Affiliation(s)
- Honghong Wang
- School of Chemistry and Biology Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Hui Wang
- School of Chemistry and Biology Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Mai Zhang
- School of Chemistry and Biology Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Yuting Jia
- School of Chemistry and Biology Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
| | - Zhengping Li
- School of Chemistry and Biology Engineering, University of Science and Technology Beijing Beijing 100083 P. R. China
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12
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Xiao M, Lai W, Man T, Chang B, Li L, Chandrasekaran AR, Pei H. Rationally Engineered Nucleic Acid Architectures for Biosensing Applications. Chem Rev 2019; 119:11631-11717. [DOI: 10.1021/acs.chemrev.9b00121] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Mingshu Xiao
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Wei Lai
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Tiantian Man
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Binbin Chang
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Hao Pei
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University, 500 Dongchuan Road, Shanghai 200241, P. R. China
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13
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Ma X, Li H, Qiao S, Huang C, Liu Q, Shen X, Geng Y, Xu W, Sun C. A simple and rapid sensing strategy based on structure-switching signaling aptamers for the sensitive detection of chloramphenicol. Food Chem 2019; 302:125359. [PMID: 31442702 DOI: 10.1016/j.foodchem.2019.125359] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 08/03/2019] [Accepted: 08/10/2019] [Indexed: 01/06/2023]
Abstract
A simple and rapid sensing strategy was proposed for chloramphenicol (CAP) detection based on structure-switching signaling aptamers. In this protocol, the aptamer can bind to both the fluorophore (FAM)-labeled complementary strand and the quencher (BHQ1)-labeled complementary strand, thus leading to the effective quenching of FAM fluorescence by BHQ1. However, when CAP is present, the structure switch is reversed because the aptamer recognizes CAP, resulting in fluorescence recovery. Such a fluorescence-sensing platform can monitor CAP within a good linear range (1-100 ng/mL), with a detection limit of 0.70 ng/mL. Cross-reactivity with other common antibiotics is negligible, indicating the excellent selectivity of the strategy. Moreover, as the aptamers are not modified, this method is simple and low-cost. The present work reveals a new direction for detecting CAP or other target compounds without prior knowledge of the secondary or tertiary structures of the aptamer.
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Affiliation(s)
- Xinyue Ma
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Hongxia Li
- State Key Laboratory on Integrated Optoelectronics, College of Electronic Science and Engineering, Jilin University, Changchun 130012, China
| | - Shangna Qiao
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Chujun Huang
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Qiuli Liu
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Xu Shen
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Yongxing Geng
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Wentao Xu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China; Beijing Laboratory for Food Quality and Safety, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China.
| | - Chunyan Sun
- Department of Food Quality and Safety, College of Food Science and Engineering, Jilin University, Changchun 130062, China.
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14
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Xie Y, Ning M, Ban J, Li Q. Novel Enzyme-Linked Aptamer Assay for the Determination of Aflatoxin B1 in Peanuts. ANAL LETT 2019. [DOI: 10.1080/00032719.2019.1632337] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Yanli Xie
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
- Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control, Zhengzhou, China
| | - Mengge Ning
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
- Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control, Zhengzhou, China
| | - Jun Ban
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
- Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control, Zhengzhou, China
| | - Qian Li
- School of Food Science and Technology, Henan University of Technology, Zhengzhou, China
- Henan Key Laboratory of Cereal and Oil Food Safety Inspection and Control, Zhengzhou, China
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15
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Pourreza N, Ghomi M. Hydrogel based aptasensor for thrombin sensing by Resonance Rayleigh Scattering. Anal Chim Acta 2019; 1079:180-191. [PMID: 31387709 DOI: 10.1016/j.aca.2019.06.049] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 06/02/2019] [Accepted: 06/22/2019] [Indexed: 12/12/2022]
Abstract
In this research, a novel Resonance Rayleigh Scattering (RRS) aptasensor was developed for thrombin monitoring using in-situ synthesized and embedded Au nanoparticles (AuNPs) into poly vinyl alcohol -borax hydrogel (PBH). Thiolated-thrombin binding aptamer (thiolated-TBA) was attached to the surface of AuNPs embedded into PBH to design the PBH-aptasensor for thrombin detection (thiolated-TBA@AuNPs-PBH). To verify the characteristic and morphology of PBH nanocomposite, energy dispersive X-ray analysis, TEM, average particle size analizer and UV-Vis spectra were performed. The difference in RRS intensities in the absence and presence of thrombin was calculated and selected as the monitoring signal. Effect of different parameters on the RRS signal was investigated at excitation wavelength of 500 nm. Under the approved conditions, the linear detection range was validated over the concentration of 0.70 pM- 0.02 μM. The limit of detection based on 3Sb was 0.10 pM. The relative standard deviation for 5.6 pM and 3.6 nM were 4.0 and 2.7% (n = 10), respectively. The proposed aptasensor was successfully applied as an experimental model for thrombin detection in serum samples of healthy volunteers with acceptable results.
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Affiliation(s)
- Nahid Pourreza
- Department of Chemistry, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran.
| | - Matineh Ghomi
- Department of Chemistry, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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16
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Qu H, Wang L, Liu J, Zheng L. Direct Screening for Cytometric Bead Assays for Adenosine Triphosphate. ACS Sens 2018; 3:2071-2078. [PMID: 30084633 DOI: 10.1021/acssensors.8b00224] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Cytometric bead assays have caught much attention because of their many exceptional advantages. Unfortunately, the immobilization of existing molecular recognition elements including monoclonal antibodies and aptamers onto solid particles may lead to the functional failure of the molecular recognition elements since they are generally obtained in free state. Herein we develop a powerful screening approach for direct and rapid discovery of aptamer based cytometric bead assays (AB-CBAs) by individually measuring the functional activity of every aptamer particles in a library and sorting them at rates of up to 108 particles per hour. The strategy is based on the transformation of molecular libraries into pools of monoclonal aptamer particles so that one individual particle displays ∼105 copies of an identical aptamer sequence. Our library design incorporates a two-color fluorescent reporter system in which changes in aptamer structure generate an optical readout, such that we can use fluorescence-activated cell sorting to rapidly and selectively separate the individual aptamer particles that exhibit large fluorescent signal change upon target binding. For demonstration, we isolated AB-CBA aptamer particles with high signaling performance for ATP after just 3 rounds of screening. We believe that the rapid and direct screening features of this strategy make it an excellent platform for generating AB-CBAs for for a wide range of important analytes.
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Affiliation(s)
- Hao Qu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
- CAS Key Laboratory of Bio-inspired Materials and Interfacial Science, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Lu Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Jian Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
| | - Lei Zheng
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, Anhui 230009, China
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17
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Dual functional extracellular recording using a light-addressable potentiometric sensor for bitter signal transduction. Anal Chim Acta 2018; 1022:106-112. [PMID: 29729730 DOI: 10.1016/j.aca.2018.03.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2018] [Revised: 03/05/2018] [Accepted: 03/10/2018] [Indexed: 11/24/2022]
Abstract
This paper presents a dual functional extracellular recording biosensor based on a light-addressable potentiometric sensor (LAPS). The design and fabrication of this biosensor make it possible to record both extracellular membrane potential changes and ATP release from a single taste bud cell for the first time. For detecting ATP release, LAPS chip was functionalized with ATP-sensitive DNA aptamer by covalent immobilization. Taste bud cells isolated from rat were cultured on LAPS surface. When the desired single taste bud cell was illuminated by modulated light, ATP release from single taste bud cells can be measured by recording the shifts of bias voltage-photocurrent curves (I-V curves) when the LAPS chip is working in discrete mode. On the other hand, extracellular membrane potential changes can be monitored by recording the fluctuation of LAPS photocurrent when the LAPS chip is working in continuous mode. The results show this biosensor can effectively record the enhancive effect of the bitter substance and inhibitory effect of the carbenoxolone (CBX) on the extracellular membrane potential changes and ATP release of single taste bud cells. In addition, the inhibitory effect of CBX also confirms LAPS extracellular recordings are originated from bitter signal transduction. It is proved this biosensor is suitable for extracellular recording of ATP release and membrane potential changes of single taste bud cells. It is suggested this biosensor could be applied to investigating taste signal transduction at the single-cell level as well as applied to other types of cells which have similar functions to taste bud cells.
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18
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Sun N, Ding Y, Tao Z, You H, Hua X, Wang M. Development of an upconversion fluorescence DNA probe for the detection of acetamiprid by magnetic nanoparticles separation. Food Chem 2018; 257:289-294. [PMID: 29622212 DOI: 10.1016/j.foodchem.2018.02.148] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 02/24/2018] [Accepted: 02/27/2018] [Indexed: 01/21/2023]
Abstract
An upconversion fluorescence DNA probe which consists of aptamer-conjugated magnet nanoparticles (apt-MNPs) and complementary DNA-conjugated upconversion nanoparticles (cDNA-UCNPs) was developed to detect acetamiprid. Acetamiprid can specifically conjugate with the apt-MNPs to dissociate the cDNA-UCNPs from the apt-MNPs and resulted in reduced fluorescence intensity through an external magnet. The change of fluorescence intensity (△I) is positively related to the concentration of acetamiprid, which can be applied for the quantification of acetamiprid. Under optimal conditions, a linear detection range and detection limit are 0.89-114.18 μg/L and 0.65 μg/L, respectively. The probe was successfully used to detect acetamiprid in spiked paddy water, soil, pear, apple, wheat and cucumber. Average recoveries are 78.2%-103.5% with intra-day relative standard deviations (RSDs) of 2.6%-10.9% and inter-day RSDs of 4.3%-10.2%. The amounts of acetamiprid in the authentic paddy water and pear samples detected by the DNA probe are significantly correlated with that detected by high-performance liquid chromatography (HPLC).
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Affiliation(s)
- Nana Sun
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Yuan Ding
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Zhexuan Tao
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Hongjie You
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Xiude Hua
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China
| | - Minghua Wang
- College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China; State & Local Joint Engineering Research Center of Green Pesticide Invention and Application, Nanjing 210095, China.
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19
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Specific Light-Up System for Protein and Metabolite Targets Triggered by Initiation Complex Formation. Sci Rep 2017; 7:15191. [PMID: 29123195 PMCID: PMC5680199 DOI: 10.1038/s41598-017-15697-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 11/01/2017] [Indexed: 12/11/2022] Open
Abstract
Gene regulation systems are mimicked by simple quantitative detection of non-nucleic acid molecular targets such as protein and metabolite. Here, we describe a one-tube, one-step real-time quantitative detection methodology for isothermal signal amplification of those targets. Using this system, real-time quantitative detection of thrombin and streptomycin, which were used as examples for protein and metabolite targets, was successfully demonstrated with detection limits of at most 50 pM and 75 nM, respectively. Notably, the dynamic range of target concentrations could be obtained for over four orders of magnitude. Thus, our method is expected to serve as a point-of-care or on-site test for medical diagnosis and food and environmental hygiene.
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20
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Liu M, Yin Q, Brennan JD, Li Y. Selection and characterization of DNA aptamers for detection of glutamate dehydrogenase from Clostridium difficile. Biochimie 2017; 145:151-157. [PMID: 28882627 DOI: 10.1016/j.biochi.2017.08.015] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 08/31/2017] [Indexed: 12/18/2022]
Abstract
Rapid and accurate diagnosis of Clostridium difficile infections (CDI) is crucial for patient treatment, infection control and epidemiological monitoring. As an important antigen, glutamate dehydrogenase (GDH) has been proposed as a preliminary screening test target for CDI. However, current assays based on GDH activity or GDH immunoassays have suboptimal sensitivity and specificity. Herein, we describe the selection and characterization of single-stranded DNA aptamers that specifically target GDH. After 10 rounds of selection, high-throughput sequencing was used to identify enriched aptamer candidates. Of 10 candidates, three aptamers for GDH were identified. Gel shift assays showed that these aptamers exhibited low nanomolar affinities. One aptamer was optimized based on structural analysis and further engineered into a structure-switching fluorescence signaling aptamer, wherein desorption from reduced graphene oxide (RGO) upon binding of GDH led to an increase in fluorescence emission. This method allowed for quantitative detection of GDH with a detection limit of 1 nM, providing great potential for its further application in CDI diagnosis.
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Affiliation(s)
- Meng Liu
- Department of Biochemistry and Biomedical Sciences, and Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada; Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 0A3, Canada; School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | - Qingxin Yin
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education), Dalian University of Technology, Dalian, 116024, China
| | - John D Brennan
- Department of Biochemistry and Biomedical Sciences, and Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada; Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 0A3, Canada; The Michael G. DeGroote Institute for Infectious Disease Research (IIDR), McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada.
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, and Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada; Biointerfaces Institute, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 0A3, Canada; The Michael G. DeGroote Institute for Infectious Disease Research (IIDR), McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada.
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21
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Carrasquilla C, Kapteyn E, Li Y, Brennan JD. Sol-Gel-Derived Biohybrid Materials Incorporating Long-Chain DNA Aptamers. Angew Chem Int Ed Engl 2017; 56:10686-10690. [PMID: 28556430 DOI: 10.1002/anie.201702859] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2017] [Indexed: 11/10/2022]
Abstract
Sol-gel-derived bio/inorganic hybrid materials have been examined for diverse applications, including biosensing, affinity chromatography and drug discovery. However, such materials have mostly been restricted to the interaction between entrapped biorecognition elements and small molecules, owing to the requirement for nanometer-scale mesopores in the matrix to retain entrapped biorecognition elements. Herein, we report on a new class of macroporous bio/inorganic hybrids, engineered through a high-throughput materials screening approach, that entrap micron-sized concatemeric DNA aptamers. We demonstrate that the entrapment of these long-chain DNA aptamers allows their retention within the macropores of the silica material, so that aptamers can interact with high molecular weight targets such as proteins. Our approach overcomes the major limitation of previous sol-gel-derived biohybrid materials by enabling molecular recognition for targets beyond small molecules.
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Affiliation(s)
- Carmen Carrasquilla
- Biointerfaces Institute and the Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 0A3, Canada), or
| | - Emily Kapteyn
- Biointerfaces Institute and the Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 0A3, Canada), or
| | - Yingfu Li
- Biointerfaces Institute and the Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 0A3, Canada), or
| | - John D Brennan
- Biointerfaces Institute and the Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 0A3, Canada), or
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22
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Carrasquilla C, Kapteyn E, Li Y, Brennan JD. Sol-Gel-Derived Biohybrid Materials Incorporating Long-Chain DNA Aptamers. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201702859] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Carmen Carrasquilla
- Biointerfaces Institute and the Department of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 0A3 Canada), or
| | - Emily Kapteyn
- Biointerfaces Institute and the Department of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 0A3 Canada), or
| | - Yingfu Li
- Biointerfaces Institute and the Department of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 0A3 Canada), or
| | - John D. Brennan
- Biointerfaces Institute and the Department of Biochemistry and Biomedical Sciences; McMaster University; 1280 Main Street West Hamilton ON L8S 0A3 Canada), or
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23
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Jeddi I, Saiz L. Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors. Sci Rep 2017; 7:1178. [PMID: 28446765 PMCID: PMC5430850 DOI: 10.1038/s41598-017-01348-5] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/24/2017] [Indexed: 12/11/2022] Open
Abstract
Aptamers consist of short oligonucleotides that bind specific targets. They provide advantages over antibodies, including robustness, low cost, and reusability. Their chemical structure allows the insertion of reporter molecules and surface-binding agents in specific locations, which have been recently exploited for the development of aptamer-based biosensors and direct detection strategies. Mainstream use of these devices, however, still requires significant improvements in optimization for consistency and reproducibility. DNA aptamers are more stable than their RNA counterparts for biomedical applications but have the disadvantage of lacking the wide array of computational tools for RNA structural prediction. Here, we present the first approach to predict from sequence the three-dimensional structures of single stranded (ss) DNA required for aptamer applications, focusing explicitly on ssDNA hairpins. The approach consists of a pipeline that integrates sequentially building ssDNA secondary structure from sequence, constructing equivalent 3D ssRNA models, transforming the 3D ssRNA models into ssDNA 3D structures, and refining the resulting ssDNA 3D structures. Through this pipeline, our approach faithfully predicts the representative structures available in the Nucleic Acid Database and Protein Data Bank databases. Our results, thus, open up a much-needed avenue for integrating DNA in the computational analysis and design of aptamer-based biosensors.
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Affiliation(s)
- Iman Jeddi
- Modeling of Biological Networks and Systems Therapeutics Laboratory, Department of Biomedical Engineering, University of California, 451 East Health Sciences Drive, Davis, CA, 95616, USA
| | - Leonor Saiz
- Modeling of Biological Networks and Systems Therapeutics Laboratory, Department of Biomedical Engineering, University of California, 451 East Health Sciences Drive, Davis, CA, 95616, USA.
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24
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Zhang A, Chang D, Zhang Z, Li F, Li W, Wang X, Li Y, Hua Q. In Vitro Selection of DNA Aptamers that Binds Geniposide. Molecules 2017; 22:molecules22030383. [PMID: 28264528 PMCID: PMC6155188 DOI: 10.3390/molecules22030383] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2017] [Accepted: 02/21/2017] [Indexed: 12/25/2022] Open
Abstract
Geniposide is a key iridoid glycoside from Gardenia jasminoides fructus widely used in traditional Chinese herbal medicine. However, detection of this small molecule represents a significant challenge mostly due to the lack of specific molecular recognition elements. In this study, we have performed in vitro selection experiments to isolate DNA aptamers that can specifically bind geniposide. Using a stringent selection procedure, we have isolated DNA aptamers that can distinguish geniposide from genipin and glucose, two structural analogs of geniposide. Two top aptamers exhibit low micromolar binding affinity towards geniposide, but show significantly reduced affinity to genipin and glucose. These aptamers have the potential to be further developed into analytical tools for the detection of geniposide.
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Affiliation(s)
- Aozhe Zhang
- School of Basic Medical Science, Beijing University of Chinese Medicine, 11 East Road, North 3rd Ring Road, Chaoyang District, Beijing 100029, China.
| | - Dingran Chang
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada.
| | - Zijian Zhang
- Beijing Institute of Traditional Chinese Medicine, Beijing University of Chinese Medicine, 11 East Road, North 3rd Ring Road, Chaoyang District, Beijing 100029, China.
| | - Fan Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada.
| | - Weihong Li
- School of Basic Medical Science, Beijing University of Chinese Medicine, 11 East Road, North 3rd Ring Road, Chaoyang District, Beijing 100029, China.
| | - Xu Wang
- School of Basic Medical Science, Beijing University of Chinese Medicine, 11 East Road, North 3rd Ring Road, Chaoyang District, Beijing 100029, China.
| | - Yingfu Li
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada.
| | - Qian Hua
- School of Basic Medical Science, Beijing University of Chinese Medicine, 11 East Road, North 3rd Ring Road, Chaoyang District, Beijing 100029, China.
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25
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Miao H, Wang L, Zhuo Y, Zhou Z, Yang X. Label-free fluorimetric detection of CEA using carbon dots derived from tomato juice. Biosens Bioelectron 2016; 86:83-89. [DOI: 10.1016/j.bios.2016.06.043] [Citation(s) in RCA: 154] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Revised: 06/13/2016] [Accepted: 06/14/2016] [Indexed: 11/17/2022]
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26
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Perez-Gonzalez C, Lafontaine DA, Penedo JC. Fluorescence-Based Strategies to Investigate the Structure and Dynamics of Aptamer-Ligand Complexes. Front Chem 2016; 4:33. [PMID: 27536656 PMCID: PMC4971091 DOI: 10.3389/fchem.2016.00033] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 07/11/2016] [Indexed: 12/11/2022] Open
Abstract
In addition to the helical nature of double-stranded DNA and RNA, single-stranded oligonucleotides can arrange themselves into tridimensional structures containing loops, bulges, internal hairpins and many other motifs. This ability has been used for more than two decades to generate oligonucleotide sequences, so-called aptamers, that can recognize certain metabolites with high affinity and specificity. More recently, this library of artificially-generated nucleic acid aptamers has been expanded by the discovery that naturally occurring RNA sequences control bacterial gene expression in response to cellular concentration of a given metabolite. The application of fluorescence methods has been pivotal to characterize in detail the structure and dynamics of these aptamer-ligand complexes in solution. This is mostly due to the intrinsic high sensitivity of fluorescence methods and also to significant improvements in solid-phase synthesis, post-synthetic labeling strategies and optical instrumentation that took place during the last decade. In this work, we provide an overview of the most widely employed fluorescence methods to investigate aptamer structure and function by describing the use of aptamers labeled with a single dye in fluorescence quenching and anisotropy assays. The use of 2-aminopurine as a fluorescent analog of adenine to monitor local changes in structure and fluorescence resonance energy transfer (FRET) to follow long-range conformational changes is also covered in detail. The last part of the review is dedicated to the application of fluorescence techniques based on single-molecule microscopy, a technique that has revolutionized our understanding of nucleic acid structure and dynamics. We finally describe the advantages of monitoring ligand-binding and conformational changes, one molecule at a time, to decipher the complexity of regulatory aptamers and summarize the emerging folding and ligand-binding models arising from the application of these single-molecule FRET microscopy techniques.
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Affiliation(s)
- Cibran Perez-Gonzalez
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
| | - Daniel A. Lafontaine
- RNA Group, Department of Biology, Faculty of Science, Université de SherbrookeSherbrooke, QC, Canada
| | - J. Carlos Penedo
- Laboratory for Biophysics and Biomolecular Dynamics, SUPA School of Physics and Astronomy, University of St. AndrewsSt Andrews, UK
- Laboratory for Biophysics and Biomolecular Dynamics, Biomedical Sciences Research Complex, School of Biology, University of St. AndrewsSt. Andrews, UK
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Ng S, Lim HS, Ma Q, Gao Z. Optical Aptasensors for Adenosine Triphosphate. Theranostics 2016; 6:1683-702. [PMID: 27446501 PMCID: PMC4955066 DOI: 10.7150/thno.15850] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 05/09/2016] [Indexed: 12/16/2022] Open
Abstract
Nucleic acids are among the most researched and applied biomolecules. Their diverse two- and three-dimensional structures in conjunction with their robust chemistry and ease of manipulation provide a rare opportunity for sensor applications. Moreover, their high biocompatibility has seen them being used in the construction of in vivo assays. Various nucleic acid-based devices have been extensively studied as either the principal element in discrete molecule-like sensors or as the main component in the fabrication of sensing devices. The use of aptamers in sensors - aptasensors, in particular, has led to improvements in sensitivity, selectivity, and multiplexing capacity for a wide verity of analytes like proteins, nucleic acids, as well as small biomolecules such as glucose and adenosine triphosphate (ATP). This article reviews the progress in the use of aptamers as the principal component in sensors for optical detection of ATP with an emphasis on sensing mechanism, performance, and applications with some discussion on challenges and perspectives.
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Affiliation(s)
| | | | | | - Zhiqiang Gao
- Department of Chemistry, National University of Singapore, Singapore 117543
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28
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Zhang H, Zhou L, Zhu Z, Yang C. Recent Progress in Aptamer-Based Functional Probes for Bioanalysis and Biomedicine. Chemistry 2016; 22:9886-900. [PMID: 27243551 DOI: 10.1002/chem.201503543] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 02/16/2016] [Indexed: 01/01/2023]
Abstract
Nucleic acid aptamers are short synthetic DNA or RNA sequences that can bind to a wide range of targets with high affinity and specificity. In recent years, aptamers have attracted increasing research interest due to their unique features of high binding affinity and specificity, small size, excellent chemical stability, easy chemical synthesis, facile modification, and minimal immunogenicity. These properties make aptamers ideal recognition ligands for bioanalysis, disease diagnosis, and cancer therapy. This review highlights the recent progress in aptamer selection and the latest applications of aptamer-based functional probes in the fields of bioanalysis and biomedicine.
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Affiliation(s)
- Huimin Zhang
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Leiji Zhou
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Zhi Zhu
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China
| | - Chaoyong Yang
- College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China.
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Marton S, Cleto F, Krieger MA, Cardoso J. Isolation of an Aptamer that Binds Specifically to E. coli. PLoS One 2016; 11:e0153637. [PMID: 27104834 PMCID: PMC4841571 DOI: 10.1371/journal.pone.0153637] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 04/01/2016] [Indexed: 01/24/2023] Open
Abstract
Escherichia coli is a bacterial species found ubiquitously in the intestinal flora of animals, although pathogenic variants cause major public health problems. Aptamers are short oligonucleotides that bind to targets with high affinity and specificity, and have great potential for use in diagnostics and therapy. We used cell-based Systematic Evolution of Ligands by EXponential enrichment (cell-SELEX) to isolate four single stranded DNA (ssDNA) aptamers that bind strongly to E. coli cells (ATCC generic strain 25922), with Kd values in the nanomolar range. Fluorescently labeled aptamers label the surface of E. coli cells, as viewed by fluorescent microscopy. Specificity tests with twelve different bacterial species showed that one of the aptamers–called P12-31—is highly specific for E. coli. Importantly, this aptamer binds to Meningitis/sepsis associated E. coli (MNEC) clinical isolates, and is the first aptamer described with potential for use in the diagnosis of MNEC-borne pathologies.
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Affiliation(s)
- Soledad Marton
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil
| | - Fernanda Cleto
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil
| | - Marco Aurélio Krieger
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil.,Instituto Carlos Chagas, Laboratório de Genomica Functional, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil
| | - Josiane Cardoso
- Instituto de Biologia Molecular do Paraná, Department of Research and Development, 3375 Professor Algacyr Munhoz Mader Street, Curitiba, Brazil
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30
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Durand G, Dausse E, Goux E, Fiore E, Peyrin E, Ravelet C, Toulmé JJ. A combinatorial approach to the repertoire of RNA kissing motifs; towards multiplex detection by switching hairpin aptamers. Nucleic Acids Res 2016; 44:4450-9. [PMID: 27067541 PMCID: PMC4872101 DOI: 10.1093/nar/gkw206] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 03/15/2016] [Indexed: 01/22/2023] Open
Abstract
Loop–loop (also known as kissing) interactions between RNA hairpins are involved in several mechanisms in both prokaryotes and eukaryotes such as the regulation of the plasmid copy number or the dimerization of retroviral genomes. The stability of kissing complexes relies on loop parameters (base composition, sequence and size) and base combination at the loop–loop helix - stem junctions. In order to identify kissing partners that could be used as regulatory elements or building blocks of RNA scaffolds, we analysed a pool of 5.2 × 106 RNA hairpins with randomized loops. We identified more than 50 pairs of kissing RNA hairpins. Two kissing motifs, 5′CCNY and 5′RYRY, generate highly stable complexes with KDs in the low nanomolar range. Such motifs were introduced in the apical loop of hairpin aptamers that switch between unfolded and folded state upon binding to their cognate target molecule, hence their name aptaswitch. The aptaswitch–ligand complex is specifically recognized by a second RNA hairpin named aptakiss through loop–loop interaction. Taking advantage of our kissing motif repertoire we engineered aptaswitch–aptakiss modules for purine derivatives, namely adenosine, GTP and theophylline and demonstrated that these molecules can be specifically and simultaneously detected by surface plasmon resonance or by fluorescence anisotropy.
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Affiliation(s)
- Guillaume Durand
- University of Bordeaux, ARNA Laboratory, 146 rue Léo Saignat, 33076 Bordeaux, France Inserm U1212, 146 rue Léo Saignat, 33076 Bordeaux, France CNRS UMR5320, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Eric Dausse
- University of Bordeaux, ARNA Laboratory, 146 rue Léo Saignat, 33076 Bordeaux, France Inserm U1212, 146 rue Léo Saignat, 33076 Bordeaux, France CNRS UMR5320, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Emma Goux
- University Grenoble Alpes, Département de Pharmacochimie Moléculaire, CNRS UMR5063, 38400 St Martin d'Hères, France
| | - Emmanuelle Fiore
- University Grenoble Alpes, Département de Pharmacochimie Moléculaire, CNRS UMR5063, 38400 St Martin d'Hères, France
| | - Eric Peyrin
- University Grenoble Alpes, Département de Pharmacochimie Moléculaire, CNRS UMR5063, 38400 St Martin d'Hères, France
| | - Corinne Ravelet
- University Grenoble Alpes, Département de Pharmacochimie Moléculaire, CNRS UMR5063, 38400 St Martin d'Hères, France
| | - Jean-Jacques Toulmé
- University of Bordeaux, ARNA Laboratory, 146 rue Léo Saignat, 33076 Bordeaux, France Inserm U1212, 146 rue Léo Saignat, 33076 Bordeaux, France CNRS UMR5320, 146 rue Léo Saignat, 33076 Bordeaux, France
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31
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Abstract
Nucleic acid aptamers are promising alternatives to antibodies in analytics. They are generally obtained through an iterative SELEX protocol that enriches a population of synthetic oligonucleotides to a subset that can recognize the chosen target molecule specifically and avidly. A wide range of targets is recognized by aptamers. Once identified and optimized for performance, aptamers can be reproducibly synthesized and offer other key features, like small size, low cost, sensitivity, specificity, rapid response, stability, and reusability. This makes them excellent options for sensory units in a variety of analytical platforms including those with electrochemical, optical, and mass sensitive transduction detection. Many novel sensing strategies have been developed by rational design to take advantage of the tendency of aptamers to undergo conformational changes upon target/analyte binding and employing the principles of base complementarity that can drive the nucleic acid structure. Despite their many advantages over antibodies, surprisingly few aptamers have yet been integrated into commercially available analytical devices. In this review, we discuss how to select and engineer aptamers for their identified application(s), some of the challenges faced in developing aptamers for analytics and many examples of their reported successful performance as sensors in a variety of analytical platforms.
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Affiliation(s)
- Muslum Ilgu
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames IA 50011, USA. and Aptalogic Inc., Ames IA 50014, USA
| | - Marit Nilsen-Hamilton
- Roy J Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames IA 50011, USA. and Aptalogic Inc., Ames IA 50014, USA and Ames Laboratory, US DOE, Ames IA 50011, USA
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32
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Du Y, Zhen SJ, Li B, Byrom M, Jiang YS, Ellington AD. Engineering Signaling Aptamers That Rely on Kinetic Rather Than Equilibrium Competition. Anal Chem 2016; 88:2250-7. [PMID: 26750592 DOI: 10.1021/acs.analchem.5b03930] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
During the past decade, aptasensors have largely been designed on the basis of the notion that ligand-modulated equilibration between aptamer conformations could be exploited for sensing. One implementation of this strategy has been to denature the aptamer with an antisense oligonucleotide, wait for dissociation of the antisense oligonucleotide, and stabilize the folded, signaling conformer with a ligand. However, there is a large kinetic barrier associated with releasing the oligonucleotide from the aptamer to again obtain an active, binding conformation. If the length of the antisense oligonucleotide is decreased to make dissociation from the aptamer more favorable, higher background signals are observed. To improve the general methodology for developing aptasensors, we have developed a novel and robust strategy for aptasensor design in which an oligonucleotide kinetically competes with the ligand for binding rather than having to be released from a stable duplex. While the oligonucleotide can induce conformational change, it initially chooses between the aptamer and a molecular beacon (MB), a process that does not require a lengthy pre-equilibration. Using an anti-ricin aptamer as a starting point, we developed a "competitive" aptasensor with a measured limit of detection (LOD) of 30 nM with an optical readout and as low as 3 nM for ricin toxin A-chain (RTA) detection on an electrochemical platform.
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Affiliation(s)
- Yan Du
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Shu Jun Zhen
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States.,Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University), Ministry of Education, College of Chemistry and Chemical Engineering, Southwest University , 400715, Chongqing, P.R. China
| | - Bingling Li
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Michelle Byrom
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Yu Sherry Jiang
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
| | - Andrew D Ellington
- Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, and Department of Chemistry, The University of Texas at Austin , Austin, Texas 78712, United States
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Ha TH. Recent Advances for the Detection of Ochratoxin A. Toxins (Basel) 2015; 7:5276-300. [PMID: 26690216 PMCID: PMC4690132 DOI: 10.3390/toxins7124882] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Revised: 11/25/2015] [Accepted: 11/26/2015] [Indexed: 12/15/2022] Open
Abstract
Ochratoxin A (OTA) is one of the mycotoxins secreted by Aspersillus and Penicillium that can easily colonize various grains like coffee, peanut, rice, and maize. Since OTA is a chemically stable compound that can endure the physicochemical conditions of modern food processing, additional research efforts have been devoted to develop sensitive and cost-effective surveillance solutions. Although traditional chromatographic and immunoassays appear to be mature enough to attain sensitivity up to the regulation levels, alternative detection schemes are still being enthusiastically pursued in an attempt to meet the requirements of rapid and cost-effective detections. Herein, this review presents recent progresses in OTA detections with minimal instrumental usage, which have been facilitated by the development of OTA aptamers and by the innovations in functional nanomaterials. In addition to the introduction of aptamer-based OTA detection techniques, OTA-specific detection principles are also presented, which exclusively take advantage of the unique chemical structure and related physicochemical characteristics.
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Affiliation(s)
- Tai Hwan Ha
- BioNanotechnology Research Centre, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea.
- Nanobiotechnology (Major), Korea University of Science & Technology, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Korea.
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34
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Screening and Identification of ssDNA Aptamer for Human GP73. BIOMED RESEARCH INTERNATIONAL 2015; 2015:610281. [PMID: 26583119 PMCID: PMC4637037 DOI: 10.1155/2015/610281] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 09/08/2015] [Indexed: 12/11/2022]
Abstract
As one tumor marker of HCC, Golgi Protein 73 (GP73) is given more promise in the early diagnosis of HCC, and aptamers have been developed to compete with antibodies as biorecognition probes in different detection system. In this study, we utilized GP73 to screen specific ssDNA aptamers by SELEX technique. First, GP73 proteins were expressed and purified by prokaryotic expression system and Nickle ion affinity chromatography, respectively. At the same time, the immunogenicity of purified GP73 was confirmed by Western blotting. The enriched ssDNA library with high binding capacity for GP73 was obtained after ten rounds of SELEX. Then, thirty ssDNA aptamers were sequenced, in which two ssDNA aptamers with identical DNA sequence were confirmed, based on the alignment results, and designated as A10-2. Furthermore, the specific antibody could block the binding of A10-2 to GP73, and the specific binding of A10-2 to GP73 was also supported by the observation that several tumor cell lines exhibited variable expression level of GP73. Significantly, the identified aptamer A10-2 could distinguish normal and cancerous liver tissues. So, our results indicate that the aptamer A10-2 might be developed into one molecular probe to detect HCC from normal liver specimens.
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35
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van den Kieboom CH, van der Beek SL, Mészáros T, Gyurcsányi RE, Ferwerda G, de Jonge MI. Aptasensors for viral diagnostics. Trends Analyt Chem 2015; 74:58-67. [PMID: 32287539 PMCID: PMC7112930 DOI: 10.1016/j.trac.2015.05.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We discuss progress in aptamer-based detection of viruses. We consider the use of aptasensors for point-of-care diagnostics of viruses. Aptamers have distinct advantages over antibodies for virus recognition. There is strong demand for multiplexed diagnostic measurement of pathogens.
Novel viral diagnostic tools need to be affordable, fast, accurate and easy to use with sensitivity and specificity equivalent or superior to current standards. At present, viral diagnostics are based on direct detection of viral components or indirect detection by measuring antibodies generated in response to viral infection. While sensitivity of detection and quantification are still important challenges, we expect major advances from new assay formats and synthetic binding molecules, such as aptamers. Compared to traditional antibody-based detection, aptamers could provide faster adaptation to continuously evolving virus strains and higher discriminating capacity between specific virus serotypes. Aptamers are very stable and easily modifiable, so are ideal molecules for detection and chemical sensing applications. Here, we review the use of aptasensors for detection of viral pathogens and consider the feasibility of aptasensors to become standard devices for point-of-care diagnostics of viruses.
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Affiliation(s)
- Corné H van den Kieboom
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Center, Nijmegen, Netherlands.,Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | | | - Tamás Mészáros
- Department of Medical Chemistry, Molecular Biology and Pathobiochemistry, Semmelweis University, Budapest, Hungary.,MTA-BME Research Group for Technical Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary
| | - Róbert E Gyurcsányi
- MTA-BME Lendület Chemical Nanosensors Research Group, Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Budapest, Hungary
| | - Gerben Ferwerda
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Center, Nijmegen, Netherlands
| | - Marien I de Jonge
- Laboratory of Pediatric Infectious Diseases, Department of Pediatrics, Radboud University Medical Center, Nijmegen, Netherlands
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36
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Goux E, Lespinasse Q, Guieu V, Perrier S, Ravelet C, Fiore E, Peyrin E. Fluorescence anisotropy-based structure-switching aptamer assay using a peptide nucleic acid (PNA) probe. Methods 2015; 97:69-74. [PMID: 26455538 DOI: 10.1016/j.ymeth.2015.09.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/04/2015] [Accepted: 09/18/2015] [Indexed: 01/04/2023] Open
Abstract
This study describes for the first time the feasibility of using peptide nucleic acids (PNAs) as an alternative to the DNA probes in structure-switching aptamer fluorescence polarisation assays. The effects of experimental parameters such as the length of the PNA strand, the nature of dye and the buffer conditions on the assay performances are first explored using two different methodologies based on the competition between the PNA/aptamer hydribridisation and the target/aptamer complexation. D-ATP can be detected from 1 to 25 μM in a linear range and a detection limit (LOD) of 3 μM can be reached. For this target, this lowers by a factor >5 the LOD reported with conventional DNA-based fluorescent structure switching aptamer-based assays and by a factor 3 the LOD observed with non-competitive fluorescent sensing platform indicating the usefulness of the PNA-based approach.
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Affiliation(s)
- Emma Goux
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France
| | - Quentin Lespinasse
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France
| | - Valérie Guieu
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France.
| | - Sandrine Perrier
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France
| | - Corinne Ravelet
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France
| | - Emmanuelle Fiore
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France
| | - Eric Peyrin
- Département de Pharmacochimie Moléculaire, Université Grenoble Alpes, UMR 5063 CNRS, ICMG FR 2607, Campus universitaire, Saint-Martin d'Hères, France.
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37
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Abstract
Aptamers, as a novel class of molecular probes for diagnosis, imaging and targeting therapy, have attracted increasing attention in recent years. Aptamers are generated from libraries of single-stranded nucleic acids against different molecules via the "systematic evolution of ligands by exponential enrichment" (SELEX) method. SELEX is a repetitive process of a sequential selection procedure in which a DNA or RNA library pool is incubated separately with target and control molecules to select specific oligonucleotide aptamers with high affinities and specificities. Cell-SELEX is a modified version of the SELEX process in which whole living cells are used as targets for the aptamers. Dendritic cell (DC) targeting, as a new therapeutic approach, can improve the efficiency of immunotherapy in the treatment of allergies and cancers. DCs use various receptors to continuously induce adaptive immunity via capture and presentation of antigens to naïve T cells. DCs are considered as the best targets in modulating immune responses against cancer, autoimmunity, allergy and transplantation. Aptamers, as a new agent, can be applied in DC targeting. The purpose of this review is to present some general concepts of aptamer production and DC targeting by aptamer molecules.
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Affiliation(s)
- A Ganji
- a Student Research Committee , Mashhad University of Medical Sciences , Mashhad , Iran .,b Immunology Research Center, Medical School, Mashhad University of Medical Sciences , Mashhad , Iran , and
| | - A Varasteh
- c Allergy Research Center, Medical School, Mashhad University of Medical Sciences , Mashhad , Iran
| | - M Sankian
- b Immunology Research Center, Medical School, Mashhad University of Medical Sciences , Mashhad , Iran , and
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38
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Verchère A, Dezi M, Adrien V, Broutin I, Picard M. In vitro transport activity of the fully assembled MexAB-OprM efflux pump from Pseudomonas aeruginosa. Nat Commun 2015; 6:6890. [PMID: 25901994 DOI: 10.1038/ncomms7890] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2014] [Accepted: 03/10/2015] [Indexed: 11/09/2022] Open
Abstract
Antibiotic resistance is a major public health issue and many bacteria responsible for human infections have now developed a variety of antibiotic resistance mechanisms. For instance, Pseudomonas aeruginosa, a disease-causing Gram-negative bacteria, is now resistant to almost every class of antibiotics. Much of this resistance is attributable to multidrug efflux pumps, which are tripartite membrane protein complexes that span both membranes and actively expel antibiotics. Here we report an in vitro procedure to monitor transport by the tripartite MexAB-OprM pump. By combining proteoliposomes containing the MexAB and OprM portions of the complex, we are able to assay energy-dependent substrate translocation in a system that mimics the dual-membrane architecture of Gram-negative bacteria. This assay facilitates the study of pump transport dynamics and could be used to screen pump inhibitors with potential clinical use in restoring therapeutic activity of old antibiotics.
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Affiliation(s)
- Alice Verchère
- Laboratoire de Cristallographie et RMN Biologiques, UMR 8015, CNRS, Université Paris Descartes, Faculté de Pharmacie de Paris, 4 Avenue de l'Observatoire, 75006 Paris, France
| | - Manuela Dezi
- Laboratoire de Cristallographie et RMN Biologiques, UMR 8015, CNRS, Université Paris Descartes, Faculté de Pharmacie de Paris, 4 Avenue de l'Observatoire, 75006 Paris, France
| | - Vladimir Adrien
- Laboratoire de physique statistique de l'École Normale Supérieure, UMR 8550, CNRS, Université Pierre et Marie Curie, 24 rue Lhomond, 75005 Paris, France
| | - Isabelle Broutin
- Laboratoire de Cristallographie et RMN Biologiques, UMR 8015, CNRS, Université Paris Descartes, Faculté de Pharmacie de Paris, 4 Avenue de l'Observatoire, 75006 Paris, France
| | - Martin Picard
- Laboratoire de Cristallographie et RMN Biologiques, UMR 8015, CNRS, Université Paris Descartes, Faculté de Pharmacie de Paris, 4 Avenue de l'Observatoire, 75006 Paris, France
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Ying G, Zhu F, Yi Y, Chen J, Mei J, Zhang Y, Chen S. Selecting DNA aptamers for endotoxin separation. Biotechnol Lett 2015; 37:1601-5. [PMID: 25896682 DOI: 10.1007/s10529-015-1839-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 04/11/2015] [Indexed: 11/26/2022]
Abstract
OBJECTIVES To select aptamers for endotoxin separation from a 75-nucleotide single-stranded DNA random library using systematic evolution of ligands by exponential enrichment. RESULTS After 15 rounds of selection, the final pool of aptamers was specific to endotoxin. Structural analysis of aptamers that appeared more than once suggested that one aptamer can form a G-quartet structure. Tests for binding affinity and specificity showed that this aptamer exhibited a high affinity for endotoxin. Using this aptamer, aptamer-magnetic beads were designed to separate endotoxin. CONCLUSIONS Using these aptamer-magnetic beads, a new method to separate endotoxin was developed to enable specific separation of endotoxin that can be applied to drug and food products.
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Affiliation(s)
- GuoQing Ying
- College of Pharmaceutical Science, ZheJiang University, Hangzhou, 310013, China,
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40
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Jeon JH, Kakuta T, Tanaka K, Chujo Y. Facile design of organic-inorganic hybrid gels for molecular recognition of nucleoside triphosphates. Bioorg Med Chem Lett 2015; 25:2050-5. [PMID: 25862197 DOI: 10.1016/j.bmcl.2015.03.093] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 03/24/2015] [Accepted: 03/30/2015] [Indexed: 01/31/2023]
Abstract
We report the molecular recognition for nucleoside triphosphates inside the ligand-modified water-soluble organic-inorganic hybrid gels composed of polyhedral oligomeric silsesquioxane (POSS). The series of ligands were designed to make hydrogen bonds with each nucleobase and introduced into the hybrid gels. From the titration experiments, the binding constants between the ligand inside the gels and nucleosides were evaluated. Accordingly, it was found that the ligands inside the gels can form a stable complex only with the target nucleoside triphosphate which has the complementary pattern of the hydrogen bonds (Ka=G-gel/cytidine triphosphate (CTP), 3.5×10(8)M(-1); U-gel/adenosine triphosphate (ATP), 1.6×10(3)M(-1); A-gel/uridine triphosphate (UTP), 1.9×10(7), respectively). With other nucleoside derivatives which have different numbers of phosphate units or different types of nucleobases, the much weaker interaction was detected. These data indicate that the complex formation only with nucleoside triphosphates should occur inside the hybrid gels, and selective recognition of each nucleoside triphosphate can be accomplished.
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Affiliation(s)
- Jong-Hwan Jeon
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takahiro Kakuta
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Kazuo Tanaka
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Yoshiki Chujo
- Department of Polymer Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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41
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Wu S, Zhang H, Shi Z, Duan N, Fang C, Dai S, Wang Z. Aptamer-based fluorescence biosensor for chloramphenicol determination using upconversion nanoparticles. Food Control 2015. [DOI: 10.1016/j.foodcont.2014.10.003] [Citation(s) in RCA: 164] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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42
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Carrasquilla C, Little JRL, Li Y, Brennan JD. Patterned paper sensors printed with long-chain DNA aptamers. Chemistry 2015; 21:7369-73. [PMID: 25820300 DOI: 10.1002/chem.201500949] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Indexed: 01/02/2023]
Abstract
There is growing interest in developing printable paper sensors to enable rapid testing of analytes for environmental, food safety, and clinical applications. A major challenge is to find suitable bioinks that are amenable to high-speed printing and remain functional after printing. We report on a simple and effective approach wherein an aqueous ink composed of megadalton-sized tandem repeating structure-switching DNA aptamers (concatemeric aptamers) is used to rapidly create patterned paper sensors on filter paper by inkjet printing. These concatemeric aptamer reporters remain immobilized at the point of printing through strong adsorption but retain sufficient segmental mobility to undergo structure switching and fluorescence signaling to provide both qualitative and quantitative detection of small molecules and protein targets. The convenience of inkjet printing allows for the patterning of internally referenced sensors with multiplexed detection, and provides a generic platform for on-demand printing of sensors even in remote locations.
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Affiliation(s)
- Carmen Carrasquilla
- Biointerfaces Institute and Department of Chemistry and Chemical Biology, McMaster University, 1280 Main St. W., Hamilton, ON, L8S 4L8 (Canada)
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43
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Sadana A, Sadana N. Detection of Biomarkers for Different Diseases on Biosensor Surfaces Part II. BIOMARKERS AND BIOSENSORS 2015. [PMCID: PMC7151883 DOI: 10.1016/b978-0-444-53794-2.00011-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this chapter the authors analyze the binding and dissociation kinetics (if applicable) of (1) interferon-gamma as a function of aptamer variants and inclusion of spacer, (2) GST-N protein in PBS and GST-N protein in 10-fold diluted serum to a localized surface plasmon resonance coupled fluorescence biosensor, (3) cytochrome c mutant to a superoxide biosensor, (4) Carbonic Anhydrase-II to an 4-(2-aminoethyl)-benzene sulfonamide ligand on an surface plasmon resonance biosensor surface, (5) glycerol secretion from differentiated (murine 3T3-L1) adipocytes to a microfluidic platform for fluorescence-based assay, and (6) different concentrations of C-reactive protein in solution to a sandwich-type assay using reflectometric interference spectroscopy (label-free detection method).
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Song J, Lau PS, Liu M, Shuang S, Dong C, Li Y. A general strategy to create RNA aptamer sensors using "regulated" graphene oxide adsorption. ACS APPLIED MATERIALS & INTERFACES 2014; 6:21806-21812. [PMID: 24992732 DOI: 10.1021/am502138n] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Aptamers have been used as molecular recognition elements for sensor development in combination with graphene oxide (GO), a nanomaterial with properties including fluorescence quenching, and selective adsorption of single-stranded nucleic acids. However, previous sensor designs based on aptamer-GO adsorption have not demonstrated wide applicability, and few studies have explored the potential of RNA aptamers. Herein, we present a new sensing strategy based on "regulated" GO adsorption that can accommodate various RNA aptamers. First, adsorption of a fluorophore-labeled RNA aptamer to GO results in fluorescence quenching due to close proximity of the fluorophore to GO. The addition of a complementary, "blocking" DNA strand (BDNA) that hybridizes to the 3'-end of the aptamer, weakens aptamer-GO interaction, and enables increased fluorescent signal generation upon the addition of target, as the sensing system becomes completely separated from GO. Our findings can be applied toward different aptamers, and adapted to enhance generality of existing sensing applications.
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Affiliation(s)
- Jinping Song
- Department of Biochemistry and Biomedical Sciences, Department of Chemistry and Chemical Biology, McMaster University , 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
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Heilkenbrinker A, Reinemann C, Stoltenburg R, Walter JG, Jochums A, Stahl F, Zimmermann S, Strehlitz B, Scheper T. Identification of the target binding site of ethanolamine-binding aptamers and its exploitation for ethanolamine detection. Anal Chem 2014; 87:677-85. [PMID: 25435319 DOI: 10.1021/ac5034819] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Aptamers are promising recognition elements for sensitive and specific detection of small molecules. We have previously selected ssDNA aptamers for ethanolamine, one of the smallest aptamer targets so far. The work presented here focuses on the determination of the binding region within the aptamer structure and its exploitation for the development of an aptamer-based assay for detection of ethanolamine. Sequence analysis of the aptamers resulted in the identification of a G-rich consensus sequence, which was able to fold in a typical two- or three-layered G-quartet structure. Experiments with stepwise truncated variants of the aptamers revealed that the consensus sequence is responsible and sufficient for binding to the target. On the basis of the knowledge of the aptamers binding site, we developed an aptamer-based microarray assay relying on competition between ethanolamine and an oligonucleotide complementary to the consensus sequence. Competitive binding of ethanolamine and fluorescently labeled complementary oligonucleotides resulted in fluorescence intensities dependent on ethanolamine concentration with a limit of detection of 10 pM. This method enables detection of small molecules without any labeling of analytes. The competitive assay could potentially be transferred to other aptamers and thus provides a promising system for aptamer-based detection of diverse small molecules.
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Affiliation(s)
- Alexandra Heilkenbrinker
- Gottfried Wilhelm Leibniz Universität Hannover, Institut für Technische Chemie, Callinstr. 5, D-30167 Hannover, Germany
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46
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Yang X, Zhuo Y, Zhu S, Luo Y, Feng Y, Xu Y. Selectively assaying CEA based on a creative strategy of gold nanoparticles enhancing silver nanoclusters' fluorescence. Biosens Bioelectron 2014; 64:345-51. [PMID: 25259877 DOI: 10.1016/j.bios.2014.09.029] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Revised: 09/02/2014] [Accepted: 09/04/2014] [Indexed: 02/02/2023]
Abstract
Herein, we have successfully built up connections between nanoparticles and nanoclusters, and further constructed a surface-enhanced fluorescence (SEF) strategy based on the two types of nanomaterials for selectively assaying carcinoembryonic antigen (CEA). Specifically, silver nanoclusters provided the original fluorescence signal, while gold nanoparticles modified with DNA served as the fluorescence enhancer simultaneously. On the basis of this proposed nano-system, the two nanomaterials were linked by CEA-aptamer, thus facilitating SEF occurring. Nevertheless, more competitive interactions between CEA and CEA-aptamer emerged once CEA added, leading to SEF failed and their fluorescence decreased. Significantly, this creative method was further applied to detect CEA, and showed the linear relationship between the fluorescence intensity and CEA concentrations in the range of 0.01-1 ng mL(-1) with a detection limit of 3 pg mL(-1) at a signal-to-noise ratio of 3, demonstrating its sensitivity and promising towards multiple applications. On the whole, this approach we established may broaden potential ways of combining nanoparticles and nanoclusters for detecting trace targets in bioanalytical fields.
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Affiliation(s)
- Xiaoming Yang
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China.
| | - Yan Zhuo
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Shanshan Zhu
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Yawen Luo
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Yuanjiao Feng
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
| | - Yan Xu
- College of Pharmaceutical Sciences, Southwest University, Chongqing 400716, China
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47
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Goodwin AP, Nakatsuka MA, Mattrey RF. Stimulus-responsive ultrasound contrast agents for clinical imaging: motivations, demonstrations, and future directions. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2014; 7:111-23. [PMID: 25195785 DOI: 10.1002/wnan.1285] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 06/23/2014] [Accepted: 07/06/2014] [Indexed: 12/17/2022]
Abstract
Microbubble ultrasound contrast agents allow imaging of the vasculature with excellent resolution and signal-to-noise ratios. Contrast in microbubbles derives from their interaction with an ultrasound wave to generate signal at harmonic frequencies of the stimulating pulse; subtracting the elastic echo caused by the surrounding tissue can enhance the specificity of these harmonic signals significantly. The nonlinear acoustic emission is caused by pressure-driven microbubble size fluctuations, which in both theoretical descriptions and empirical measurements was found to depend on the mechanical properties of the shell that encapsulates the microbubble as well as stabilizes it against the surrounding aqueous environment. Thus biochemically induced switching between a rigid 'off' state and a flexible 'on' state provides a mechanism for sensing chemical markers for disease. In our research, we coupled DNA oligonucleotides to a stabilizing lipid monolayer to modulate stiffness of the shell and thereby induce stimulus-responsive behavior. In initial proof-of-principle studies, it was found that signal modulation came primarily from DNA crosslinks preventing the microbubble size oscillations rather than merely damping the signal. Next, these microbubbles were redesigned to include an aptamer sequence in the crosslinking strand, which not only allowed the sensing of the clotting enzyme thrombin but also provided a general strategy for sensing other soluble biomarkers in the bloodstream. Finally, the thrombin-sensitive microbubbles were validated in a rabbit model, presenting the first example of an ultrasound contrast agent that could differentiate between active and inactive clots for the diagnosis of deep venous thrombosis.
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Affiliation(s)
- Andrew P Goodwin
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, CO, USA
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48
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Trevino SG, Levy M. High-throughput bead-based identification of structure-switching aptamer beacons. Chembiochem 2014; 15:1877-81. [PMID: 25056925 PMCID: PMC4161366 DOI: 10.1002/cbic.201402037] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Indexed: 12/29/2022]
Abstract
We describe a new platform to identify structure-switching DNA beacon aptamers, which detect small molecules in a specific manner. By clonally amplifying a DNA library designed to fluoresce in response to binding events onto microbeads, aptamer beacons can be selected by stringent fluorescence-assisted sorting. We validated this method by isolating known and novel anti-steroid aptamers from two separate DNA libraries that were structurally enriched with three-way junctions. Importantly, aptamers were retrieved in only a few (three) rounds of selection by this approach and did not require further optimization, significantly streamlining the process of beacon development.
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Affiliation(s)
- Simon G Trevino
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY 10461 (USA)
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49
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An aptamer-based dipstick assay for the rapid and simple detection of aflatoxin B1. Biosens Bioelectron 2014; 62:288-94. [PMID: 25032679 DOI: 10.1016/j.bios.2014.06.059] [Citation(s) in RCA: 148] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 06/10/2014] [Accepted: 06/30/2014] [Indexed: 12/20/2022]
Abstract
A rapid and simple dipstick assay based on an aptamer has been developed for the determination of aflatoxin B1 (AFB1). The dipstick assay format was based on a competitive reaction of the biotin-modified aptamer specific to AFB1 between target and cy5-modified DNA probes. Streptavidin and anti-cy5 antibody as capture reagents were immobilized at test and control lines on a membrane of the dipstick assay. After optimization, the limit of detection for the dipstick assay was 0.1 ng/ml AFB1 in buffer. The method was confirmed to be specific to AFB1, and the entire process of the assay can be completed within 30 min. Aqueous methanol (20%) provided a good extraction efficiency, and the matrix influence from corn extracts was successfully reduced through 2-fold dilution. The results of AFB1 analysis for corn samples spiked with known concentration of AFB1 by the dipstick assay and ELISA showed good agreement. The cut-off value of the dipstick assay for corn samples was 0.3 ng/g AFB1. Therefore, the dipstick assay is first reported and considered as a rapid, simple, on-site and inexpensive screening tool for AFB1 determination in grains as well as a corn.
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50
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Lee JW, Cho JH, Cho EJ. Aptamer-based optical switch for biosensors. ANALYTICAL SCIENCE AND TECHNOLOGY 2014. [DOI: 10.5806/ast.2014.27.3.121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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