1
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Fallah A, Havaei SA, Sedighian H, Kachuei R, Fooladi AAI. Prediction of aptamer affinity using an artificial intelligence approach. J Mater Chem B 2024; 12:8825-8842. [PMID: 39158322 DOI: 10.1039/d4tb00909f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/20/2024]
Abstract
Aptamers are oligonucleotide sequences that can connect to particular target molecules, similar to monoclonal antibodies. They can be chosen by systematic evolution of ligands by exponential enrichment (SELEX), and are modifiable and can be synthesized. Even if the SELEX approach has been improved a lot, it is frequently challenging and time-consuming to identify aptamers experimentally. In particular, structure-based methods are the most used in computer-aided design and development of aptamers. For this purpose, numerous web-based platforms have been suggested for the purpose of forecasting the secondary structure and 3D configurations of RNAs and DNAs. Also, molecular docking and molecular dynamics (MD), which are commonly utilized in protein compound selection by structural information, are suitable for aptamer selection. On the other hand, from a large number of sequences, artificial intelligence (AI) may be able to quickly discover the possible aptamer candidates. Conversely, sophisticated machine and deep-learning (DL) models have demonstrated efficacy in forecasting the binding properties between ligands and targets during drug discovery; as such, they may provide a reliable and precise method for forecasting the binding of aptamers to targets. This research looks at advancements in AI pipelines and strategies for aptamer binding ability prediction, such as machine and deep learning, as well as structure-based approaches, molecular dynamics and molecular docking simulation methods.
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Affiliation(s)
- Arezoo Fallah
- Department of Bacteriology and Virology, Faculty of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Seyed Asghar Havaei
- Department of Microbiology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.
| | - Hamid Sedighian
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
| | - Reza Kachuei
- Molecular Biology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Abbas Ali Imani Fooladi
- Applied Microbiology Research Center, Biomedicine Technologies Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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2
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Dong R, Yi N, Jiang D. Advances in single molecule arrays (SIMOA) for ultra-sensitive detection of biomolecules. Talanta 2024; 270:125529. [PMID: 38091745 DOI: 10.1016/j.talanta.2023.125529] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/25/2023] [Accepted: 12/05/2023] [Indexed: 01/27/2024]
Abstract
In the contemporary era of scientific and medical advancements, the accurate and ultra-sensitive detection of proteins, nucleic acids and metabolites plays a pivotal role in disease diagnosis and treatment monitoring. Single-molecule detection technologies play a great role in achieving this goal. In recent years, digital detection methods based on single molecule arrays (SIMOA) have brought groundbreaking contributions to the field of single-molecule detection. By confining the target molecules to femtoliter-sized containers, the SIMOA technology achieves detection sensitivity of attomolar. This review delves into the historical evolution and fundamentals of SIMOA technology, summarizes various approaches to optimize its performance, and describes the applications of SIMOA for the ultrasensitive detection of biomarkers for diseases such as cancer, COVID-19, and neurological disorders, as well as in DNA detection. Currently, some SIMOA technologies have been realized for high-throughput and multiplexed detection. It is believed that SIMOA technology will play a significant role in medical monitoring and disease prevention in the future.
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Affiliation(s)
- Renkai Dong
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Ning Yi
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China
| | - Dechen Jiang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, 210023, China.
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3
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Li Y, Cui Z, Shi L, Shan J, Zhang W, Wang Y, Ji Y, Zhang D, Wang J. Perovskite Nanocrystals: Superior Luminogens for Food Quality Detection Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:4493-4517. [PMID: 38382051 DOI: 10.1021/acs.jafc.3c06660] [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: 02/23/2024]
Abstract
With the global limited food resources receiving grievous damage from frequent climate changes and ascending global food demand resulting from increasing population growth, perovskite nanocrystals with distinctive photoelectric properties have emerged as attractive and prospective luminogens for the exploitation of rapid, easy operation, low cost, highly accurate, excellently sensitive, and good selective biosensors to detect foodborne hazards in food practices. Perovskite nanocrystals have demonstrated supreme advantages in luminescent biosensing for food products due to their high photoluminescence (PL) quantum yield, narrow full width at half-maximum PL, tunable PL in the entire visible spectrum, easy preparation, and various modification strategies compared with conventional semiconductors. Herein, we have carried out a comprehensive discussion concerning perovskite nanocrystals as luminogens in the application of high-performance biosensing of foodborne hazards for food products, including a brief introduction of perovskite nanocrystals, perovskite nanocrystal-based biosensors, and their application in different categories of food products. Finally, the challenges and opportunities faced by perovskite nanocrystals as superior luminogens were proposed to promote their practicality in the future food supply.
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Affiliation(s)
- Yuechun Li
- College of Food Science and Engineering, Northwest A&F University, 22 Xinong Road, Yangling 712100, Shaanxi, China
| | - Zhaowen Cui
- College of Food Science and Engineering, Northwest A&F University, 22 Xinong Road, Yangling 712100, Shaanxi, China
| | - Longhua Shi
- College of Food Science and Engineering, Northwest A&F University, 22 Xinong Road, Yangling 712100, Shaanxi, China
| | - Jinrui Shan
- College of Food Science and Engineering, Northwest A&F University, 22 Xinong Road, Yangling 712100, Shaanxi, China
| | - Wentao Zhang
- College of Food Science and Engineering, Northwest A&F University, 22 Xinong Road, Yangling 712100, Shaanxi, China
| | - Yanru Wang
- College of Food Science and Engineering, Northwest A&F University, 22 Xinong Road, Yangling 712100, Shaanxi, China
| | - Yanwei Ji
- College of Food Science and Engineering, Northwest A&F University, 22 Xinong Road, Yangling 712100, Shaanxi, China
| | - Daohong Zhang
- College of Food Science and Engineering, Northwest A&F University, 22 Xinong Road, Yangling 712100, Shaanxi, China
| | - Jianlong Wang
- College of Food Science and Engineering, Northwest A&F University, 22 Xinong Road, Yangling 712100, Shaanxi, China
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4
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Qin Y, Zhang S, Qian J, Meng F, Yao J, Zhang M. Lable-free aptamer portable colorimetric smartphone for gliadin detection in food. Front Bioeng Biotechnol 2024; 12:1338408. [PMID: 38440327 PMCID: PMC10910070 DOI: 10.3389/fbioe.2024.1338408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/05/2024] [Indexed: 03/06/2024] Open
Abstract
For individuals with celiac disease (CD), the current clinical therapy option available is a lifelong gluten-free diet. Therefore, it is essential to swiftly and efficiently detect gluten in foods. A colorimetric sensor has been developed, which operates by regulating the aggregation and dispersion state of AuNPs induced by high concentration NaCl through the specific binding of gliadin and aptamer, thereby achieving rapid detection of gliadin in flour. It is found that the sensor exhibits good linearity in the concentration range of 0.67-10 μM and the LOD (3σ/S) is 12 nM. And it can accurately distinguish various types of free-gliadin samples, with a spiked recovery rate of 85%-122.3%. To make the detection process more convenient, the colorimetric results of the biosensor were translated into RGB color-gamut parameters by a smartphone color-picking program for further analysis. Gliadin can still be accurately quantified with the established smartphone platform, and a correlation coefficient of 0.988 was found. The proposed portable smartphone aptamer colorimetric sensing device has achieved satisfactory results in the rapid detection of gliadin in food.
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Affiliation(s)
- Yadi Qin
- School of Pharmacy, Xinjiang Medical University, Urumqi, China
| | - Sicheng Zhang
- School of Pharmacy, Xinjiang Medical University, Urumqi, China
| | - Jie Qian
- School of Pharmacy, Xinjiang Medical University, Urumqi, China
| | - Fanxing Meng
- College life Science and Technology, Xinjiang University, Urumqi, China
| | - Jun Yao
- School of Pharmacy, Xinjiang Medical University, Urumqi, China
- Key Laboratory of Active Components and Drug Release Technology of Natural Medicines in Xinjiang, Xinjiang Medical University, Urumqi, China
| | - Minwei Zhang
- College life Science and Technology, Xinjiang University, Urumqi, China
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5
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Mir TUG, Wani AK, Akhtar N, Katoch V, Shukla S, Kadam US, Hong JC. Advancing biological investigations using portable sensors for detection of sensitive samples. Heliyon 2023; 9:e22679. [PMID: 38089995 PMCID: PMC10711145 DOI: 10.1016/j.heliyon.2023.e22679] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/29/2023] [Accepted: 11/16/2023] [Indexed: 01/14/2024] Open
Abstract
Portable biosensors are emerged as powerful diagnostic tools for analyzing intricately complex biological samples. These biosensors offer sensitive detection capabilities by utilizing biomolecules such as proteins, nucleic acids, microbes or microbial products, antibodies, and enzymes. Their speed, accuracy, stability, specificity, and low cost make them indispensable in forensic investigations and criminal cases. Notably, portable biosensors have been developed to rapidly detect toxins, poisons, body fluids, and explosives; they have proven invaluable in forensic examinations of suspected samples, generating efficient results that enable effective and fair trials. One of the key advantages of portable biosensors is their ability to provide sensitive and non-destructive detection of forensic samples without requiring extensive sample preparation, thereby reducing the possibility of false results. This comprehensive review provides an overview of the current advancements in portable biosensors for the detection of sensitive materials, highlighting their significance in advancing investigations and enhancing sensitive sample detection capabilities.
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Affiliation(s)
- Tahir ul Gani Mir
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
- State Forensic Science Laboratory, Srinagar, Jammu and Kashmir, 190001, India
| | - Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Vaidehi Katoch
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Saurabh Shukla
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, Punjab, 144411, India
| | - Ulhas Sopanrao Kadam
- Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, South Korea
| | - Jong Chan Hong
- Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam, 52828, South Korea
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
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6
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Gaviria-Arroyave MI, Arango JP, Barrientos Urdinola K, Cano JB, Peñuela Mesa GA. Fluorescent nanostructured carbon dot-aptasensor for chlorpyrifos detection: Elucidating the interaction mechanism for an environmentally hazardous pollutant. Anal Chim Acta 2023; 1278:341711. [PMID: 37709453 DOI: 10.1016/j.aca.2023.341711] [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: 04/04/2023] [Revised: 08/10/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023]
Abstract
Chlorpyrifos (CPF) is a commonly used insecticide found in many water sources and is related to several health and environmental effects. Biosensors based on aptamers (single-stranded nucleic acid oligonucleotides) are promising alternatives to achieve the detection of CPF and other pesticides in natural waters. However, several challenges need to be addressed to promote the real application of functional aptasensing devices. In this work, an ssDNA aptamer (S1) is combined with carbon quantum dots (CD) and graphene oxide (GO) to produce a stable fluorescent aptasensor characterized through spectrophotometric and electrophoretic techniques. For a deeper understanding of the system, the mechanism of molecular interaction was studied through docking modeling using free bioinformatic tools like HDOCK, showing that the stem-loops and the higher guanine (G) content are crucial for better interaction. The model also suggests the possibility of generating a truncated aptamer to improve the binding affinity. The biosensor was evaluated for CPF detection, showing a low LOD of 0.01 μg L-1 and good specificity in tap water, even compared to other organophosphates pesticides (OPs) like profenofos. Finally, the recovery of the proposed aptasensor was evaluated in some natural water using spiked samples and compared with UPLC MS-MS chromatography as the gold standard, showing a good recovery above 2.85 nM and evidencing the need of protecting ssDNA aptamers from an erratic interaction with the aromatic groups of dissolved organic matter (humic substances). This work paves the way for a better aptasensors design and the on-site implementation of novel devices for environmental monitoring.
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Affiliation(s)
| | - Juan Pablo Arango
- GIBEC Research Group, Life Sciences Faculty, Universidad EIA, Colombia
| | | | - Juan Bernardo Cano
- GIMEL Research Group. Engineering Faculty, Universidad de Antioquia, Colombia
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7
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Ghuge SA, Nikalje GC, Kadam US, Suprasanna P, Hong JC. Comprehensive mechanisms of heavy metal toxicity in plants, detoxification, and remediation. JOURNAL OF HAZARDOUS MATERIALS 2023; 450:131039. [PMID: 36867909 DOI: 10.1016/j.jhazmat.2023.131039] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/07/2023] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
Natural and anthropogenic causes are continually growing sources of metals in the ecosystem; hence, heavy metal (HM) accumulation has become a primary environmental concern. HM contamination poses a serious threat to plants. A major focus of global research has been to develop cost-effective and proficient phytoremediation technologies to rehabilitate HM-contaminated soil. In this regard, there is a need for insights into the mechanisms associated with the accumulation and tolerance of HMs in plants. It has been recently suggested that plant root architecture has a critical role in the processes that determine sensitivity or tolerance to HMs stress. Several plant species, including those from aquatic habitats, are considered good hyperaccumulators for HM cleanup. Several transporters, such as the ABC transporter family, NRAMP, HMA, and metal tolerance proteins, are involved in the metal acquisition mechanisms. Omics tools have shown that HM stress regulates several genes, stress metabolites or small molecules, microRNAs, and phytohormones to promote tolerance to HM stress and for efficient regulation of metabolic pathways for survival. This review presents a mechanistic view of HM uptake, translocation, and detoxification. Sustainable plant-based solutions may provide essential and economical means of mitigating HM toxicity.
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Affiliation(s)
- Sandip A Ghuge
- Agricultural Research Organization (ARO), The Volcani Institute, P.O. Box 15159, 7505101 Rishon LeZion, Israel
| | - Ganesh Chandrakant Nikalje
- Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, South Korea; Department of Botany, Seva Sadan's R. K. Talreja College of Arts, Science and Commerce, Affiliated to University of Mumbai, Ulhasnagar 421003, India
| | - Ulhas Sopanrao Kadam
- Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, South Korea.
| | - Penna Suprasanna
- Amity Centre for Nuclear Biotechnology, Amity Institute of Biotechnology, Amity University Maharashtra, Mumbai 410206, India
| | - Jong Chan Hong
- Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam 52828, South Korea; Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA.
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8
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Chen DN, Mao YW, Qu P, Wang AJ, Mei LP, Feng JJ. Bimetallic AuPt alloy/rod-like CeO 2 nanojunctions with high peroxidase-like activity for colorimetric sensing of organophosphorus pesticides. Mikrochim Acta 2023; 190:220. [PMID: 37178236 DOI: 10.1007/s00604-023-05757-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 03/17/2023] [Indexed: 05/15/2023]
Abstract
Organophosphorus pesticides (OP) have extensive applications in agriculture, while their overuse causes inevitable residues in food, soil, and water, ultimately being harmful to human health and even causing diverse dysfunctions. Herein, a novel colorimetric platform was established for quantitative determination of malathion based on peroxidase mimic AuPt alloy decorated on CeO2 nanorods (CeO2@AuPt NRs). The synthesized nanozyme oxidized colorless 3,3',5,5'-tetramethylbenzidine (TMB) in the presence of H2O2. Besides, the oxidized TMB was inversely reduced by ascorbic acid (AA), which were originated from hydrolysis of L-ascorbic acid-2-phosphate (AA2P) with the assistance of acid phosphatase (ACP). Based upon this observation ACP analysis was explored by colorimetry, showing a wid linear range of 0.2 ~ 3.5 U L-1 and a low limit of detection (LOD = 0.085 U L-1, S/N = 3). Furthermore, malathion present in the colorimetric system inhibited the activity of ACP and simultaneously affected the generation of AA, in turn promoting the recovery of the chromogenic reaction. Based on this, the LOD was decreased to 1.5 nM (S/N = 3) for the assay of malathion with a wide linear range of 6 ~ 100 nM. This simple colorimetric platform provides some informative guidelines for determination of other pesticides and disease markers.
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Affiliation(s)
- Di-Nan Chen
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Yan-Wen Mao
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Ping Qu
- Zhejiang Jinhua Ecological and Environmental Monitoring Center, Jinhua, China.
| | - Ai-Jun Wang
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Li-Ping Mei
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, China
| | - Jiu-Ju Feng
- Key Laboratory of the Ministry of Education for Advanced Catalysis Materials, College of Chemistry and Materials Science, College of Geography and Environmental Sciences, Zhejiang Normal University, Jinhua, 321004, China.
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9
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Jiang W, Li Z, Yang Q, Hou X. Integration of Metallic Nanomaterials and Recognition Elements for the Specifically Monitoring of Pesticides in Electrochemical Sensing. Crit Rev Anal Chem 2023:1-22. [DOI: 10.1080/10408347.2023.2189955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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10
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A novel biosensing platform for detection of glaucoma biomarker GDF15 via an integrated BLI-ELASA strategy. Biomaterials 2023; 294:121997. [PMID: 36638554 DOI: 10.1016/j.biomaterials.2023.121997] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 12/26/2022] [Accepted: 01/07/2023] [Indexed: 01/11/2023]
Abstract
Glaucoma is a leading cause of irreversible blindness worldwide. Early discovery and prioritized intervention significantly impact its prognosis. Precise monitoring of the biomarker GDF15 contributes towards effective diagnosis and assessment of glaucoma. In this study, we demonstrate that GDF15 monitoring can also aid screening for glaucoma risk and early diagnosis. We obtained an aptamer (APT2TM) with high affinity, high specificity, and high stability for binding to both human-derived and rat-derived GDF15. Simulation results showed that the binding capabilities of APT2TM are mainly affected by the interplay between van der Waals forces and polar solvation energy, and that salt bridges and hydrogen bonds play critical roles. We then integrated an enzyme-linked aptamer sandwich assay (ELASA) into a biolayer interferometry (BLI) system to develop an automated, high-throughput, real-time monitoring BLI-ELASA biosensing platform. This platform exhibited a wide linear detection window (10-810 pg/mL range) and high sensitivity for GDF15 (detection limit of 5-6 pg/mL). Moreover, we confirmed its excellent performance when applied to GDF15 quantification in real samples from glaucomatous rats and clinical patients. We believe that this technology represents a robust, convenient, and cost-effective approach for risk screening, early diagnosis, and animal modeling evaluation of glaucoma in the near future.
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Upconversion nanoparticles-based background-free selective fluorescence sensor developed for immunoassay of fipronil pesticide. JOURNAL OF FOOD MEASUREMENT AND CHARACTERIZATION 2023. [DOI: 10.1007/s11694-023-01849-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
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12
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Kadam US, Cho Y, Park TY, Hong JC. Aptamer-based CRISPR-Cas powered diagnostics of diverse biomarkers and small molecule targets. APPLIED BIOLOGICAL CHEMISTRY 2023; 66:13. [PMID: 36843874 PMCID: PMC9937869 DOI: 10.1186/s13765-023-00771-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 02/03/2023] [Indexed: 06/06/2023]
Abstract
CRISPR-Cas systems have been widely used in genome editing and transcriptional regulation. Recently, CRISPR-Cas effectors are adopted for biosensor construction due to its adjustable properties, such as simplicity of design, easy operation, collateral cleavage activity, and high biocompatibility. Aptamers' excellent sensitivity, specificity, in vitro synthesis, base-pairing, labeling, modification, and programmability has made them an attractive molecular recognition element for inclusion in CRISPR-Cas systems. Here, we review current advances in aptamer-based CRISPR-Cas sensors. We briefly discuss aptamers and the knowledge of Cas effector proteins, crRNA, reporter probes, analytes, and applications of target-specific aptamers. Next, we provide fabrication strategies, molecular binding, and detection using fluorescence, electrochemical, colorimetric, nanomaterials, Rayleigh, and Raman scattering. The application of CRISPR-Cas systems in aptamer-based sensing of a wide range of biomarkers (disease and pathogens) and toxic contaminants is growing. This review provides an update and offers novel insights into developing CRISPR-Cas-based sensors using ssDNA aptamers with high efficiency and specificity for point-of-care setting diagnostics.
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Affiliation(s)
- Ulhas Sopanrao Kadam
- Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam-do 52828 Republic of Korea
| | - Yuhan Cho
- Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam-do 52828 Republic of Korea
| | - Tae Yoon Park
- Graduate School of Education, Yonsei University, Seoul, 03722 Republic of Korea
| | - Jong Chan Hong
- Division of Life Science and Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, Gyeongnam-do 52828 Republic of Korea
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211 USA
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Serebrennikova KV, Komova NS, Aybush AV, Zherdev AV, Dzantiev BB. Flexible Substrate of Cellulose Fiber/Structured Plasmonic Silver Nanoparticles Applied for Label-Free SERS Detection of Malathion. MATERIALS (BASEL, SWITZERLAND) 2023; 16:1475. [PMID: 36837103 PMCID: PMC9963878 DOI: 10.3390/ma16041475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/20/2023] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Surface-enhanced Raman scattering (SERS) is considered an efficient technique providing high sensitivity and fingerprint specificity for the detection of pesticide residues. Recent developments in SERS-based detection aim to create flexible plasmonic substrates that meet the requirements for non-destructive analysis of contaminants on curved surfaces by simply wrapping or wiping. Herein, we reported a flexible SERS substrate based on cellulose fiber (CF) modified with silver nanostructures (AgNS). A silver film was fabricated on the membrane surface with an in situ silver mirror reaction leading to the formation of a AgNS-CF substrate. Then, the substrate was decorated through in situ synthesis of raspberry-like silver nanostructures (rAgNS). The SERS performance of the prepared substrate was tested using 4-mercaptobenzoic acid (4-MBA) as a Raman probe and compared with that of the CF-based plasmonic substrates. The sensitivity of the rAgNS/AgNS-CF substrate was evaluated by determining the detection limit of 4-MBA and an analytical enhancement factor, which were 10 nM and ~107, respectively. Further, the proposed flexible rAgNS/AgNS-CF substrate was applied for SERS detection of malathion. The detection limit for malathion reached 0.15 mg/L, which meets the requirements about its maximum residue level in food. Thus, the characteristics of the rAgNS/AgNS-CF substrate demonstrate the potential of its application as a label-free and ready-to-use sensing platform for the SERS detection of trace hazardous substances.
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Affiliation(s)
- Kseniya V. Serebrennikova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky prospect 33, 119071 Moscow, Russia
| | - Nadezhda S. Komova
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky prospect 33, 119071 Moscow, Russia
| | - Arseniy V. Aybush
- N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Kosygin Street 4, 119991 Moscow, Russia
| | - Anatoly V. Zherdev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky prospect 33, 119071 Moscow, Russia
| | - Boris B. Dzantiev
- A.N. Bach Institute of Biochemistry, Research Center of Biotechnology, Russian Academy of Sciences, Leninsky prospect 33, 119071 Moscow, Russia
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14
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Method Validation for Multi-Pesticide Residue Determination in Chrysanthemum. Molecules 2023; 28:molecules28031291. [PMID: 36770967 PMCID: PMC9921869 DOI: 10.3390/molecules28031291] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/18/2023] [Accepted: 01/22/2023] [Indexed: 01/31/2023] Open
Abstract
The chrysanthemum can be consumed in various forms, representing the "integration of medicine and food". Quantitative analysis of multi-pesticide residues in chrysanthemum matrices is therefore crucial for both product-safety assurance and consumer-risk evaluation. In the present study, a simple and effective method was developed for simultaneously detecting 15 pesticides frequently used in chrysanthemum cultivation in three matrices, including fresh flowers, dry chrysanthemum tea, and infusions. The calibration curves for the pesticides were linear in the 0.01-1 mg kg-1 range, with correlation coefficients greater than 0.99. The limits of quantification (LOQs) for fresh flowers, dry chrysanthemum tea, and infusions were 0.01-0.05 mg kg-1, 0.05 mg kg-1, and 0.001-0.005 mg L-1, respectively. In all selected matrices, satisfactory accuracy and precision were achieved, with recoveries ranging from 75.7 to 118.2% and relative standard deviations (RSDs) less than 20%. The validated method was then used to routinely monitor pesticide residues in 50 commercial chrysanthemum-tea samples. As a result, 56% of samples were detected with 5-13 pesticides. This research presents a method for the efficient analysis of multi-pesticide residues in chrysanthemum matrices.
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Lee SJ, Cho J, Lee BH, Hwang D, Park JW. Design and Prediction of Aptamers Assisted by In Silico Methods. Biomedicines 2023; 11:356. [PMID: 36830893 PMCID: PMC9953197 DOI: 10.3390/biomedicines11020356] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/21/2023] [Accepted: 01/23/2023] [Indexed: 01/28/2023] Open
Abstract
An aptamer is a single-stranded DNA or RNA that binds to a specific target with high binding affinity. Aptamers are developed through the process of systematic evolution of ligands by exponential enrichment (SELEX), which is repeated to increase the binding power and specificity. However, the SELEX process is time-consuming, and the characterization of aptamer candidates selected through it requires additional effort. Here, we describe in silico methods in order to suggest the most efficient way to develop aptamers and minimize the laborious effort required to screen and optimise aptamers. We investigated several methods for the estimation of aptamer-target molecule binding through conformational structure prediction, molecular docking, and molecular dynamic simulation. In addition, examples of machine learning and deep learning technologies used to predict the binding of targets and ligands in the development of new drugs are introduced. This review will be helpful in the development and application of in silico aptamer screening and characterization.
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Affiliation(s)
- Su Jin Lee
- Drug Manufacturing Center, Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDI Hub), Daegu 41061, Republic of Korea
| | - Junmin Cho
- Medical Device Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDI Hub), Daegu 41061, Republic of Korea
| | - Byung-Hoon Lee
- Medical Device Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDI Hub), Daegu 41061, Republic of Korea
| | - Donghwan Hwang
- Medical Device Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDI Hub), Daegu 41061, Republic of Korea
| | - Jee-Woong Park
- Medical Device Development Center, Daegu-Gyeongbuk Medical Innovation Foundation (K-MEDI Hub), Daegu 41061, Republic of Korea
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Gong Z, Huang Y, Hu X, Zhang J, Chen Q, Chen H. Recent Progress in Electrochemical Nano-Biosensors for Detection of Pesticides and Mycotoxins in Foods. BIOSENSORS 2023; 13:140. [PMID: 36671974 PMCID: PMC9856537 DOI: 10.3390/bios13010140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/04/2023] [Accepted: 01/11/2023] [Indexed: 06/17/2023]
Abstract
Pesticide and mycotoxin residues in food are concerning as they are harmful to human health. Traditional methods, such as high-performance liquid chromatography (HPLC) for such detection lack sensitivity and operation convenience. Efficient, accurate detection approaches are needed. With the recent development of nanotechnology, electrochemical biosensors based on nanomaterials have shown solid ability to detect trace pesticides and mycotoxins quickly and accurately. In this review, English articles about electrochemical biosensors in the past 11 years (2011-2022) were collected from PubMed database, and various nanomaterials are discussed, including noble metal nanomaterials, magnetic metal nanoparticles, metal-organic frameworks, carbon nanotubes, as well as graphene and its derivatives. Three main roles of such nanomaterials in the detection process are summarized, including biomolecule immobilization, signal generation, and signal amplification. The detection targets involve two types of pesticides (organophosphorus and carbamate) and six types of mycotoxins (aflatoxin, deoxynivalenol, zearalenone, fumonisin, ochratoxin A, and patulin). Although significant achievements have been made in the evolution of electrochemical nano-biosensors, many challenges remain to be overcome.
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Affiliation(s)
- Zhaoyuan Gong
- Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700, China
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China
| | - Yueming Huang
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China
| | - Xianjing Hu
- Guangdong Provincial Key Laboratory of Research and Development of Natural Drugs, School of Pharmacy, Guangdong Medical University, Dongguan 523808, China
| | - Jianye Zhang
- Guangzhou Municipal and Guangdong Provincial Key Laboratory of Molecular Target and Clinical Pharmacology, The NMPA and State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences and the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 510000, China
| | - Qilei Chen
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China
| | - Hubiao Chen
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong 999077, China
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Qiao L, Zhao Y, Zhang Y, Zhang M, Tao Y, Xiao Y, Zeng X, Zhang Y, Zhu Y. Designing a Stable g-C 3N 4/BiVO 4-Based Photoelectrochemical Aptasensor for Tetracycline Determination. TOXICS 2022; 11:17. [PMID: 36668743 PMCID: PMC9865260 DOI: 10.3390/toxics11010017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 12/07/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
The excessive consumption of tetracycline (TC) could bring a series of unpredictable health and ecological risks. Therefore, it is crucial to develop convenient and effective detection technology for TC. Herein, a "signal on" photoelectrochemical (PEC) aptasensor was constructed for the stable detection of TC. Specifically, the g-C3N4/BiVO4 were used to promote the migration of photo-generated charges to an enhanced photocurrent response. TC aptamer probes were stably fixed on the g-C3N4/BiVO4/FTO electrode as a recognition element via covalent bonding interaction. In the presence of TC, the aptamer probes could directly recognize and capture TC. Subsequently, TC was oxidized by the photogenerated holes of g-C3N4/BiVO4, causing an enhanced photocurrent. The "signal on" PEC aptasensor displayed a distinguished detection performance toward TC in terms of a wide linear range from 0.1 to 500 nM with a low detection limit of 0.06 nM, and possessed high stability, great selectivity, and good application prospects.
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Affiliation(s)
- Lu Qiao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, China
| | - Yue Zhao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, China
| | - Yuanyuan Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, China
| | - Mingjuan Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, China
| | - Yani Tao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, China
| | - Yao Xiao
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, China
| | - Xinxia Zeng
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, China
| | - Yi Zhang
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, China
| | - Yuan Zhu
- College of Environmental Science and Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Environmental Biology and Pollution Control, Hunan University, Ministry of Education, Changsha 410082, China
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Koo KM, Kim CD, Ju FN, Kim H, Kim CH, Kim TH. Recent Advances in Electrochemical Biosensors for Monitoring Animal Cell Function and Viability. BIOSENSORS 2022; 12:bios12121162. [PMID: 36551129 PMCID: PMC9775431 DOI: 10.3390/bios12121162] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/02/2022] [Accepted: 12/08/2022] [Indexed: 05/28/2023]
Abstract
Redox reactions in live cells are generated by involving various redox biomolecules for maintaining cell viability and functions. These qualities have been exploited in the development of clinical monitoring, diagnostic approaches, and numerous types of biosensors. Particularly, electrochemical biosensor-based live-cell detection technologies, such as electric cell-substrate impedance (ECIS), field-effect transistors (FETs), and potentiometric-based biosensors, are used for the electrochemical-based sensing of extracellular changes, genetic alterations, and redox reactions. In addition to the electrochemical biosensors for live-cell detection, cancer and stem cells may be immobilized on an electrode surface and evaluated electrochemically. Various nanomaterials and cell-friendly ligands are used to enhance the sensitivity of electrochemical biosensors. Here, we discuss recent advances in the use of electrochemical sensors for determining cell viability and function, which are essential for the practical application of these sensors as tools for pharmaceutical analysis and toxicity testing. We believe that this review will motivate researchers to enhance their efforts devoted to accelerating the development of electrochemical biosensors for future applications in the pharmaceutical industry and stem cell therapeutics.
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Lam SY, Lau HL, Kwok CK. Capture-SELEX: Selection Strategy, Aptamer Identification, and Biosensing Application. BIOSENSORS 2022; 12:1142. [PMID: 36551109 PMCID: PMC9776347 DOI: 10.3390/bios12121142] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 06/01/2023]
Abstract
Small-molecule contaminants, such as antibiotics, pesticides, and plasticizers, have emerged as one of the substances most detrimental to human health and the environment. Therefore, it is crucial to develop low-cost, user-friendly, and portable biosensors capable of rapidly detecting these contaminants. Antibodies have traditionally been used as biorecognition elements. However, aptamers have recently been applied as biorecognition elements in aptamer-based biosensors, also known as aptasensors. The systematic evolution of ligands by exponential enrichment (SELEX) is an in vitro technique used to generate aptamers that bind their targets with high affinity and specificity. Over the past decade, a modified SELEX method known as Capture-SELEX has been widely used to generate DNA or RNA aptamers that bind small molecules. In this review, we summarize the recent strategies used for Capture-SELEX, describe the methods commonly used for detecting and characterizing small-molecule-aptamer interactions, and discuss the development of aptamer-based biosensors for various applications. We also discuss the challenges of the Capture-SELEX platform and biosensor development and the possibilities for their future application.
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Affiliation(s)
- Sin Yu Lam
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China
| | - Hill Lam Lau
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China
| | - Chun Kit Kwok
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Hong Kong SAR 999077, China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen 518057, China
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Qin Y, Qin Y, Bubiajiaer H, Chen F, Yao J, Zhang M. Engineering constructed of high selectivity dexamethasone aptamer based on truncation and mutation technology. Front Bioeng Biotechnol 2022; 10:994711. [PMID: 36177181 PMCID: PMC9513367 DOI: 10.3389/fbioe.2022.994711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/22/2022] [Indexed: 11/13/2022] Open
Abstract
Various biosensors based on aptamers are currently the most popular rapid detection approaches, but the performance of these sensors is closely related to the affinity of aptamers. In this work, a strategy for constructed high-affinity aptamer was proposed. By truncating the bases flanking the 59 nt dexamethasones (DEX) original aptamer sequence to improve the sensitivity of the aptamer to DEX, and then base mutation was introduced to further improve the sensitivity and selectivity of aptamers. Finally, the 33 nt aptamer Apt-M13 with G-quadruplex structures was obtained. The dissociation constant (Kd) was determined to be 200 nM by Graphene oxide (GO)-based fluorometry. As-prepared Apt-M13 was used for a label-free colorimetric aptamer sensor based on gold nanoparticles, the LOD was 3.2-fold lower than the original aptamer described in previous works. The anti-interference ability of DEX analogs is also further improved. It indicates that truncation technology effectively improves the specificity of the aptamer to DEX in this work, and the introduction of mutation further improves the affinity and selectivity of the aptamer to DEX. Therefore, the proposed aptamer optimization method is also expected to become a general strategy for various aptamer sequences.
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Affiliation(s)
- Yadi Qin
- School of Pharmacy, Xinjiang Medical University, Urumqi, China
| | - Yanan Qin
- College Life Science and Technology, Xinjiang University, Urumqi, China
| | | | - Fengxia Chen
- School of Pharmacy, Xinjiang Medical University, Urumqi, China
| | - Jun Yao
- School of Pharmacy, Xinjiang Medical University, Urumqi, China
- *Correspondence: Jun Yao, ; Minwei Zhang,
| | - Minwei Zhang
- College Life Science and Technology, Xinjiang University, Urumqi, China
- *Correspondence: Jun Yao, ; Minwei Zhang,
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