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Fatemi K, Lau SY, Obayomi KS, Kiew SF, Coorey R, Chung LY, Fatemi R, Heshmatipour Z, Premarathna KSD. Carbon nanomaterial-based aptasensors for rapid detection of foodborne pathogenic bacteria. Anal Biochem 2024; 695:115639. [PMID: 39127327 DOI: 10.1016/j.ab.2024.115639] [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: 07/15/2024] [Revised: 08/06/2024] [Accepted: 08/07/2024] [Indexed: 08/12/2024]
Abstract
Each year, millions of people suffer from foodborne illness due to the consumption of food contaminated with pathogenic bacteria, which severely challenges global health. Therefore, it is essential to recognize foodborne pathogens swiftly and correctly. However, conventional detection techniques for bacterial pathogens are labor-intensive, low selectivity, and time-consuming, highlighting a notable knowledge gap. A novel approach, aptamer-based biosensors (aptasensors) linked to carbon nanomaterials (CNs), has shown the potential to overcome these limitations and provide a more reliable method for detecting bacterial pathogens. Aptamers, short single-stranded DNA (ssDNA)/RNA molecules, serve as bio-recognition elements (BRE) due to their exceptionally high affinity and specificity in identifying foodborne pathogens such as Salmonella spp., Escherichia coli (E. coli), Listeria monocytogenes, Campylobacter jejuni, and other relevant pathogens commonly associated with foodborne illnesses. Carbon nanomaterials' high surface area-to-volume ratio contributes unique characteristics crucial for bacterial sensing, as it improves the binding capacity and signal amplification in the design of aptasensors. Furthermore, aptamers can bind to CNs and create aptasensors with improved signal specificity and sensitivity. Hence, this review intends to critically review the current literature on developing aptamer functionalized CN-based biosensors by transducer optical and electrochemical for detecting foodborne pathogens and explore the advantages and challenges associated with these biosensors. Aptasensors conjugated with CNs offers an efficient tool for identifying foodborne pathogenic bacteria that is both precise and sensitive to potentially replacing complex current techniques that are time-consuming.
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Affiliation(s)
- Kiyana Fatemi
- Department of Chemical Engineering, Faculty of Engineering and Science, Curtin University Malaysia, Miri, Sarawak, Malaysia
| | - Sie Yon Lau
- Department of Chemical Engineering, Faculty of Engineering and Science, Curtin University Malaysia, Miri, Sarawak, Malaysia.
| | - Kehinde Shola Obayomi
- Department of Chemical Engineering, Faculty of Engineering and Science, Curtin University Malaysia, Miri, Sarawak, Malaysia; Zuckerberg Institute for Water Research (ZIWR), The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 84990, Israel
| | - Siaw Fui Kiew
- Department of Chemical Engineering, Faculty of Engineering and Science, Curtin University Malaysia, Miri, Sarawak, Malaysia; Sarawak Biovalley Pilot Plant, Curtin University Malaysia, CDT 250, 98009, Miri, Sarawak, Malaysia
| | - Ranil Coorey
- School of Molecular and Life Sciences, Curtin University, Bentley, Western Australia, Australia
| | - Lip Yong Chung
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Reza Fatemi
- Department of Electrical Engineering, College of Technical and Engineering, West Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Zoheir Heshmatipour
- Department of Microbiology, Faculty of Science, Tonekabon Branch, Islamic Azad University, Tonekabon, Iran
| | - K S D Premarathna
- Department of Chemical Engineering, Faculty of Engineering and Science, Curtin University Malaysia, Miri, Sarawak, Malaysia
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2
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Urmi R, Banerjee P, Singh M, Singh R, Chhillar S, Sharma N, Chandra A, Singh N, Qamar I. Revolutionizing biomedicine: Aptamer-based nanomaterials and nanodevices for therapeutic applications. BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2024; 42:e00843. [PMID: 38881649 PMCID: PMC11179248 DOI: 10.1016/j.btre.2024.e00843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 04/28/2024] [Accepted: 05/24/2024] [Indexed: 06/18/2024]
Abstract
With the progress in two distinct areas of nanotechnology and aptamer identification technologies, the two fields have merged to what is known as aptamer nanotechnology. Aptamers have varying properties in the biomedical field include their small size, non-toxicity, ease of manufacturing, negligible immunogenicity, ability to identify a wide range of targets, and high immobilizing capacity. Nevertheless, aptamers can utilize the distinct characteristics offered by nanomaterials like optical, magnetic, thermal, electronic properties to become more versatile and function as a novel device in diagnostics and therapeutics. This engineered aptamer conjugated nanomaterials, in turn provides a potentially new and unique properties apart from the pre-existing characteristics of aptamer and nanomaterials, where they act to offer wide array of applications in the biomedical field ranging from drug targeting, delivery of drugs, biosensing, bioimaging. This review gives comprehensive insight of the different aptamer conjugated nanomaterials and their utilization in biomedical field. Firstly, it introduces on the aptamer selection methods and roles of nanomaterials offered. Further, different conjugation strategies are explored in addition, the class of aptamer conjugated nanodevices being discussed. Typical biomedical examples and studies specifically, related to drug delivery, biosensing, bioimaging have been presented.
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Affiliation(s)
- Rajkumari Urmi
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Pallabi Banerjee
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Manisha Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Risha Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Sonam Chhillar
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Neha Sharma
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Anshuman Chandra
- School of Physical Sciences, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Nagendra Singh
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
| | - Imteyaz Qamar
- School of Biotechnology, Gautam Buddha University, Greater Noida, U.P. 201312, India
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3
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Wada M, Endo T, Hisamoto H, Sueyoshi K. Assessment of the structural change of DNA by binding with a small molecule based on capillary sieving electrophoresis. ANAL SCI 2024; 40:773-780. [PMID: 38413474 DOI: 10.1007/s44211-024-00524-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 01/24/2024] [Indexed: 02/29/2024]
Abstract
In this study, capillary sieving electrophoresis (CSE) using polymer solutions was used to evaluate the structural changes in nucleic acids upon complexation with small molecules. As the model target and nucleic acids, L-tyrosinamide (Tyr-Am) and its aptamer, which is a type of DNA specifically binding to Tyr-Am, were selected. CSE was conducted using a capillary filled with background solution (BGS) containing hydroxypropyl cellulose (HPC) as a sieving matrix. When Tyr-Am or tyrosine was added to the BGS in CSE, the ratio of mobility differences of the Tyr-Am-aptamer complex increased compared to that of the free aptamer without the addition of Tyr-Am. In contrast, when other amino acids or their analogs were added, results showed no apparent change or decreases in electrophoretic mobility. These results indicate that the proposed method can be applied to assess structural changes in nucleic acids that target small molecules.
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Affiliation(s)
- Masahide Wada
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, Osaka, Japan.
| | - Tatsuro Endo
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, Osaka, Japan
| | - Hideaki Hisamoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, Osaka, Japan
| | - Kenji Sueyoshi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, Osaka, Japan
- CREST, Japan Science and Technology Agency, Tokyo, Japan
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4
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Hu C, Li S, Zhou J, Wei D, Liu X, Chen Z, Peng H, Liu X, Deng Y. In vitro SELEX and application of an African swine fever virus (ASFV) p30 protein specific aptamer. Sci Rep 2024; 14:4078. [PMID: 38374125 PMCID: PMC10876938 DOI: 10.1038/s41598-024-53619-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 02/02/2024] [Indexed: 02/21/2024] Open
Abstract
The African swine fever virus (ASFV) has caused severe economic losses in the pig industry. To monitor ASFV spread, the p30 protein has been identified as an ideal infection marker due to its early and long-term expression during the ASFV infection period. Timely monitoring of ASFV p30 enables the detection of ASFV infection and assessment of disease progression. Aptamers are an outstanding substitute for antibodies to develop an efficient tool for ASFV p30 protein detection. In this study, a series of aptamer candidates were screened by in vitro magnetic bead-based systematic evolution of ligands by exponential enrichment (MB-SELEX). An aptamer (Atc-20) finally showed high specificity and affinity (Kd = 140 ± 10 pM) against ASFV p30 protein after truncation and affinity assessment. Furthermore, an aptamer/antibody heterogeneous sandwich detection assay was designed based on Atc20, achieving a linear detection of ASFV p30 ranging from 8 to 125 ng/ml and a detection limit (LOD) of 0.61 ng/ml. This assay showed good analytical performances and effectively detected p30 protein in diluted serum samples, presenting promising potential for the development of ASFV biosensors.
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Affiliation(s)
- Changchun Hu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Hunan, 412007, Zhuzhou, China
| | - Shuo Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Hunan, 412007, Zhuzhou, China
| | - Jie Zhou
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Hunan, 412007, Zhuzhou, China
| | - Dan Wei
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Hunan, 412007, Zhuzhou, China
| | - Xueying Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Hunan, 412007, Zhuzhou, China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Hunan, 412007, Zhuzhou, China
| | - Hongquan Peng
- Department of Nephrology, Kiang Wu Hospital, Macau, SAR, China
| | - Xun Liu
- Department of Nephrology, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Hunan, 412007, Zhuzhou, China.
- Institute for Future Sciences, University of South China, Changsha, Hunan, China.
- Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China.
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5
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Patil AVP, Yang PF, Yang CY, Gaur MS, Wu CC. A Critical Review on Detection of Foodborne Pathogens Using Electrochemical Biosensors. Crit Rev Biomed Eng 2024; 52:17-40. [PMID: 38523439 DOI: 10.1615/critrevbiomedeng.2023049469] [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: 03/26/2024]
Abstract
An outbreak of foodborne pathogens would cause severe consequences. Detecting and diagnosing foodborne diseases is crucial for food safety, and it is increasingly important to develop fast, sensitive, and cost-effective methods for detecting foodborne pathogens. In contrast to traditional methods, such as medium-based culture, nucleic acid amplification test, and enzyme-linked immunosorbent assay, electrochemical biosensors possess the advantages of simplicity, rapidity, high sensitivity, miniaturization, and low cost, making them ideal for developing pathogen-sensing devices. The biorecognition layer, consisting of recognition elements, such as aptamers, antibodies and bacteriophages, and other biomolecules or polymers, is the most critical component to determine the selectivity, specificity, reproducibility, and lifetime of a biosensor when detecting pathogens in a biosample. Furthermore, nanomaterials have been frequently used to improve electrochemical biosensors for sensitively detecting foodborne pathogens due to their high conductivity, surface-to-volume ratio, and electrocatalytic activity. In this review, we survey the characteristics of biorecognition elements and nanomaterials in constructing electrochemical biosensors applicable for detecting foodborne pathogens during the past five years. As well as the challenges and opportunities of electrochemical biosensors in the application of foodborne pathogen detection are discussed.
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Affiliation(s)
- Avinash V Police Patil
- Department of Bio-Industrial Mechatronics Engineering, National Chung Hsing University, Taichung City 402, Taiwan R.O.C
| | - Ping-Feng Yang
- Department of Bio-Industrial Mechatronics Engineering, National Chung Hsing University, Taichung City 402, Taiwan R.O.C
| | - Chiou-Ying Yang
- Institute of Molecular Biology, National Chung Hsing University, Taichung 402, Taiwan R.O.C
| | - M S Gaur
- Department of Physics, Hindustan College of Science and Technology, Farah, Mathura, 281122 U.P., India
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6
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Duan Y, Liu F, Zhang C, Wang Y, Chen G. Screen and Optimization of an Aptamer for Alexandrium tamarense-A Common Toxin-Producing Harmful Alga. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:935-950. [PMID: 37743437 DOI: 10.1007/s10126-023-10251-2] [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: 06/26/2023] [Accepted: 09/01/2023] [Indexed: 09/26/2023]
Abstract
Among all the paralytic shellfish toxins (PSTs)-producing algae, Alexandrium tamarense is one of the most widespread harmful species posing a serious threat to marine resources and human health. Therefore, it is extremely important to establish a rapid and accurate monitoring method for A. tamarense that can provide early warnings of harmful algal blooms (HABs) caused by this alga and limit the contamination due to PSTs. In this study, an ssDNA library was first obtained by whole cell systematic evolution of ligands by exponential enrichment after 18 consecutive rounds of iterative screening. After sequencing in combination with subsequent multiple alignment of sequences and secondary structure simulation, the library could be classified into 2 families, namely, Family1 and Family2, according to sequence similarity. Flow cytometry was used to test the affinity and cross-reactivity of Ata19, Ata6, Ata25 and Ata29 belonging to Family2. Ata19 was selected to be modified by truncation, through which a new resultant aptamer named as Ata19-1-1 was obtained. Ata19-1-1 with a KD of 75.16 ± 11.10 nM displayed a much higher affinity than Ata19. The specificity test showed that Ata19-1-1 has the same discrimination ability as Ata19 and can at least distinguish the target microalga from other microalgae. The observation under a fluorescence microscopy showed that the A. tamarense cells labeled with Ata19-1-1 are exhibiting bright green fluorescence and could be easily identified, factually confirming the binding of the aptamer with target cells. In summary, the aptamer Ata19-1-1 produced in this study may serve as an ideal molecular recognition element for A. tamarense, which has the potential to be developed into a novel detection method for this harmful alga in the future.
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Affiliation(s)
- Yu Duan
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, People's Republic of China
- School of Environment, Harbin Institute of Technology, Harbin, 150001, People's Republic of China
| | - Fuguo Liu
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, People's Republic of China
- School of Environment, Harbin Institute of Technology, Harbin, 150001, People's Republic of China
| | - Chunyun Zhang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, People's Republic of China.
| | - Yuanyuan Wang
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, People's Republic of China
| | - Guofu Chen
- School of Marine Science and Technology, Harbin Institute of Technology (Weihai), Wenhua West Road, 2#, Weihai, 264209, People's Republic of China.
- School of Environment, Harbin Institute of Technology, Harbin, 150001, People's Republic of China.
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7
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Manfredini A, Malusà E, Canfora L. Aptamer-based technology for detecting Bacillus subtilis in soil. Appl Microbiol Biotechnol 2023; 107:6963-6972. [PMID: 37698608 DOI: 10.1007/s00253-023-12765-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/12/2023] [Accepted: 08/28/2023] [Indexed: 09/13/2023]
Abstract
The uncertainty associated with the impact of a bioinoculant on soil microbial community and, as a consequence, on soil quality, as well as the need to define its persistence, has prompted the demand for an accurate detection and tracking of the presence and the quantification of a target microbial inoculant in soil. Although DNA or RNA-based molecular detection are well established and commonly applied in this regard, alternative ligands such as DNA-aptamers have several advantages over them, such as low cost, ease of modification, ease of immobilisation on lab-on-chip or nanosensors, high stability and not thermolability. In this study, we used a toggle-cell SELEX method to isolate, select and characterise ssDNA (single-strand DNA) aptamers to detect a Bacillus subtilis strain which is being tested as a plant growth promoting rhizobacteria (PGPR) formulation. Two ssDNA aptamers (patenting application n.102022000022590) showed strong affinity and specificity for B. subtilis strains, with values of the kinetic parameters Kd (dissociation constant) in the nanomolar range and Bmax (maximum intensity of binding) around 1. Validation of the suitability of the aptamers was validated on three inoculated soils characterised by different chemical-physical features and in soil from a field trial with the formulated B. subtilis PCM/B 00105 strain. These are considered significant features to monitor B. subtilis strains in soil, practical to optimise bioinoculant application methods, support regulatory processes and foster the shift of agricultural production toward more sustainable cropping systems. KEY POINTS: • First DNA aptamers binding a B. subtilis strain included in a bioinoculum formulation. • First DNA aptamer binding B. subtilis in soil. • Aptamer may be a method for microbial inoculant detection in soil.
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Affiliation(s)
| | - Eligio Malusà
- CREA Centro di Ricerca Viticoltura ed Enologia, 31015, Conegliano, Italy
- National Institute of Horticultural Research, 96-100, Skierniewice, Poland
| | - Loredana Canfora
- CREA Centro di Ricerca Agricoltura e Ambiente, 00184, Rome, Italy
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8
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P U A, Raj G, John J, Mohan K M, John F, George J. Aptamers: Features, Synthesis and Applications. Chem Biodivers 2023; 20:e202301008. [PMID: 37709723 DOI: 10.1002/cbdv.202301008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 09/11/2023] [Accepted: 09/14/2023] [Indexed: 09/16/2023]
Abstract
Aptamers have become a topic of interest among the researchers and scientists since they not only possess all of the benefits of antibodies but also possess special qualities including heat stability, low cost, and limitless uses⋅ Here we give a review about the features, applications, and challenges of aptamers and also how they are beneficial over the antibodies for biomedical applications. Their unique features make aptamers a prominent tool in therapeutics, diagnostics, biosensors and targeted drug delivery. In conclusion, aptamers represent exciting materials for a variety of applications and can be modified to improve their properties and to extend their applications in biomedical field.
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Affiliation(s)
- Aiswarya P U
- Bio-organic Laboratory, Department of Chemistry, Sacred Heart College, Kochi, 682013, India
| | - Gopika Raj
- Bio-organic Laboratory, Department of Chemistry, Sacred Heart College, Kochi, 682013, India
| | - Jinju John
- Bio-organic Laboratory, Department of Chemistry, Sacred Heart College, Kochi, 682013, India
| | - Malavika Mohan K
- Bio-organic Laboratory, Department of Chemistry, Sacred Heart College, Kochi, 682013, India
| | - Franklin John
- Bio-organic Laboratory, Department of Chemistry, Sacred Heart College, Kochi, 682013, India
| | - Jinu George
- Bio-organic Laboratory, Department of Chemistry, Sacred Heart College, Kochi, 682013, India
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9
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Tsujimura H, Naganuma M, Ohoka N, Inoue T, Naito M, Tsuji G, Demizu Y. Development of DNA Aptamer-Based PROTACs That Degrade the Estrogen Receptor. ACS Med Chem Lett 2023; 14:827-832. [PMID: 37312841 PMCID: PMC10258903 DOI: 10.1021/acsmedchemlett.3c00126] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 05/16/2023] [Indexed: 06/15/2023] Open
Abstract
Targeted protein degradation (TPD), using chimeric molecules such as proteolysis-targeting chimeras (PROTACs), has attracted attention as a strategy for selective degradation of intracellular proteins by hijacking the ubiquitin-proteasome system (UPS). However, it is often difficult to develop such degraders due to the absence of appropriate ligands for target proteins. In targeting proteins for degradation, the application of nucleic acid aptamers is considered to be effective because these can be explored using systematic evolution of ligand by exponential enrichment (SELEX) methods. In this study, we constructed chimeric molecules in which nucleic acid aptamers capable of binding to the estrogen receptor α (ERα) and E3 ubiquitin ligase ligands were linked via a linker. ERα aptamer-based PROTACs were found to degrade ERα via the UPS. These findings represent the development of novel aptamer-based PROTACs that target intracellular proteins and are potentially applicable to other proteins.
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Affiliation(s)
- Haruna Tsujimura
- Division
of Organic Chemistry, National Institute
of Health Sciences, Kanagawa 210-9501, Japan
- Graduate
School of Medical Life Science, Yokohama
City University, Kanagawa 236-0027, Japan
| | - Miyako Naganuma
- Division
of Organic Chemistry, National Institute
of Health Sciences, Kanagawa 210-9501, Japan
- Graduate
School of Medical Life Science, Yokohama
City University, Kanagawa 236-0027, Japan
| | - Nobumichi Ohoka
- Division
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kanagawa 210-9501, Japan
| | - Takao Inoue
- Division
of Molecular Target and Gene Therapy Products, National Institute of Health Sciences, Kanagawa 210-9501, Japan
| | - Mikihiko Naito
- Laboratory
of Targeted Protein Degradation, Graduate School of Pharmaceutical
Sciences, The University of Tokyo, Tokyo 113-0033, Japan
| | - Genichiro Tsuji
- Division
of Organic Chemistry, National Institute
of Health Sciences, Kanagawa 210-9501, Japan
| | - Yosuke Demizu
- Division
of Organic Chemistry, National Institute
of Health Sciences, Kanagawa 210-9501, Japan
- Graduate
School of Medical Life Science, Yokohama
City University, Kanagawa 236-0027, Japan
- Graduate
School of Medicine, Dentistry and Pharmaceutical Sciences, Division
of Pharmaceutical Science, Okayama University, Okayama 700-8530, Japan
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10
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Yang LF, Ling M, Kacherovsky N, Pun SH. Aptamers 101: aptamer discovery and in vitro applications in biosensors and separations. Chem Sci 2023; 14:4961-4978. [PMID: 37206388 PMCID: PMC10189874 DOI: 10.1039/d3sc00439b] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 04/14/2023] [Indexed: 05/21/2023] Open
Abstract
Aptamers are single-stranded nucleic acids that bind and recognize targets much like antibodies. Recently, aptamers have garnered increased interest due to their unique properties, including inexpensive production, simple chemical modification, and long-term stability. At the same time, aptamers possess similar binding affinity and specificity as their protein counterpart. In this review, we discuss the aptamer discovery process as well as aptamer applications to biosensors and separations. In the discovery section, we describe the major steps of the library selection process for aptamers, called systematic evolution of ligands by exponential enrichment (SELEX). We highlight common approaches and emerging strategies in SELEX, from starting library selection to aptamer-target binding characterization. In the applications section, we first evaluate recently developed aptamer biosensors for SARS-CoV-2 virus detection, including electrochemical aptamer-based sensors and lateral flow assays. Then we discuss aptamer-based separations for partitioning different molecules or cell types, especially for purifying T cell subsets for therapeutic applications. Overall, aptamers are promising biomolecular tools and the aptamer field is primed for expansion in biosensing and cell separation.
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Affiliation(s)
- Lucy F Yang
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Melissa Ling
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Nataly Kacherovsky
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
| | - Suzie H Pun
- Department of Bioengineering and Molecular Engineering and Sciences Institute, University of Washington Seattle Washington USA
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11
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Kong F, Luo J, Jing L, Wang Y, Shen H, Yu R, Sun S, Xing Y, Ming T, Liu M, Jin H, Cai X. Reduced Graphene Oxide and Gold Nanoparticles-Modified Electrochemical Aptasensor for Highly Sensitive Detection of Doxorubicin. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:1223. [PMID: 37049316 PMCID: PMC10096947 DOI: 10.3390/nano13071223] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
Doxorubicin (DOX) is the most clinically important antibiotic in cancer treatment, but its severe cardiotoxicity and other side effects limit its clinical use. Therefore, monitoring DOX concentrations during therapy is essential to improve efficacy and reduce adverse effects. Here, we fabricated a sensitive electrochemical aptasensor for DOX detection. The sensor used gold wire as the working electrode and was modified with reduced graphene oxide (rGO)/gold nanoparticles (AuNPs) to improve the sensitivity. An aptamer was used as the recognition element for the DOX. The 5' end of the aptamer was modified with a thiol group, and thus immobilized to the AuNPs, and the 3' end was modified with methylene blue, which acts as the electron mediator. The combination between the aptamer and DOX would produce a binding-induced conformation, which changes the electron transfer rate, yielding a current change that correlates with the concentration of DOX. The aptasensor exhibited good linearity in the DOX concentration range of 0.3 μM to 6 μM, with a detection limit of 0.1 μM. In addition, the aptasensor was used for DOX detection in real samples and results, and showed good recovery. The proposed electrochemical aptasensor will provide a sensitive, fast, simple, and reliable new platform for detecting DOX.
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Affiliation(s)
- Fanli Kong
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinping Luo
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Luyi Jing
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiding Wang
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huayu Shen
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China
| | - Rong Yu
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China
| | - Shuai Sun
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Xing
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Ming
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Meiting Liu
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyan Jin
- Obstetrics and Gynecology Department, Peking University First Hospital, Beijing 100034, China
| | - Xinxia Cai
- State Key Laboratory of Transducer Technology, Aerospace Information Research Institute, Chinese Academy of Sciences, Beijing 100190, China
- School of Electronic, Electrical and Communication Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
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12
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Zhou Z, Lan X, Zhu L, Zhang Y, Chen K, Zhang W, Xu W. Portable dual-aptamer microfluidic chip biosensor for Bacillus cereus based on aptamer tailoring and dumbbell-shaped probes. JOURNAL OF HAZARDOUS MATERIALS 2023; 445:130545. [PMID: 36493638 DOI: 10.1016/j.jhazmat.2022.130545] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 11/21/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
As food-borne pathogens, Bacillus cereus not only produce toxins that contaminate food and threaten human health, but also rely on spores to resist extreme environments. At present, the detection of B. cereus is still at the genome level and it is not easily distinguished from other Bacilli of the same group. Herein, we obtained the aptamers of B. cereus in different phases through Cell-SELEX technology. Then, through step-by-step tailoring and molecular docking, the two best performing aptamers were ascertained and the interaction revealed between the repeated G bases in the aptamer and the polar amino acids in the α-helix of the epiprotein. Based on these aptamers, a multifunctional dumbbell-shaped probe and an ultrasensitive microfluidic chip biosensor were designed. Tests showed that the novel sensor is able to complete detection within 1 h with a limit of detection (LOD) of 9.27 CFU/mL. Moreover, the sensor can be used in complex food environments, such as milk and rice, is able to detect both vegetative cells and spores, and it can also distinguish B. thuringiensis from the same flora. This study can provide a reference for the future development of food-borne pathogenic bacteria aptamer selecting, target interaction analysis, detection methods and equipment.
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Affiliation(s)
- Ziqi Zhou
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) (MOA), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xinyue Lan
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) (MOA), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China
| | - Yangzi Zhang
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Key Laboratory of Safety Assessment of Genetically Modified Organism (Food Safety) (MOA), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Kehan Chen
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China; Department of Mechanical Design and Manufacturing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Wenqiang Zhang
- Department of Mechanical Design and Manufacturing, College of Engineering, China Agricultural University, Beijing 100083, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100193, China.
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13
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Sung TC, Wang T, Liu Q, Ling QD, Subbiah SK, Renuka RR, Hsu ST, Umezawa A, Higuchi A. Cell-binding peptides on the material surface guide stem cell fate of adhesion, proliferation and differentiation. J Mater Chem B 2023; 11:1389-1415. [PMID: 36727243 DOI: 10.1039/d2tb02601e] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Human cells, especially stem cells, need to communicate and interact with extracellular matrix (ECM) proteins, which not only serve as structural components but also guide and support cell fate and properties such as cell adhesion, proliferation, survival and differentiation. The binding of the cells with ECM proteins or ECM-derived peptides via cell adhesion receptors such as integrins activates several signaling pathways that determine the cell fate, morphological change, proliferation and differentiation. The development of synthetic ECM protein-derived peptides that mimic the biological and biochemical functions of natural ECM proteins will benefit academic and clinical application. Peptides derived from or inspired by specific ECM proteins can act as agonists of each ECM protein receptor. Given that most ECM proteins function in cell adhesion via integrin receptors, many peptides have been developed that bind to specific integrin receptors. In this review, we discuss the peptide sequence, immobilization design, reaction method, and functions of several ECM protein-derived peptides. Various peptide sequences derived from mainly ECM proteins, which are used for coating or grafting on dishes, scaffolds, hydrogels, implants or nanofibers, have been developed to improve the adhesion, proliferation or differentiation of stem cells and to culture differentiated cells. This review article will help to inform the optimal choice of ECM protein-derived peptides for the development of scaffolds, implants, hydrogels, nanofibers and 2D cell culture dishes to regulate the proliferation and direct the differentiation of stem cells into specific lineages.
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Affiliation(s)
- Tzu-Cheng Sung
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, No. 270, Xueyuan Road, Wenzhou, Zhejiang, 325027, China.
| | - Ting Wang
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, No. 270, Xueyuan Road, Wenzhou, Zhejiang, 325027, China.
| | - Qian Liu
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, No. 270, Xueyuan Road, Wenzhou, Zhejiang, 325027, China.
| | - Qing-Dong Ling
- Cathay Medical Research Institute, Cathay General Hospital, No. 32, Ln 160, Jian-Cheng Road, Hsi-Chi City, Taipei 221, Taiwan
| | - Suresh Kumar Subbiah
- Centre for Materials Engineering and Regenerative Medicine, Bharath Institute of Higher Education and Research, 173, Agaram Road, Tambaram East, Chennai-73, 600078, India
| | - Remya Rajan Renuka
- Centre for Materials Engineering and Regenerative Medicine, Bharath Institute of Higher Education and Research, 173, Agaram Road, Tambaram East, Chennai-73, 600078, India
| | - Shih-Tien Hsu
- Department of Internal Medicine, Taiwan Landseed Hospital, 77 Kuangtai Road, Pingjen City, Tao-Yuan County 32405, Taiwan
| | - Akihiro Umezawa
- Department of Reproduction, National Center for Child Health and Development, 2-10-1 Okura, Setagaya-ku, Tokyo, 157-8535, Japan
| | - Akon Higuchi
- State Key Laboratory of Ophthalmology, Optometry and Visual Science, Eye Hospital, Wenzhou Medical University, No. 270, Xueyuan Road, Wenzhou, Zhejiang, 325027, China. .,Department of Chemical and Materials Engineering, National Central University, No. 300, Jhongda RD., Jhongli, Taoyuan, 32001, Taiwan. .,R & D Center for Membrane Technology, Chung Yuan Christian University, 200 Chung-Bei Rd., Jhongli, Taoyuan 320, Taiwan
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14
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A review: Construction of aptamer screening methods based on improving the screening rate of key steps. Talanta 2023. [DOI: 10.1016/j.talanta.2022.124003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Yue Y, Zhang D, Tian K, Ni D, Guo F, Yu Z, Wang P, Liang P. Screening and Evaluation of Thiamethoxam Aptamer Based on Pressurized GO-SELEX and Its Sensor Application. BIOSENSORS 2023; 13:155. [PMID: 36831921 PMCID: PMC9953353 DOI: 10.3390/bios13020155] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/09/2023] [Accepted: 01/17/2023] [Indexed: 06/18/2023]
Abstract
Thiamethoxam, a nicotinic pesticide used worldwide, can cause great harm to the environment and even to human health, and aptamers, known as chemical antibodies, have high affinity and specificity for the target, as well as great potential in detecting small molecules such as pesticides. In this paper, we report a highly sensitive biosensor system for thiamethoxam residue detection based on aptamer technology. After 15 rounds of screening with the pressurized GO-SELEX technology, we found that the aptamer libraries of the 5th and 9th rounds showed high affinity by the capture method. Four candidate aptamers were obtained by high-throughput sequencing and secondary structure prediction. Among them, the aptamer named Thi-5R-18 from the 5th round was demonstrated to possess the highest affinity by isothermal titration calorimetry, with a dissociation constant (Kd) of 4.935 × 10-5 M. The results of molecular docking showed that thiamethoxam and Thi-5R-18 were combined with bases G-15, A-19, and T-71 through hydrogen bonding and π-π interaction.Thi-5R-18 was used as a recognition element to construct a AuNPs colorimetric aptasensor, achieving an ultralow detection limit of 0.37 nM. More importantly, this colorimetric aptasensor can be used for quantitative detection of thiamethoxam on tea leaves, with a recovery of 96.94%~105.86%. This study provides a highly sensitive biosensor for detection of thiamethoxam residue.
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Affiliation(s)
- Yaqi Yue
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - De Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Kangfei Tian
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Dejiang Ni
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Fei Guo
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhi Yu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Pu Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture & Forestry Sciences, Huazhong Agricultural University, Wuhan 430070, China
| | - Pei Liang
- College of Optical and Electronic Technology, China Jiliang University, Hangzhou 310018, China
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16
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Shafiei N, Mahmoodzadeh Hosseini H, Amani J, Mirhosseini SA, Jafary H. Screening and Identification of DNA Nanostructure Aptamer Using the SELEX Method for Detection of Epsilon Toxin. IRANIAN JOURNAL OF PHARMACEUTICAL RESEARCH : IJPR 2023; 22:e140505. [PMID: 38444705 PMCID: PMC10912870 DOI: 10.5812/ijpr-140505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 03/07/2024]
Abstract
Background Epsilon toxin (ETX), produced by Clostridium perfringens, is one of the most potent toxins known, with a lethal potency approaching that of botulinum neurotoxins. Epsilon toxin is responsible for enteritis. Therefore, the development of rapid and simple methods to detect ETX is imperative. Aptamers are single-stranded oligonucleotides that can bind tightly to specific target molecules with an affinity comparable to that of monoclonal antibodies (mAbs). DNA aptamers can serve as tools for the molecular identification of organisms, such as pathogen subspecies. Objectives This study aimed to isolate high-affinity single-stranded DNA (ssDNA) aptamers against ETX. Methods This study identified aptamers using the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) method, enzyme-linked apta-sorbent assay (ELASA), and surface plasmon resonance (SPR) to determine the affinity and specificity of the newly obtained aptamers targeting ETX. Results Several aptamers obtained through the SELEX process were studied. Among them, 2 aptamers, ETX clone 3 (ETX3; dissociation constant (Kd = 8.4 ± 2.4E-9M) and ETX11 (Kd = 6.3 ± 1.3E-9M) had favorable specificity for ETX. The limits of detection were 0.21 and 0.08 μg/mL for ETX3 and ETX11, respectively.. Conclusions The discovered aptamers can be used in various aptamer-based rapid diagnostic tests for the detection of ETX.
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Affiliation(s)
- Nafiseh Shafiei
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hamideh Mahmoodzadeh Hosseini
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Jafar Amani
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Seyed Ali Mirhosseini
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Hanieh Jafary
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
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17
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Wei Z, Zhou Y, Wang R, Wang J, Chen Z. Aptamers as Smart Ligands for Targeted Drug Delivery in Cancer Therapy. Pharmaceutics 2022; 14:pharmaceutics14122561. [PMID: 36559056 PMCID: PMC9781707 DOI: 10.3390/pharmaceutics14122561] [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: 09/30/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 11/25/2022] Open
Abstract
Undesirable side effects and multidrug tolerance are the main holdbacks to the treatment of cancer in conventional chemotherapy. Fortunately, targeted drug delivery can improve the enrichment of drugs at the target site and reduce toxicity to normal tissues and cells. A targeted drug delivery system is usually composed of a nanocarrier and a targeting component. The targeting component is called a "ligand". Aptamers have high target affinity and specificity, which are identified as attractive and promising ligands. Therefore, aptamers have potential application in the development of smart targeting systems. For instance, aptamers are able to efficiently recognize tumor markers such as nucleolin, mucin, and epidermal growth factor receptor (EGFR). Besides, aptamers can also identify glycoproteins on the surface of tumor cells. Thus, the aptamer-mediated targeted drug delivery system has received extensive attention in the application of cancer therapy. This article reviews the application of aptamers as smart ligands for targeted drug delivery in cancer therapy. Special interest is focused on aptamers as smart ligands, aptamer-conjugated nanocarriers, aptamer targeting strategy for tumor microenvironment (TME), and aptamers that are specified to crucial cancer biomarkers for targeted drug delivery.
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Affiliation(s)
| | | | | | - Jin Wang
- Correspondence: (J.W.); (Z.C.); Tel.: +86-18616-819-730 (J.W.); +86-13767-154-425 (Z.C.)
| | - Zhenhua Chen
- Correspondence: (J.W.); (Z.C.); Tel.: +86-18616-819-730 (J.W.); +86-13767-154-425 (Z.C.)
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18
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Franco-Urquijo PA, Sierra-Martínez M, Jarquín-Martínez M, Martínez-Roque MA, García-Velásquez VM, Acosta-Altamirano G, Ruiz-Pérez NJ, Toscano-Garibay JD, Alvarez-Salas LM. Fluorescence-Linked Aptamer Assay for SARS-CoV-2 Spike-Protein: A Step-by-Step Performance Analysis in Clinical Samples. Diagnostics (Basel) 2022; 12:diagnostics12112829. [PMID: 36428893 PMCID: PMC9689637 DOI: 10.3390/diagnostics12112829] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 11/01/2022] [Accepted: 11/09/2022] [Indexed: 11/19/2022] Open
Abstract
The COVID-19 pandemic has been a main concern over the last two years and has become one of the most important crises in the history of human health. Today, there is still a need for affordable and reliable diagnostic tests for massive disease monitoring. Previously, a set of highly specific DNA-aptamers (C7/C9) binding to the SARS-CoV-2 Spike (S) protein were isolated but its performance in clinical samples remained to be tested. Here, 242 samples were collected through three different methods and subjected to florescence-linked aptamer assays (FLAA) based on C7/C9 aptamers through two readout protocols. Then, a step-by-step statistical approach which included agreement tests, proportion comparisons and binomial and multinomial logistic regressions was used to predict optimal conditions for the novel C7/C9 FLAA test. RTqPCR threshold cycles, symptoms onset and processing time were influential factors on FLAA test results. Naturally occurring mutations on S were also detected and analyzed. Aminoacidic substitutions D614G and T732A appeared relevant for aptamer recognition although further studies are necessary. The methodology presented here is the first step to determine the performance and diagnosis across a range of clinical contexts and it might serve as a base for a complete analysis applicable to other designs of new diagnostic tests.
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Affiliation(s)
- Pablo Alberto Franco-Urquijo
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City 07360, Mexico
| | - Mónica Sierra-Martínez
- Unidad de Investigación en Salud, Hospital Regional de Alta Especialidad de Ixtapaluca, Ixtapaluca 56530, Mexico
| | - Mariana Jarquín-Martínez
- Unidad de Investigación en Salud, Hospital Regional de Alta Especialidad de Ixtapaluca, Ixtapaluca 56530, Mexico
| | - Mateo Alejandro Martínez-Roque
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City 07360, Mexico
| | - Victor Miguel García-Velásquez
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City 07360, Mexico
| | | | | | - Julia Dolores Toscano-Garibay
- Unidad de Desarrollo en Soluciones Diagnósticas, Hospital Regional de Alta Especialidad de Ixtapaluca, Ixtapaluca 56530, Mexico
- Correspondence: (J.D.T.-G.); (L.M.A.-S.); Tel.: +52-(55)5972-9800 (ext. 1202) (J.D.T.-G.); +52-(55)5747-3800 (ext. 5387 or 5388) (L.M.A.-S.)
| | - Luis Marat Alvarez-Salas
- Laboratorio de Terapia Génica, Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Mexico City 07360, Mexico
- Correspondence: (J.D.T.-G.); (L.M.A.-S.); Tel.: +52-(55)5972-9800 (ext. 1202) (J.D.T.-G.); +52-(55)5747-3800 (ext. 5387 or 5388) (L.M.A.-S.)
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19
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da Silva AG, Goulart LR, Löffler P, Code C, Neves AF. Development of a Molecular Aptamer Beacon Applied to Magnetic-Assisted RNA Extraction for Detection of Dengue and Zika Viruses Using Clinical Samples. Int J Mol Sci 2022; 23:ijms232213866. [PMID: 36430340 PMCID: PMC9693377 DOI: 10.3390/ijms232213866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/27/2022] [Accepted: 11/03/2022] [Indexed: 11/12/2022] Open
Abstract
Limitations in the detection of cocirculating flaviviruses such as Dengue and Zika lead us to propose the use of aptameric capture of the viral RNA in combination with RT-PCR (APTA-RT-PCR). Aptamers were obtained via SELEX and next-generation sequencing, followed by colorimetric and fluorescent characterizations. An APTA-RT-PCR assay was developed, optimized, and tested against the viral RNAs in 108 serum samples. After selection, sequence APTAZC10 was designed as a bifunctional molecular beacon (APTAZC10-MB), exhibiting affinity for the viral targets. APTA-RT-PCR was able to detect Dengue and Zika RNA in 43% and 8% of samples, respectively. Our results indicate that APTAZC10-MB and APTA-RT-PCR will be useful to improve the detection of Dengue and Zika viruses in a fast molecular assay for the improvement of infectious disease surveillance.
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Affiliation(s)
- Amanda Gabrielle da Silva
- Institute of Physics, Postgraduate Program in Exact and Technological Sciences, Universidade Federal de Catalão, Catalão 75704-020, Brazil
| | - Luiz Ricardo Goulart
- Nanobiotechnology Laboratory, Institute of Biotechnology, Universidade Federal de Uberlândia, Uberlândia 38402-022, Brazil
| | - Philipp Löffler
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Christian Code
- Dianox ApS, Fruebjergvej 3, 2100 København, Denmark
- PhyLife Physical Life Sciences, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
| | - Adriana Freitas Neves
- Institute of Biotechnology, Molecular Biology Laboratory, Universidade Federal de Catalão, Catalão 75704-020, Brazil
- Correspondence:
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20
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Yang CH, Tsai CH. Aptamer against Aflatoxin B1 Obtained by SELEX and Applied in Detection. BIOSENSORS 2022; 12:848. [PMID: 36290985 PMCID: PMC9599246 DOI: 10.3390/bios12100848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 09/26/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Aflatoxins, especially aflatoxin B1 (AFB1), are the most prevalent mycotoxins in nature. They contaminate various crops and cause global food and feed safety concerns. Therefore, a simple, rapid, sensitive, and specific AFB1 detection tool is urgently needed. Aptamers generated by SELEX technology can specifically bind the desired targets with high affinity. The broad range of targets expands the scope of applications for aptamers. We used an AFB1-immobilized magnetic nanoparticle for SELEX to select AFB1-specific aptamers. One aptamer, fl-2CS1, revealed a dissociation constant (Kd = 2.5 μM) with AFB1 determined by isothermal titration calorimetry. Furthermore, no interaction was shown with other toxins (AFB2, AFG1, AFG2, OTA, and FB1). According to structural prediction and analysis, we identified a short version of the AFB1-specific aptamer, fl-2CS1/core, with a minimum length of 39-mer used in the AFB1-aptasensor system by real-time qPCR. The aptasensor showed a broad range of detection from 50 ppt to 50 ppb with an accuracy of 90% in the spiked peanut extract samples. With the application of the AFB1-aptasensor we have constructed, a wide range detection tool with high accuracy might be developed as a point-of-care testing tool in agriculture.
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Affiliation(s)
- Chung-Hsuan Yang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
| | - Ching-Hsiu Tsai
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Advanced Plant Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
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21
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Takao J, Nagai R, Endo T, Hisamoto H, Sueyoshi K. Aptamer Selection Based on Microscale Electrophoretic Filtration Using a Hydrogel-Plugged Capillary Device. Molecules 2022; 27:molecules27185818. [PMID: 36144553 PMCID: PMC9505737 DOI: 10.3390/molecules27185818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/20/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
This study reports a novel aptamer selection method based on microscale electrophoretic filtration. Aptamers are versatile materials that recognize specific targets and are attractive for their applications in biosensors, diagnosis, and therapy. However, their practical applications remain scarce due to issues with conventional selection methods, such as complicated operations, low-efficiency separation, and expensive apparatus. To overcome these drawbacks, a selection method based on microscale electrophoretic filtration using a capillary partially filled with hydrogel was developed. The electrophoretic filtration of model target proteins (immunoglobulin E (IgE)) using hydrogel, the electrokinetic injection of DNAs to interact with the trapped proteins, the elimination of DNAs with weak interactions, and the selective acquisition of aptamer candidates with strong interactions were successfully demonstrated, revealing the validity of the proposed concept. Two aptamer candidates for IgE were obtained after three selection cycles, and their affinity for the target was confirmed to be less than 1 nM based on their dissociation constant (KD) values. Therefore, the proposed method allows for the selection of aptamers with simple operations, highly effective separation based on electrophoresis and filtration, and a relatively cheap apparatus with disposable devices.
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Affiliation(s)
- Junku Takao
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, Osaka 545-0051, Japan
| | - Reina Nagai
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, Osaka 545-0051, Japan
| | - Tatsuro Endo
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, Osaka 545-0051, Japan
| | - Hideaki Hisamoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, Osaka 545-0051, Japan
| | - Kenji Sueyoshi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, Osaka 545-0051, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
- Correspondence:
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22
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Luo Z, Chen S, Zhou J, Wang C, Li K, Liu J, Tang Y, Wang L. Application of aptamers in regenerative medicine. Front Bioeng Biotechnol 2022; 10:976960. [PMID: 36105606 PMCID: PMC9465253 DOI: 10.3389/fbioe.2022.976960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/08/2022] [Indexed: 12/03/2022] Open
Abstract
Regenerative medicine is a discipline that studies how to use biological and engineering principles and operation methods to repair and regenerate damaged tissues and organs. Until now, regenerative medicine has focused mainly on the in-depth study of the pathological mechanism of diseases, the further development and application of new drugs, and tissue engineering technology strategies. The emergence of aptamers has supplemented the development methods and types of new drugs and enriched the application elements of tissue engineering technology, injecting new vitality into regenerative medicine. The role and application status of aptamers screened in recent years in various tissue regeneration and repair are reviewed, and the prospects and challenges of aptamer technology are discussed, providing a basis for the design and application of aptamers in long-term transformation.
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Affiliation(s)
- Zhaohui Luo
- Youjiang Medical University for Nationalities, Baise, Guangxi, China
- Guangxi Key Laboratory of basic and translational research of Bone and Joint Degenerative Diseases, Guangxi Biomedical Materials Engineering Research Center for Bone and Joint Degenerative Diseases, Department of Orthopedics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Shimin Chen
- Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Jing Zhou
- Youjiang Medical University for Nationalities, Baise, Guangxi, China
| | - Chong Wang
- School of Mechanical Engineering, Dongguan University of Technology, Dongguan, Guangdong, China
| | - Kai Li
- Academy of Orthopedics, Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diseases, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
- *Correspondence: Kai Li, ; Jia Liu, ; Yujin Tang,
| | - Jia Liu
- Guangxi Key Laboratory of basic and translational research of Bone and Joint Degenerative Diseases, Guangxi Biomedical Materials Engineering Research Center for Bone and Joint Degenerative Diseases, Department of Orthopedics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
- *Correspondence: Kai Li, ; Jia Liu, ; Yujin Tang,
| | - Yujin Tang
- Guangxi Key Laboratory of basic and translational research of Bone and Joint Degenerative Diseases, Guangxi Biomedical Materials Engineering Research Center for Bone and Joint Degenerative Diseases, Department of Orthopedics, Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi, China
- *Correspondence: Kai Li, ; Jia Liu, ; Yujin Tang,
| | - Liqiang Wang
- State Key Laboratory of Metal Matrix Composites, School of Material Science and Engineering, Shanghai Jiao Tong University, Shanghai, China
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23
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El-Husseini DM, Sayour AE, Melzer F, Mohamed MF, Neubauer H, Tammam RH. Generation and Selection of Specific Aptamers Targeting Brucella Species through an Enhanced Cell-SELEX Methodology. Int J Mol Sci 2022; 23:ijms23116131. [PMID: 35682807 PMCID: PMC9180945 DOI: 10.3390/ijms23116131] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 02/07/2023] Open
Abstract
Brucellae are Gram-negative, aerobic, non-motile coccobacilli causing brucellosis in man and animals. The disease is one of the most significant yet neglected global zoonoses. Especially in developing countries, brucellosis is causing public health problems and economic losses to private animal owners and national revenues. Composed of oligonucleotides, aptamers are chemical analogues of antibodies that are promising components for developing aptamer-based rapid, sensitive, and specific tests to identify the Brucella group of bacteria. For this purpose, aptamers were generated and selected by an enhanced protocol of cell systematic evolution of ligands by exponential enrichment (cell-SELEX). This enhanced cell-SELEX procedure involved the combination of both conventional and toggle cell-SELEX to boost the specificity and binding affinity to whole Brucella cells. This procedure, combined with high-throughput sequencing of the resulting aptamer pools, comprehensive bioinformatics analysis, and wet lab validation assays, led to the selection of a highly sensitive and specific aptamer for those Brucella species known to circulate in Egypt. The isolated candidate aptamer showed dissociation constant (KD) values of 43.5 ± 11, 61.5 ± 8, and 56 ± 10.8 nM for B. melitensis, B. abortus, and B. suis, respectively. This is the first development of a Brucella-specific aptamer using an enhanced combination of conventional and toggle cell-SELEX to the authors’ best knowledge.
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Affiliation(s)
- Dalia M. El-Husseini
- Biotechnology Department, Animal Health Research Institute, Agricultural Research Center, Dokki, Giza 12618, Egypt
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany;
- Correspondence: (D.M.E.-H.); (F.M.)
| | - Ashraf E. Sayour
- Molecular Biomimetics Research Group, Animal Health Research Institute, Agricultural Research Center, Dokki, Giza 12618, Egypt;
| | - Falk Melzer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany;
- Correspondence: (D.M.E.-H.); (F.M.)
| | - Magda F. Mohamed
- Chemistry Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (M.F.M.); (R.H.T.)
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, 07743 Jena, Germany;
| | - Reham H. Tammam
- Chemistry Department, Faculty of Science, Cairo University, Giza 12613, Egypt; (M.F.M.); (R.H.T.)
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24
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Research progress of whole-cell-SELEX selection and the application of cell-targeting aptamer. Mol Biol Rep 2022; 49:7979-7993. [PMID: 35274201 DOI: 10.1007/s11033-022-07317-0] [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: 01/19/2022] [Accepted: 03/02/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Aptamers refer to the artificially synthesized nucleic acid sequences (DNA/RNA) that can bind to a wide range of targets with high affinity and specificity, which are generally generated from systematic evolution of ligands by exponential enrichment (SELEX). As a novel method of aptamers screening, whole-cell-SELEX (WC-SELEX) has gained more and more attention in many fields such as biomedicine, analytical chemistry, and molecular diagnostics due to its ability to screen multiple potential aptamers without knowing the detailed structural information of target molecules. METHODS AND RESULTS In recent years, with the deepening of research on application of aptamers, the traditional WC-SELEX cannot meet the practical application because of long experimental period, complicated operation process and low specificity, etc. Therefore, the development of more efficient methods for screening aptamer is always on the road. This paper summarizes the current research status of WC-SELEX for bacteria, parasites and animal cells, and reviews the latest advances of WC-SELEX techniques that are dependent on novel instruments, materials and microelectronics, including fluorescence-activated cell sorting-assisted SELEX, three-dimensional assisted WC-SELEX, and microfluidic chip system-assisted WC-SELEX. In addition, the application of aptamers targeting cells was discussed. CONCLUSION Taken together, this review is aimed at providing a reference for WC-SELEX selection and application of aptamer targeting cells.
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25
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Chen XF, Zhao X, Yang Z. Aptasensors for the detection of infectious pathogens: design strategies and point-of-care testing. Mikrochim Acta 2022; 189:443. [PMID: 36350388 PMCID: PMC9643942 DOI: 10.1007/s00604-022-05533-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 10/10/2022] [Indexed: 11/11/2022]
Abstract
The epidemic of infectious diseases caused by contagious pathogens is a life-threatening hazard to the entire human population worldwide. A timely and accurate diagnosis is the critical link in the fight against infectious diseases. Aptamer-based biosensors, the so-called aptasensors, employ nucleic acid aptamers as bio-receptors for the recognition of target pathogens of interest. This review focuses on the design strategies as well as state-of-the-art technologies of aptasensor-based diagnostics for infectious pathogens (mainly bacteria and viruses), covering the utilization of three major signal transducers, the employment of aptamers as recognition moieties, the construction of versatile biosensing platforms (mostly micro and nanomaterial-based), innovated reporting mechanisms, and signal enhancement approaches. Advanced point-of-care testing (POCT) for infectious disease diagnostics are also discussed highlighting some representative ready-to-use devices to address the urgent needs of currently prevalent coronavirus disease 2019 (COVID-19). Pressing issues in aptamer-based technology and some future perspectives of aptasensors are provided for the implementation of aptasensor-based diagnostics into practical application.
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Affiliation(s)
- Xiao-Fei Chen
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou, 510070, People's Republic of China
| | - Xin Zhao
- Guangdong Provincial Key Laboratory of Chemical Measurement and Emergency Test Technology, Institute of Analysis, Guangdong Academy of Sciences (China National Analytical Center, Guangzhou), Guangzhou, 510070, People's Republic of China.
| | - Zifeng Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510120, People's Republic of China.
- Guangzhou Laboratory, Guangzhou, 510320, People's Republic of China.
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, Guangzhou, 510005, People's Republic of China.
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26
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Liu L, Han Z, An F, Gong X, Zhao C, Zheng W, Mei L, Zhou Q. Aptamer-based biosensors for the diagnosis of sepsis. J Nanobiotechnology 2021; 19:216. [PMID: 34281552 PMCID: PMC8287673 DOI: 10.1186/s12951-021-00959-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/09/2021] [Indexed: 12/15/2022] Open
Abstract
Sepsis, the syndrome of infection complicated by acute organ dysfunction, is a serious and growing global problem, which not only leads to enormous economic losses but also becomes one of the leading causes of mortality in the intensive care unit. The detection of sepsis-related pathogens and biomarkers in the early stage plays a critical role in selecting appropriate antibiotics or other drugs, thereby preventing the emergence of dangerous phases and saving human lives. There are numerous demerits in conventional detection strategies, such as high cost, low efficiency, as well as lacking of sensitivity and selectivity. Recently, the aptamer-based biosensor is an emerging strategy for reasonable sepsis diagnosis because of its accessibility, rapidity, and stability. In this review, we first introduce the screening of suitable aptamer. Further, recent advances of aptamer-based biosensors in the detection of bacteria and biomarkers for the diagnosis of sepsis are summarized. Finally, the review proposes a brief forecast of challenges and future directions with highly promising aptamer-based biosensors.
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Affiliation(s)
- Lubin Liu
- Institute for Translational Medicine, Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China
- School of Stomatology, Qingdao University, Qingdao, 266003, China
| | - Zeyu Han
- Institute for Translational Medicine, Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China
- School of Stomatology, Qingdao University, Qingdao, 266003, China
| | - Fei An
- Institute for Translational Medicine, Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China
- School of Stomatology, Qingdao University, Qingdao, 266003, China
| | - Xuening Gong
- Institute for Translational Medicine, Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China
- School of Stomatology, Qingdao University, Qingdao, 266003, China
| | - Chenguang Zhao
- Institute for Translational Medicine, Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China
- School of Stomatology, Qingdao University, Qingdao, 266003, China
| | - Weiping Zheng
- Institute for Translational Medicine, Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China
- School of Stomatology, Qingdao University, Qingdao, 266003, China
| | - Li Mei
- School of Stomatology, Qingdao University, Qingdao, 266003, China
| | - Qihui Zhou
- Institute for Translational Medicine, Department of Stomatology, The Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266003, China.
- School of Stomatology, Qingdao University, Qingdao, 266003, China.
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27
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Recent Advancements in Aptamer-Based Surface Plasmon Resonance Biosensing Strategies. BIOSENSORS-BASEL 2021; 11:bios11070233. [PMID: 34356703 PMCID: PMC8301862 DOI: 10.3390/bios11070233] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/05/2021] [Accepted: 07/08/2021] [Indexed: 12/12/2022]
Abstract
Surface plasmon resonance (SPR) can track molecular interactions in real time, and is a powerful as well as widely used biological and chemical sensing technique. Among the different SPR-based sensing applications, aptamer-based SPR biosensors have attracted significant attention because of their simplicity, feasibility, and low cost for target detection. Continuous developments in SPR aptasensing research have led to the emergence of abundant technical and design concepts. To understand the recent advances in SPR for biosensing, this paper reviews SPR-based research from the last seven years based on different sensing-type strategies and sub-directions. The characteristics of various SPR-based applications are introduced. We hope that this review will guide the development of SPR aptamer sensors for healthcare.
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28
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Wada M, Endo T, Hisamoto H, Sueyoshi K. Fractionation of Single-stranded DNAs with/without Stable Preorganized Structures Using Capillary Sieving Electrophoresis for Aptamer Selection. ANAL SCI 2021; 37:799-802. [PMID: 33952863 DOI: 10.2116/analsci.21c003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Aptamers, single-stranded DNAs/RNAs with a strong and specific interaction towards a target molecule, have wide applications in the fields of medicine and biosensors. In conventional aptamer selection methods, it is difficult to obtain "preorganized" and/or "induced-fit" type of aptamers selectively. In this study, separation and fractionation of single-stranded DNAs with/without stable preorganized structures were carried out using capillary sieving electrophoresis. The fractionated DNAs showed different mobilities and thermodynamic stabilities of their secondary structures; this outcome is deemed to be necessary for the synthesis of novel aptasensors with a desirable sensing mechanism.
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Affiliation(s)
- Masahide Wada
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University
| | - Tatsuro Endo
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University
| | - Hideaki Hisamoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University
| | - Kenji Sueyoshi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Prefecture University.,PRESTO, Japan Science and Technology Agency
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29
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Saito S, Sakamoto T, Tanaka N, Watanabe R, Kamimura T, Ota K, Riley KR, Yoshimoto K, Tasaki-Handa Y, Shibukawa M. Single-Round DNA Aptamer Selection by Combined Use of Capillary Electrophoresis and Next Generation Sequencing: An Aptaomics Approach for Identifying Unique Functional Protein-Binding DNA Aptamers. Chemistry 2021; 27:10058-10067. [PMID: 33991022 DOI: 10.1002/chem.202100177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Indexed: 11/05/2022]
Abstract
In DNA aptamer selection, existing methods do not discriminate aptamer sequences based on their binding affinity and function and the reproducibility of the selection is often poor, even for the selection of well-known aptamers like those that bind the commonly used model protein thrombin. In the present study, a novel single-round selection method (SR-CE selection) was developed by combining capillary electrophoresis (CE) with next generation sequencing. Using SR-CE selection, a successful semi-quantitative and semi-comprehensive aptamer selection for thrombin was demonstrated with high reproducibility for the first time. Selection rules based on dissociation equilibria and kinetics were devised to obtain families of analogous sequences. Selected sequences of the same family were shown to bind thrombin with high affinity. Furthermore, data acquired from SR-CE selection was mined by creating sub-libraries that were categorized by the functionality of the aptamers (e. g., pre-organized aptamers versus structure-induced aptamers). Using this approach, a novel fluorescent molecular recognition sensor for thrombin with nanomolar detection limits was discovered. Thus, in this proof-of-concept report, we have demonstrated the potential of a "DNA Aptaomics" approach to systematically design functional aptamers as well as to obtain high affinity aptamers.
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Affiliation(s)
- Shingo Saito
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Toshiki Sakamoto
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Naoki Tanaka
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Ryo Watanabe
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Takuya Kamimura
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Kazuki Ota
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Kathryn R Riley
- Chemistry and Biochemistry, Swarthmore College, Swarthmore, PA 19081, USA
| | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro-ku, Tokyo, 153-8902, Japan
| | - Yuiko Tasaki-Handa
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Masami Shibukawa
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
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30
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Guo W, Zhang C, Ma T, Liu X, Chen Z, Li S, Deng Y. Advances in aptamer screening and aptasensors' detection of heavy metal ions. J Nanobiotechnology 2021; 19:166. [PMID: 34074287 PMCID: PMC8171055 DOI: 10.1186/s12951-021-00914-4] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 05/26/2021] [Indexed: 02/07/2023] Open
Abstract
Heavy metal pollution has become more and more serious with industrial development and resource exploitation. Because heavy metal ions are difficult to be biodegraded, they accumulate in the human body and cause serious threat to human health. However, the conventional methods to detect heavy metal ions are more strictly to the requirements by detection equipment, sample pretreatment, experimental environment, etc. Aptasensor has the advantages of strong specificity, high sensitivity and simple preparation to detect small molecules, which provides a new direction platform in the detection of heavy metal ions. This paper reviews the selection of aptamers as target for heavy metal ions since the 21th century and aptasensors application for detection of heavy metal ions that were reported in the past five years. Firstly, the selection methods for aptamers with high specificity and high affinity are introduced. Construction methods and research progress on sensor based aptamers as recognition element are also introduced systematically. Finally, the challenges and future opportunities of aptasensors in detecting heavy metal ions are discussed.
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Affiliation(s)
- Wenfei Guo
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Chuanxiang Zhang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Tingting Ma
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Xueying Liu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Zhu Chen
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Song Li
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
| | - Yan Deng
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou, 412007 China
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31
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Citartan M. Aptamers as the powerhouse of dot blot assays. Talanta 2021; 232:122436. [PMID: 34074421 DOI: 10.1016/j.talanta.2021.122436] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/13/2021] [Accepted: 04/15/2021] [Indexed: 12/21/2022]
Abstract
Dot blot assays have always been associated with antibodies as the main molecular recognition element, which are widely employed in a myriad of diagnostic applications. With the rising of aptamers as the equivalent molecular recognition elements of antibodies, dot blot assays are also one of the diagnostic avenues that should be scrutinized for their amenability with aptamers as the potential surrogates of antibodies. In this review, the stepwise procedures of an aptamer-based dot blot assays are underscored before reviewing the existing aptamer-based dot blot assays developed so far. Most of the applications center on monitoring the progress of SELEX and as the validatory assays to assess the potency of aptamer candidates. For the purpose of diagnostics, the current effort is still languid and as such possible suggestions to galvanize the move to spur the aptamer-based dot blot assays to a point-of-care arena are discussed.
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Affiliation(s)
- Marimuthu Citartan
- Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, Bertam, 13200, Kepala Batas, Penang, Malaysia.
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32
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Abstract
Graphene-based FRET aptasensors can be realized only by unique combinations of aptamer that can be freely functionalized by chemical modification, and graphene/graphene oxide that works as an excellent fluorescence acceptor at the same time as aptamer adsorbates. This review describes the principles of the sensor, several applications to microchannel devices, improvement of the sensing performance by molecular design of the aptamer and remarks on future prospects based on an introduction of recent works and achievements, including the author's paper. The sensor employs DNA modified with graphene/graphene oxide at the terminal as the molecular probe. This system is supported by the excellent property of DNA that does not lose the molecular recognition ability even due to a chemical modification at the terminal. I hope that this review will be useful for developing research on higher performance of graphene aptasensors in the future.
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Affiliation(s)
- Yuko Ueno
- Department of Applied Chemistry, Faculty of Science and Engineering, Chuo University
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