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Zhang D, Liu Y, Huang H, Fu T, Bing T, Wu X, Tan W. Streamlining RNA Aptamer Selection via Unique Molecular Identifiers and High-Throughput Sequencing. Anal Chem 2024. [PMID: 39385698 DOI: 10.1021/acs.analchem.4c02984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
Abstract
Aptamers are valuable tools for applications such as cell imaging, drug delivery, and therapeutics. RNA aptamers, in particular, exhibit complex structural diversity and flexibility, affording higher affinity and specificity, broader target recognition, and easier chemical modification compared with DNA aptamers. However, traditional selection methods for RNA aptamers are time-consuming and involve numerous rounds of screening, thus limiting their widespread application. To overcome this challenge, we propose an efficient truncated selection approach termed ID-SELEX. This method incorporates a molecular identification marker whereby each template is labeled with a unique molecular identifier, or UMI. Such incorporation helps mitigate biases introduced by multiple polymerase chain reaction (PCR) amplification during high-throughput sequencing, ensuring accurate identification of aptamer candidates. Utilizing ID-SELEX, we successfully identified a panel of high-quality aptamers targeting the human colon cancer cell line HCT-8 in just 2 rounds of selection. Furthermore, we demonstrated the versatility of this strategy by selecting 6 RNA aptamers targeting mouse myoblast cell line C2C12 with only one round of selection. In summary, RNA aptamer selection based on ID-SELEX utilizes high-throughput sequencing and UMI labeling to enable the rapid screening of RNA aptamers across human and murine cell lines. As such, ID-SELEX has the potential to facilitate RNA aptamer discovery, providing a novel molecular tool for biomedical research, clinical applications, and precision medicine.
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Affiliation(s)
- Dengwei Zhang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Yuqing Liu
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Huidong Huang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Ting Fu
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/BioSensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Tao Bing
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- School of Molecular Medicine, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou 310024, China
| | - Xiaoqiu Wu
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| | - Weihong Tan
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
- Institute of Molecular Medicine (IMM), Renji Hospital, Shanghai Jiao Tong University School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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2
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Wang B, Kobeissy F, Golpich M, Cai G, Li X, Abedi R, Haskins W, Tan W, Benner SA, Wang KKW. Aptamer Technologies in Neuroscience, Neuro-Diagnostics and Neuro-Medicine Development. Molecules 2024; 29:1124. [PMID: 38474636 DOI: 10.3390/molecules29051124] [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: 01/04/2024] [Revised: 02/15/2024] [Accepted: 02/27/2024] [Indexed: 03/14/2024] Open
Abstract
Aptamers developed using in vitro Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technology are single-stranded nucleic acids 10-100 nucleotides in length. Their targets, often with specificity and high affinity, range from ions and small molecules to proteins and other biological molecules as well as larger systems, including cells, tissues, and animals. Aptamers often rival conventional antibodies with improved performance, due to aptamers' unique biophysical and biochemical properties, including small size, synthetic accessibility, facile modification, low production cost, and low immunogenicity. Therefore, there is sustained interest in engineering and adapting aptamers for many applications, including diagnostics and therapeutics. Recently, aptamers have shown promise as early diagnostic biomarkers and in precision medicine for neurodegenerative and neurological diseases. Here, we critically review neuro-targeting aptamers and their potential applications in neuroscience research, neuro-diagnostics, and neuro-medicine. We also discuss challenges that must be overcome, including delivery across the blood-brain barrier, increased affinity, and improved in vivo stability and in vivo pharmacokinetic properties.
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Affiliation(s)
- Bang Wang
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
- The Foundation for Applied Molecular Evolution, 1501 NW 68th Terrace, Gainesville, FL 32605, USA
| | - Firas Kobeissy
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
- Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
- Brain Rehabilitation Research Center, Malcom Randall VA Medical Center, North Florida/South Georgia Veterans Health System, 1601 SW Archer Road, Gainesville, FL 32608, USA
- Center for Visual and Neurocognitive Rehabilitation (CVNR), Atlanta VA Health Care System, 1670 Clairmont Rd, Decatur, GA 30033, USA
| | - Mojtaba Golpich
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Guangzheng Cai
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
| | - Xiaowei Li
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Reem Abedi
- Department of Biochemistry and Molecular Genetics, American University of Beirut, Beirut 1107-2020, Lebanon
| | - William Haskins
- Gryphon Bio, Inc., 611 Gateway Blvd. Suite 120 #253, South San Francisco, CA 94080, USA
| | - Weihong Tan
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), The Chinese Academy of Sciences, Hangzhou 310022, China
| | - Steven A Benner
- The Foundation for Applied Molecular Evolution, 1501 NW 68th Terrace, Gainesville, FL 32605, USA
| | - Kevin K W Wang
- Center for Neurotrauma, MultiOmics and Biomarkers (CNMB), Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, Atlanta, GA 30310, USA
- Department of Emergency Medicine, University of Florida, Gainesville, FL 32611, USA
- Brain Rehabilitation Research Center, Malcom Randall VA Medical Center, North Florida/South Georgia Veterans Health System, 1601 SW Archer Road, Gainesville, FL 32608, USA
- Center for Visual and Neurocognitive Rehabilitation (CVNR), Atlanta VA Health Care System, 1670 Clairmont Rd, Decatur, GA 30033, USA
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Alfinito E. TBA for Sensing Toxic Cations: A Critical Analysis of Structural and Electrical Properties. Int J Mol Sci 2023; 24:14492. [PMID: 37833940 PMCID: PMC10572628 DOI: 10.3390/ijms241914492] [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: 08/16/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023] Open
Abstract
Food and drinks can be contaminated with pollutants such as lead and strontium, which poses a serious danger to human health. For this reason, a number of effective sensors have been developed for the rapid and highly selective detection of such contaminants. TBA, a well-known aptamer developed to selectively target and thereby inhibit the protein of clinical interest α-thrombin, is receiving increasing attention for sensing applications, particularly for the sensing of different cations. Indeed, TBA, in the presence of these cations, folds into the stable G-quadruplex structure. Furthermore, different cations produce small but significant changes in this structure that result in changes in the electrical responses that TBA can produce. In this article, we give an overview of the expected data regarding the use of TBA in the detection of lead and strontium, calculating the expected electrical response using different measurement techniques. Finally, we conclude that TBA should be able to detect strontium with a sensitivity approximately double that achievable for lead.
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Affiliation(s)
- Eleonora Alfinito
- Dipartimento di Matematica e Fisica 'Ennio De Giorgi', Università del Salento, I-73100 Lecce, Italy
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Kizilkurtlu AA, Demirbas E, Agel HE. Electrochemical aptasensors for pathogenic detection toward point-of-care diagnostics. Biotechnol Appl Biochem 2023; 70:1460-1479. [PMID: 37277950 DOI: 10.1002/bab.2485] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 05/20/2023] [Indexed: 06/07/2023]
Abstract
A biosensor system refers to a biomedical device, which detects biological, chemical, or biochemical components by converting those signals to an electrical signal by utilizing and uniting physical or chemical transducer with biorecognition elements. An electrochemical biosensor is generally based on the reaction of either production or consumption of electrons under a three-electrode system. Biosensor systems are exploited in a wide range of areas, such as medicine, agriculture, husbandry, food, industry, environment protection, quality control, waste disposal, and the military. Pathogenic infections are the third leading cause of death worldwide after cardiovascular diseases and cancer. Therefore, there is an urgent need for effective diagnostic tools to control food, water, and soil contamination result in protecting human life and health. Aptamers are peptide or oligonucleotide-based molecules that show very high affinity to their targets that are produced from large pools of random amino acid or oligonucleotide sequences. Generally, aptamers have been utilized for fundamental sciences and clinical implementations for their target-specific affinity and have been intensely exploited for different kinds of biosensor applications for approximately 30 years. The convergence of aptamers with biosensor systems enabled the construction of voltammetric, amperometric, and impedimetric biosensors for the detection of specific pathogens. In this review, electrochemical aptamer biosensors were evaluated by discussing the definition, types, and production techniques of aptamers, the advantages of aptamers as a biological recognition element against their alternatives, and a wide range of aptasensor examples from literature in the detection of specific pathogens.
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Affiliation(s)
| | - Erhan Demirbas
- Department of Chemistry, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Hatice Esra Agel
- BioNano Functional Materials Technologies Research Group TÜBİTAK - Marmara Research Center, Gebze, Kocaeli, Turkey
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5
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Zhang H, Yang S, Zeng J, Li X, Chuai R. A Genosensor Based on the Modification of a Microcantilever: A Review. MICROMACHINES 2023; 14:427. [PMID: 36838127 PMCID: PMC9959632 DOI: 10.3390/mi14020427] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/28/2022] [Accepted: 01/06/2023] [Indexed: 06/18/2023]
Abstract
When the free end of a microcantilever is modified by a genetic probe, this sensor can be used for a wider range of applications, such as for chemical analysis, biological testing, pharmaceutical screening, and environmental monitoring. In this paper, to clarify the preparation and detection process of a microcantilever sensor with genetic probe modification, the core procedures, such as probe immobilization, complementary hybridization, and signal extraction and processing, are combined and compared. Then, to reveal the microcantilever's detection mechanism and analysis, the influencing factors of testing results, the theoretical research, including the deflection principle, the establishment and verification of a detection model, as well as environmental influencing factors are summarized. Next, to demonstrate the application results of the genetic-probe-modified sensors, based on the classification of detection targets, the application status of other substances except nucleic acid, virus, bacteria and cells is not introduced. Finally, by enumerating the application results of a genetic-probe-modified microcantilever combined with a microfluidic chip, the future development direction of this technology is surveyed. It is hoped that this review will contribute to the future design of a genetic-probe-modified microcantilever, with further exploration of the sensitive mechanism, optimization of the design and processing methods, expansion of the application fields, and promotion of practical application.
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Affiliation(s)
- He Zhang
- Correspondence: ; Tel.: +86-024-2549-6401
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6
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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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7
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Chen W, Lai Q, Zhang Y, Liu Z. Recent Advances in Aptasensors For Rapid and Sensitive Detection of Staphylococcus Aureus. Front Bioeng Biotechnol 2022; 10:889431. [PMID: 35677308 PMCID: PMC9169243 DOI: 10.3389/fbioe.2022.889431] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 04/12/2022] [Indexed: 12/30/2022] Open
Abstract
The infection of Staphylococcus aureus (S.aureus) and the spread of drug-resistant bacteria pose a serious threat to global public health. Therefore, timely, rapid and accurate detection of S. aureus is of great significance for food safety, environmental monitoring, clinical diagnosis and treatment, and prevention of drug-resistant bacteria dissemination. Traditional S. aureus detection methods such as culture identification, ELISA, PCR, MALDI-TOF-MS and sequencing, etc., have good sensitivity and specificity, but they are complex to operate, requiring professionals and expensive and complex machines. Therefore, it is still challenging to develop a fast, simple, low-cost, specific and sensitive S. aureus detection method. Recent studies have demonstrated that fast, specific, low-cost, low sample volume, automated, and portable aptasensors have been widely used for S. aureus detection and have been proposed as the most attractive alternatives to their traditional detection methods. In this review, recent advances of aptasensors based on different transducer (optical and electrochemical) for S. aureus detection have been discussed in details. Furthermore, the applications of aptasensors in point-of-care testing (POCT) have also been discussed. More and more aptasensors are combined with nanomaterials as efficient transducers and amplifiers, which appears to be the development trend in aptasensors. Finally, some significant challenges for the development and application of aptasensors are outlined.
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Affiliation(s)
- Wei Chen
- Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha, China
- National Clinical Research Center for Geriatric Diseases, Xiangya Hospital of Central South University, Changsha, China
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, China
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
- *Correspondence: Wei Chen, ; Zhengchun Liu,
| | - Qingteng Lai
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, China
| | - Yanke Zhang
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, China
| | - Zhengchun Liu
- Hunan Key Laboratory for Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha, China
- Department of Microbiology, School of Basic Medical Science, Central South University, Changsha, China
- *Correspondence: Wei Chen, ; Zhengchun Liu,
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8
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Chakraborty B, Das S, Gupta A, Xiong Y, Vyshnavi TV, Kizer ME, Duan J, Chandrasekaran AR, Wang X. Aptamers for Viral Detection and Inhibition. ACS Infect Dis 2022; 8:667-692. [PMID: 35220716 PMCID: PMC8905934 DOI: 10.1021/acsinfecdis.1c00546] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Indexed: 02/07/2023]
Abstract
Recent times have experienced more than ever the impact of viral infections in humans. Viral infections are known to cause diseases not only in humans but also in plants and animals. Here, we have compiled the literature review of aptamers selected and used for detection and inhibition of viral infections in all three categories: humans, animals, and plants. This review gives an in-depth introduction to aptamers, different types of aptamer selection (SELEX) methodologies, the benefits of using aptamers over commonly used antibody-based strategies, and the structural and functional mechanism of aptasensors for viral detection and therapy. The review is organized based on the different characterization and read-out tools used to detect virus-aptasensor interactions with a detailed index of existing virus-targeting aptamers. Along with addressing recent developments, we also discuss a way forward with aptamers for DNA nanotechnology-based detection and treatment of viral diseases. Overall, this review will serve as a comprehensive resource for aptamer-based strategies in viral diagnostics and treatment.
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Affiliation(s)
- Banani Chakraborty
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Sreyashi Das
- Department of Biological Sciences and Bioengineering, Indian Institute of Technology, Kanpur, Uttar Pradesh 208016, India
| | - Arushi Gupta
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Yanyu Xiong
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - T-V Vyshnavi
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, Karnataka 560012, India
| | - Megan E. Kizer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jinwei Duan
- Department of Chemistry and Materials Science, Chang’an University, Xi’an, Shaanxi 710064, China
| | - Arun Richard Chandrasekaran
- The RNA Institute, University at Albany, State University of New York, Albany, New York 12222, United States
| | - Xing Wang
- Nick Holonyak Jr. Micro and Nanotechnology Laboratory (HMNTL), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Carl R. Woese Institute for Genomic Biology (IGB), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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9
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Qian S, Chang D, He S, Li Y. Aptamers from random sequence space: Accomplishments, gaps and future considerations. Anal Chim Acta 2022; 1196:339511. [DOI: 10.1016/j.aca.2022.339511] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 01/12/2022] [Accepted: 01/15/2022] [Indexed: 02/07/2023]
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Xiao X, Li H, Zhao L, Zhang Y, Liu Z. Oligonucleotide aptamers: Recent advances in their screening, molecular conformation and therapeutic applications. Biomed Pharmacother 2021; 143:112232. [PMID: 34649356 DOI: 10.1016/j.biopha.2021.112232] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/04/2021] [Accepted: 09/19/2021] [Indexed: 01/08/2023] Open
Abstract
Aptamers are single stranded oligonucleotides with specific recognition and binding ability to target molecules, which can be obtained by Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Aptamers have the advantages of low molecular weight, low immunogenicity, easy modification and high stability. They play promising role in promoting food safety, monitoring the environment and basic research, especially in clinical diagnosis and therapeutic drugs. To date, great achievements regarding the selection, modifications and application of aptamers have been made. However, since it is still a challenge to obtain aptamers with high affinity in a more effective way, few aptamer-based products have already successfully entered into clinical use. This review aims to provide a thorough overview of the latest advances in this rapidly developing field, focusing on aptamer screening methods for different targets, the structure of the interaction between aptamers and target substances, and the challenges and potential of current therapeutic aptamers.
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Affiliation(s)
- Xueran Xiao
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Hui Li
- Department of Urology, Peking University International Hospital, Beijing 102206, China
| | - Lijian Zhao
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China
| | - Yanfen Zhang
- Technology Transfer Center, Hebei University, Baoding 071002, China.
| | - Zhongcheng Liu
- College of Pharmaceutical Sciences, Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Institute of Life Science and Green Development, Hebei University, Baoding 071002, China.
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11
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Wu L, Wang Y, Xu X, Liu Y, Lin B, Zhang M, Zhang J, Wan S, Yang C, Tan W. Aptamer-Based Detection of Circulating Targets for Precision Medicine. Chem Rev 2021; 121:12035-12105. [PMID: 33667075 DOI: 10.1021/acs.chemrev.0c01140] [Citation(s) in RCA: 252] [Impact Index Per Article: 84.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The past decade has witnessed ongoing progress in precision medicine to improve human health. As an emerging diagnostic technique, liquid biopsy can provide real-time, comprehensive, dynamic physiological and pathological information in a noninvasive manner, opening a new window for precision medicine. Liquid biopsy depends on the sensitive and reliable detection of circulating targets (e.g., cells, extracellular vesicles, proteins, microRNAs) from body fluids, the performance of which is largely governed by recognition ligands. Aptamers are single-stranded functional oligonucleotides, capable of folding into unique tertiary structures to bind to their targets with superior specificity and affinity. Their mature evolution procedure, facile modification, and affinity regulation, as well as versatile structural design and engineering, make aptamers ideal recognition ligands for liquid biopsy. In this review, we present a broad overview of aptamer-based liquid biopsy techniques for precision medicine. We begin with recent advances in aptamer selection, followed by a summary of state-of-the-art strategies for multivalent aptamer assembly and aptamer interface modification. We will further describe aptamer-based micro-/nanoisolation platforms, aptamer-enabled release methods, and aptamer-assisted signal amplification and detection strategies. Finally, we present our perspectives regarding the opportunities and challenges of aptamer-based liquid biopsy for precision medicine.
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Affiliation(s)
- Lingling Wu
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Yidi Wang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Xing Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Yilong Liu
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Bingqian Lin
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Mingxia Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Jialu Zhang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Shuang Wan
- Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Chaoyong Yang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Collaborative Innovation Center of Chemistry for Energy Materials, The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, China
| | - Weihong Tan
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China.,Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha 410082, China.,The Cancer Hospital of the University of Chinese Academy of Sciences, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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Saito S. SELEX-based DNA Aptamer Selection: A Perspective from the Advancement of Separation Techniques. ANAL SCI 2021; 37:17-26. [PMID: 33132238 DOI: 10.2116/analsci.20sar18] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 10/22/2020] [Indexed: 11/23/2022]
Abstract
DNA aptamers, which are short, single-stranded DNA sequences that selectively bind to target substances (proteins, cells, small molecules, metal ions), can be acquired by means of the systematic evolution of ligands by exponential enrichment (SELEX) methodology. In the SELEX procedure, one of the keys for the effective acquisition of high-affinity and functional aptamer sequences is the separation stage to isolate target-bound DNA from unbound DNA in a randomized DNA library. In this review, various remarkable advancements in separation techniques for SELEX-based aptamer selection developed in this decade, are described and discussed, including CE-, microfluidic chip-, solid phase-, and FACS-based SELEX along with other methods.
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Affiliation(s)
- Shingo Saito
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo Sakura, Saitama, 338-8570, Japan.
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13
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ZHAO LP, YANG G, ZHANG XM, QU F. Development of Aptamer Screening against Proteins and Its Applications. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2020. [DOI: 10.1016/s1872-2040(20)60012-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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14
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Liu J, Feng W, Zhang W. A single-molecule study reveals novel rod-like structures formed by a thrombin aptamer repeat sequence. NANOSCALE 2020; 12:4159-4166. [PMID: 32022812 DOI: 10.1039/c9nr09054a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Thrombin aptamers (TBAs) have attracted much attention due to their various applications. The structures and properties of long ssDNA chains with multiple TBA repeat sequences are interesting and distinct from those of their monomers. Due to the complexity of the sample system, it is quite difficult to reveal the structure of such a long-chain ssDNA using traditional methods. In this work, we investigated the repeated ssDNA by using single-molecule magnetic tweezers and AFM imaging. To do that we developed the polymerase change-rolling circle amplification (PC-RCA) synthetic method and prepared two-end modified repeated ssDNA. The rod-like G4 structures formed by intramolecular stacking of the repeat sequence were for the first time identified. This novel structure is different from those higher-order quadruplex structures formed by G-tetrads or loop-mediated interactions. It is also quite interesting to find that the increase of the TBA copy number can unitize the diversity of TBA conformation to the best-fit binding structure for thrombin. The methodology developed in this work can be used for studying other repeat sequences in the genome, such as telomeric DNA as well as interactions of ssDNA with the binding molecule.
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Affiliation(s)
- Jianyu Liu
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, People's Republic of China.
| | - Wei Feng
- Institute of Atomic and Molecular Physics, Jilin University, Changchun 130012, People's Republic of China
| | - Wenke Zhang
- State Key Laboratory of Supramolecular Structure and Materials, College of Chemistry, Jilin University, Changchun 130012, People's Republic of China.
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A DNA-Based Biosensor Assay for the Kinetic Characterization of Ion-Dependent Aptamer Folding and Protein Binding. Molecules 2019; 24:molecules24162877. [PMID: 31398834 PMCID: PMC6718989 DOI: 10.3390/molecules24162877] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 11/16/2022] Open
Abstract
Therapeutic and diagnostic nucleic acid aptamers are designed to bind tightly and specifically to their target. The combination of structural and kinetic analyses of aptamer interactions has gained increasing importance. Here, we present a fluorescence-based switchSENSE aptasensor for the detailed kinetic characterization of aptamer-analyte interaction and aptamer folding, employing the thrombin-binding aptamer (TBA) as a model system. Thrombin-binding aptamer folding into a G-quadruplex and its binding to thrombin strongly depend on the type and concentration of ions present in solution. We observed conformational changes induced by cations in real-time and determined the folding and unfolding kinetics of the aptamer. The aptamer's affinity for K+ was found to be more than one order of magnitude higher than for other cations (K+ > NH4+ >> Na+ > Li+). The aptamer's affinity to its protein target thrombin in the presence of different cations followed the same trend but differed by more than three orders of magnitude (KD = 0.15 nM to 250 nM). While the stability (kOFF) of the thrombin-TBA complex was similar in all conditions, the cation type strongly influenced the association rate (kON). These results demonstrated that protein-aptamer binding is intrinsically related to the correct aptamer fold and, hence, to the presence of stabilizing ions. Because fast binding kinetics with on-rates exceeding 108 M-1s-1 can be quantified, and folding-related phenomena can be directly resolved, switchSENSE is a useful analytical tool for in-depth characterization of aptamer-ion and aptamer-protein interactions.
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Zhang Y, Lai BS, Juhas M. Recent Advances in Aptamer Discovery and Applications. Molecules 2019; 24:molecules24050941. [PMID: 30866536 PMCID: PMC6429292 DOI: 10.3390/molecules24050941] [Citation(s) in RCA: 339] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 03/03/2019] [Accepted: 03/04/2019] [Indexed: 12/22/2022] Open
Abstract
Aptamers are short, single-stranded DNA, RNA, or synthetic XNA molecules that can be developed with high affinity and specificity to interact with any desired targets. They have been widely used in facilitating discoveries in basic research, ensuring food safety and monitoring the environment. Furthermore, aptamers play promising roles as clinical diagnostics and therapeutic agents. This review provides update on the recent advances in this rapidly progressing field of research with particular emphasis on generation of aptamers and their applications in biosensing, biotechnology and medicine. The limitations and future directions of aptamers in target specific delivery and real-time detection are also discussed.
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Affiliation(s)
- Yang Zhang
- College of Science, Harbin Institute of Technology, Shenzhen 518055, China.
| | - Bo Shiun Lai
- School of Medicine, Johns Hopkins University, Baltimore, MD 21205, USA.
| | - Mario Juhas
- Institute of Medical Microbiology, University of Zurich, Gloriastrasse 28/30, CH-8006 Zurich, Switzerland.
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Lu P, Zhang D, Chai Y, Yu C, Wang X, Tang Y, Ge M, Yao L. Regulatory-sequence mechanical biosensor: A versatile platform for investigation of G-quadruplex/label-free protein interactions and tunable protein detection. Anal Chim Acta 2019; 1045:1-9. [PMID: 30454563 DOI: 10.1016/j.aca.2018.09.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/07/2018] [Accepted: 09/10/2018] [Indexed: 11/16/2022]
Abstract
Mechanical biosensors can be used to quantitatively explore DNA-protein binding mechanisms by detecting targets at low concentrations or measuring force in single-molecule force spectroscopy. However, restrictions in single-molecule manipulation and labelling protocols have hindered the application for bulk analysis of label-free protein detection. Here, we present the integration of molecular force measurement and finely tunable detection of label-free proteins into one mechanical sensor. Regulatory-sequence force spectroscopy was obtained to investigate the binding force of DNA G-quadruplexes (GQ) and label-free protein. The dual control of regulatory sequences and mechanical forces induces the structure switching from DNA duplex to GQ/protein complex. It exhibits a synergistic effect, enabling the rational fine-tuning of the dynamic range for biosensing protein concentrations over eight orders of magnitude. Furthermore, this method was exploited to estimate the stability of the human telomeric DNA GQ by Ku protein and ligand methylpyridostatin. The results revealed that human telomeric GQ has two different binding sites for Ku protein and ligand. Force spectroscopy integrating label-free force measurement and tunable target detection holds great promise for use in biosensing, drug screening, targeted therapies, DNA nanotechnology, and fields in which GQ are of rapidly increasing importance.
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Affiliation(s)
- Pan Lu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Di Zhang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yahong Chai
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chanchan Yu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiuyu Wang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yalin Tang
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Maofa Ge
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Yao
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Ma Y, Li X, Li W, Liu Z. Glycan-Imprinted Magnetic Nanoparticle-Based SELEX for Efficient Screening of Glycoprotein-Binding Aptamers. ACS APPLIED MATERIALS & INTERFACES 2018; 10:40918-40926. [PMID: 30379519 DOI: 10.1021/acsami.8b14441] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Nucleic acid aptamers, as useful alternatives of antibodies, have found a large range of promising applications such as affinity separation and bioassays. The screening of aptamers is critical for their applications. Aptamers are often screened by an in vitro methodology called SELEX (systematic evolution of ligands by exponential enrichment). Although numerous SELEX methods have been established to facilitate the selection, new efficient selection methods are still much needed. Molecularly imprinted polymers, which are antibody alternatives at the material level and competitors of aptamers, have not been used as a platform for aptamer selection yet so far. In this study, a glycan-imprinted magnetic nanoparticles (MNPs)-based SELEX was developed to efficiently screen aptamers against glycoproteins. Glycan-imprinted MNPs were used as an affinity interface to bind target glycoprotein, and then the target glycoprotein-bound MNPs were used as an affinity substrate for aptamer selection. The glycan-imprinted MNPs were synthesized by a state-of-the-art imprinting approach called boronate affinity controllable oriented surface imprinting. The glycan-imprinted MNPs exhibited high affinity and specificity and therefore allowed preferential binding toward target glycoproteins while excluding unwanted species. Two representative glycoproteins, including RNase B and transferrin, were employed as target glycoproteins, and aptamers with high affinity and specificity toward the two target glycoproteins were screened out in 3 rounds. This method exhibited some merits, such as high affinity, fast speed, and avoiding negative screening. Therefore, the glycan-imprinted MNP-based SELEX approach holds great values for the efficient screening of high-performance aptamers.
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Affiliation(s)
- Yanyan Ma
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Xinglin Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Wei Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
| | - Zhen Liu
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , China
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Recent Advances in SELEX Technology and Aptamer Applications in Biomedicine. Int J Mol Sci 2017; 18:ijms18102142. [PMID: 29036890 PMCID: PMC5666824 DOI: 10.3390/ijms18102142] [Citation(s) in RCA: 249] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 12/11/2022] Open
Abstract
Aptamers are short DNA/RNA oligonucleotides capable of binding to target molecules with high affinity and specificity. The process of selecting an aptamer is called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Thanks to the inherit merits, aptamers have been used in a wide range of applications, including disease diagnosis, targeted delivery agents and therapeutic uses. To date, great achievements regarding the selection, modifications and application of aptamers have been made. However, few aptamer-based products have already successfully entered into clinical and industrial use. Besides, it is still a challenge to obtain aptamers with high affinity in a more efficient way. Thus, it is important to comprehensively review the current shortage and achievement of aptamer-related technology. In this review, we first present the limitations and notable advances of aptamer selection. Then, we compare the different methods used in the kinetic characterization of aptamers. We also discuss the impetus and developments of the clinical application of aptamers.
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20
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Volk DE, Lokesh GLR. Development of Phosphorothioate DNA and DNA Thioaptamers. Biomedicines 2017; 5:E41. [PMID: 28703779 PMCID: PMC5618299 DOI: 10.3390/biomedicines5030041] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 07/03/2017] [Accepted: 07/11/2017] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid aptamers are short RNA- or DNA-based affinity reagents typically selected from combinatorial libraries to bind to a specific target such as a protein, a small molecule, whole cells or even animals. Aptamers have utility in the development of diagnostic, imaging and therapeutic applications due to their size, physico-chemical nature and ease of synthesis and modification to suit the application. A variety of oligonucleotide modifications have been used to enhance the stability of aptamers from nuclease degradation in vivo. The non-bridging oxygen atoms of the phosphodiester backbones of RNA and DNA aptamers can be substituted with one or two sulfur atoms, resulting in thioaptamers with phosphorothioate or phosphorodithioate linkages, respectively. Such thioaptamers are known to have increased binding affinity towards their target, as well as enhanced resistance to nuclease degradation. In this review, we discuss the development of phosphorothioate chemistry and thioaptamers, with a brief review of selection methods.
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Affiliation(s)
- David E Volk
- McGovern Medical School, Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, University of Texas Health Science Center, Houston, TX 77030, USA.
| | - Ganesh L R Lokesh
- McGovern Medical School, Brown Foundation Institute of Molecular Medicine for the Prevention of Human Diseases, University of Texas Health Science Center, Houston, TX 77030, USA.
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Abstract
Nucleic acid aptamers, often termed 'chemical antibodies', are functionally comparable to traditional antibodies, but offer several advantages, including their relatively small physical size, flexible structure, quick chemical production, versatile chemical modification, high stability and lack of immunogenicity. In addition, many aptamers are internalized upon binding to cellular receptors, making them useful targeted delivery agents for small interfering RNAs (siRNAs), microRNAs and conventional drugs. However, several crucial factors have delayed the clinical translation of therapeutic aptamers, such as their inherent physicochemical characteristics and lack of safety data. This Review discusses these challenges, highlighting recent clinical developments and technological advances that have revived the impetus for this promising class of therapeutics.
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Affiliation(s)
- Jiehua Zhou
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
| | - John Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
- Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, 1500 E. Duarte Rd, Duarte, CA 91010, USA
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Sharma TK, Bruno JG, Dhiman A. ABCs of DNA aptamer and related assay development. Biotechnol Adv 2017; 35:275-301. [PMID: 28108354 DOI: 10.1016/j.biotechadv.2017.01.003] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 11/19/2016] [Accepted: 01/17/2017] [Indexed: 12/14/2022]
Abstract
This review is intended to guide the novice in aptamer research and development to understand virtually all of the aptamer development options and currently available assay modalities. Aptamer development topics range from discussions of basic and advanced versions of Systematic Evolution of Ligands by EXponential Enrichment (SELEX) and SELEX variations involving incorporation of exotic unnatural nucleotides to expand library diversity for even greater aptamer affinity and specificity to improved next generation methods of DNA sequencing, screening and tracking aptamer development throughout the SELEX process and characterization of lead aptamer candidates. Aptamer assay development topics include descriptions of various colorimetric and fluorescent assays in microplates or on membranes including homogeneous beacon and multiplexed Fluorescence Resonance Energy Transfer (FRET) assays. Finally, a discussion of the potential for marketing successful aptamer-based assays or test kits is included.
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Affiliation(s)
- Tarun Kumar Sharma
- Center for Biodesign and Diagnostics, Translational Health Science and Technology Institute, Faridabad, Haryana 121001, India; AptaBharat Innovation Private Limited, Translational Health Science and Technology Institute Incubator, Haryana 121001, India.
| | - John G Bruno
- Operational Technologies Corporation, 4100 NW Loop 410, Suite, 230, San Antonio, TX 78229, USA..
| | - Abhijeet Dhiman
- Department of Biotechnology, All India Institute of Medical Sciences, New Delhi 110029, India.; Faculty of Pharmacy, Uttarakhand Technical University, Dehradun 248007, Uttarakhand, India
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23
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Ospina-Villa JD, Zamorano-Carrillo A, Castañón-Sánchez CA, Ramírez-Moreno E, Marchat LA. Aptamers as a promising approach for the control of parasitic diseases. Braz J Infect Dis 2016; 20:610-618. [PMID: 27755981 PMCID: PMC9427573 DOI: 10.1016/j.bjid.2016.08.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/15/2016] [Accepted: 08/16/2016] [Indexed: 01/31/2023] Open
Abstract
Aptamers are short single-stranded RNA or DNA oligonucleotides that are capable of binding various biological targets with high affinity and specificity. Their identification initially relies on a molecular process named SELEX (Systematic Evolution of Ligands by EXponential enrichment) that has been later modified in order to improve aptamer sensitivity, minimize duration and cost of the assay, as well as increase target types. Several biochemical modifications can help to enhance aptamer stability without affecting significantly target interaction. As a result, aptamers have generated a large interest as promising tools to compete with monoclonal antibodies for detection and inhibition of specific markers of human diseases. One aptamer-based drug is currently authorized and several others are being clinically evaluated. Despite advances in the knowledge of parasite biology and host–parasite interactions from “omics” data, protozoan parasites still affect millions of people around the world and there is an urgent need for drug target discovery and novel therapeutic concepts. In this context, aptamers represent promising tools for pathogen identification and control. Recent studies have reported the identification of “aptasensors” for parasite diagnosis, and “intramers” targeting intracellular proteins. Here we discuss various strategies that have been employed for intracellular expression of aptamers and expansion of their possible application, and propose that they may be suitable for the clinical use of aptamers in parasitic infections.
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Affiliation(s)
- Juan David Ospina-Villa
- Instituto Politécnico Nacional, Escuela Nacional de Medicina y Homeopatía, Ciudad de Mexico, Mexico
| | | | - Carlos A Castañón-Sánchez
- Hospital Regional de Alta Especialidad de Oaxaca, Subdirección de Enseñanza e Investigación, Oaxaca, Mexico
| | - Esther Ramírez-Moreno
- Instituto Politécnico Nacional, Escuela Nacional de Medicina y Homeopatía, Ciudad de Mexico, Mexico
| | - Laurence A Marchat
- Instituto Politécnico Nacional, Escuela Nacional de Medicina y Homeopatía, Ciudad de Mexico, Mexico.
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Chumakov AM, Yuhina ES, Frolova EI, Kravchenko JE, Chumakov SP. Expanding the application potential of DNA aptamers by their functionalization. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1068162016010027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Prakash JS, Rajamanickam K. Aptamers and Their Significant Role in Cancer Therapy and Diagnosis. Biomedicines 2015; 3:248-269. [PMID: 28536411 PMCID: PMC5344239 DOI: 10.3390/biomedicines3030248] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 08/07/2015] [Indexed: 02/07/2023] Open
Abstract
Aptamers are nucleic acid/peptide molecules that can be generated by a sophisticated, well-established technique known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Aptamers can interact with their targets through structural recognition, as in antibodies, though with higher specificity. With this added advantage, they can be made useful for clinical applications such as targeted therapy and diagnosis. In this review, we have discussed the steps involved in SELEX process and modifications executed to attain high affinity nucleic acid aptamers. Moreover, our review also highlights the therapeutic applications of aptamer functionalized nanoparticles and nucleic acids as chemo-therapeutic agents. In addition, we have described the development of "aptasensor" in clinical diagnostic application for detecting cancer cells and the use of aptamers in different routine imaging techniques, such as Positron Emission Tomography/Computed Tomography, Ultrasound, and Magnetic Resonance Imaging.
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Affiliation(s)
- Joy Sebastian Prakash
- Faculty of Allied Health Sciences (FAHS), Chettinad Academy of Research and Education, Kelambakkam, Chennai 603103, Tamil Nadu, India.
| | - Karunanithi Rajamanickam
- Faculty of Allied Health Sciences (FAHS), Chettinad Academy of Research and Education, Kelambakkam, Chennai 603103, Tamil Nadu, India.
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Friedman AD, Kim D, Liu R. Highly stable aptamers selected from a 2'-fully modified fGmH RNA library for targeting biomaterials. Biomaterials 2015; 36:110-23. [PMID: 25443790 DOI: 10.1016/j.biomaterials.2014.08.046] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 08/29/2014] [Indexed: 11/26/2022]
Abstract
When developed as targeting ligands for the in vivo delivery of biomaterials to biological systems, RNA aptamers immediately face numerous obstacles, in particular nuclease degradation and post-selection 2' modification. This study aims to develop a novel class of highly stable, 2'-fully modified RNA aptamers that are ideal for the targeted delivery of biomaterials. We demonstrated the facile transcription of a fGmH (2'-F-dG, 2'-OMe-dA/dC/dU) RNA library with unexpected hydrophobicity, the direct selection of aptamers from a fGmH RNA library that bind Staphylococcus aureus Protein A (SpA) as a model target, and the superior nuclease and serum stability of these aptamers compared to 2'-partially modified RNA variants. Characterizations of fGmH RNA aptamers binding to purified SpA and to endogenous SpA present on the surface of S. aureus cells demonstrate fGmH RNA aptamer selectivity and stability. Significantly, fGmH RNA aptamers were able to functionalize, stabilize, and specifically deliver aggregation-prone silver nanoparticles (AgNPs) to S. aureus with SpA-dependent antimicrobial effects. This study describes a novel aptamer class with considerable potential to improve the in vivo applicability of nucleic acid-based affinity molecules to biomaterials.
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Zhou W, Huang PJJ, Ding J, Liu J. Aptamer-based biosensors for biomedical diagnostics. Analyst 2015; 139:2627-40. [PMID: 24733714 DOI: 10.1039/c4an00132j] [Citation(s) in RCA: 337] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aptamers are single-stranded nucleic acids that selectively bind to target molecules. Most aptamers are obtained through a combinatorial biology technique called SELEX. Since aptamers can be isolated to bind to almost any molecule of choice, can be readily modified at arbitrary positions and they possess predictable secondary structures, this platform technology shows great promise in biosensor development. Over the past two decades, more than one thousand papers have been published on aptamer-based biosensors. Given this progress, the application of aptamer technology in biomedical diagnosis is still in a quite preliminary stage. Most previous work involves only a few model aptamers to demonstrate the sensing concept with limited biomedical impact. This Critical Review aims to summarize progress that might enable practical applications of aptamers for biological samples. First, general sensing strategies based on the unique properties of aptamers are summarized. Each strategy can be coupled to various signaling methods. Among these, a few detection methods including fluorescence lifetime, flow cytometry, upconverting nanoparticles, nanoflare technology, magnetic resonance imaging, electronic aptamer-based sensors, and lateral flow devices have been discussed in more detail since they are more likely to work in a complex sample matrix. The current limitations of this field include the lack of high quality aptamers for clinically important targets. In addition, the aptamer technology has to be extensively tested in a clinical sample matrix to establish reliability and accuracy. Future directions are also speculated to overcome these challenges.
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Affiliation(s)
- Wenhu Zhou
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Central South University, Tongzipo Road #172, Changsha 410013, Hunan, PR China.
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28
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Zhang Y, Li X, Zou R, Xue Y, Lou X, He M. Bovine thrombin enhances the efficiency and specificity of polymerase chain reaction. Biotechniques 2014; 57:289-94. [PMID: 25495728 DOI: 10.2144/000114237] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 09/25/2014] [Indexed: 11/23/2022] Open
Abstract
The polymerase chain reaction (PCR) has become one of the central techniques in molecular biology since its invention. However, PCR can be fraught with difficulties in various situations, and it is desirable to find novel PCR enhancers suitable for universal applications. Here we show that bovine thrombin (BT), a well-known coagulation protein, is exceptionally effective at preventing the formation of primer dimers and enhancing the formation of the desired PCR products. The PCR enhancement effects of BT were demonstrated by testing various types of samples, including low-copy synthetic single-stranded DNAs (ssDNAs), synthetic ssDNA pools, human genomic DNA, and hepatitis B virus genomic DNA. In addition, BT was also able to effectively relieve PCR inhibition by nanomaterial inhibitors such as gold nanoparticles (AuNPs) and graphene oxide (GO). Compared with BSA, one of the most popular PCR enhancers, BT was more effective and required concentrations 18-178 times less than that of BSA to achieve a similar level of PCR enhancement.
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Affiliation(s)
- Ying Zhang
- Department of Chemistry, Capital Normal University, Beijing, China
| | - Xiaoning Li
- Department of Chemistry, Capital Normal University, Beijing, China
| | - Ruxing Zou
- Department of Chemistry, Capital Normal University, Beijing, China
| | - Ying Xue
- Beijing Municipal Center for Disease Prevention and Control, Beijing, China
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Beijing, China
| | - Miao He
- School of Environment, Tsinghua University, Beijing, China
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Liao J, Liu B, Liu J, Zhang J, Chen K, Liu H. Cell-specific aptamers and their conjugation with nanomaterials for targeted drug delivery. Expert Opin Drug Deliv 2014; 12:493-506. [PMID: 25430795 DOI: 10.1517/17425247.2015.966681] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
INTRODUCTION Aptamers are short, single-stranded DNA or RNA sequences that can fold into complex secondary and tertiary structures and bind to various target molecules with high affinity and specificity. These properties, as well as rapid tissue penetration and ease of chemical modification, make aptamers ideal recognition elements for in vivo targeted drug delivery and attractive molecules for use in disease diagnosis and therapy. AREAS COVERED The general properties of aptamers as well as advantages over their counterpart antibodies are briefly discussed. Next, aptamer selection by cell- systematic evolution of ligands by exponential enrichment is described in detail. Finally, the review summarizes recent progress in the field of targeted drug delivery based on aptamers and their conjugation to liposomes, micelles and other nanomaterials. EXPERT OPINION Advances in nanotechnology have led to new and improved nanomaterials for biomedical applications. Conjugation of nanoparticles (NPs) with aptamers exploits both technologies, making aptamer-NP conjugates ideal agents for drug delivery with proven therapeutic effects and the reduction of toxicity to normal tissue. The use of multivalent aptamer-conjugated nanomaterials represents one of the new directions for drug development in the future; as such, continuing studies of these multivalent aptamers and bioconjugates should result in important clinical applications in targeted drug delivery.
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Affiliation(s)
- Jie Liao
- Central South University, Xiang Ya Hospital , Changsha , China
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30
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Miyachi Y, Ogino C, Kondo A. Structural evaluation of the DNA aptamer for ATP DH25.42 by AFM. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2014; 33:31-9. [PMID: 24588754 DOI: 10.1080/15257770.2013.857029] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Atomic force microscopy (AFM) can dynamically detect the adhesion or affinity force between a sample surface and a cantilever. This feature could be used to analyze bio-molecular interactions between a DNA aptamer and a target molecule. In this study, the binding force between adenosine triphosphate (ATP) and the anti-ATP DNA aptamer DH25.42, based on structural changes was measured using AFM. In addition, the relationship between the cations in the binding buffer, and the affinity and structure formation of the DNA aptamer was also evaluated using AFM and circular dichroism (CD) spectrum analysis. As a result, the specific force between DH25.42 and ATP could be measured by AFM. Moreover, it was suggested that Mg(2+) in the binding buffer was critical to the binding function of DH25.42 to ATP.
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Affiliation(s)
- Yusuke Miyachi
- a Department of Chemical Science and Engineering , Graduate School of Engineering, Kobe University , Nada , Kobe , Japan
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Ivanov YD, Bukharina NS, Pleshakova TO, Frantsuzov PA, Andreeva EY, Kaysheva AL, Zgoda VG, Izotov AA, Pavlova TI, Ziborov VS, Radko SP, Moshkovskii SA, Archakov AI. Atomic force microscopy fishing and mass spectrometry identification of gp120 on immobilized aptamers. Int J Nanomedicine 2014; 9:4659-70. [PMID: 25336946 PMCID: PMC4200055 DOI: 10.2147/ijn.s66946] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Atomic force microscopy (AFM) was applied to carry out direct and label-free detection of gp120 human immunodeficiency virus type 1 envelope glycoprotein as a target protein. This approach was based on the AFM fishing of gp120 from the analyte solution using anti-gp120 aptamers immobilized on the AFM chip to count gp120/aptamer complexes that were formed on the chip surface. The comparison of image contrasts of fished gp120 against the background of immobilized aptamers and anti-gp120 antibodies on the AFM images was conducted. It was shown that an image contrast of the protein/aptamer complexes was two-fold higher than the contrast of the protein/antibody complexes. Mass spectrometry identification provided an additional confirmation of the target protein presence on the AFM chips after biospecific fishing to avoid any artifacts.
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Affiliation(s)
- Yuri D Ivanov
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Natalia S Bukharina
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Tatyana O Pleshakova
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Pavel A Frantsuzov
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Elena Yu Andreeva
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Anna L Kaysheva
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
- PostgenTech Ltd., Moscow, Russia
| | - Victor G Zgoda
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Alexander A Izotov
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Tatyana I Pavlova
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Vadim S Ziborov
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Sergey P Radko
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Sergei A Moshkovskii
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
| | - Alexander I Archakov
- Department of Personalized Medicine, Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Moscow, Russia
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New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e183. [PMID: 25093707 PMCID: PMC4221594 DOI: 10.1038/mtna.2014.34] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 06/10/2014] [Indexed: 12/24/2022]
Abstract
Single-stranded oligonucleotide aptamers have attracted great attention in the past decade because of their diagnostic and therapeutic potential. These versatile, high affinity and specificity reagents are selected by an iterative in vitro process called SELEX, Systematic Evolution of Ligands by Exponential Enrichment. Numerous SELEX methods have been developed for aptamer selections; some that are simple and straightforward, and some that are specialized and complicated. The method of SELEX is crucial for selection of an aptamer with desired properties; however, success also depends on the starting aptamer library, the target molecule, aptamer enrichment monitoring assays, and finally, the analysis and characterization of selected aptamers. Here, we summarize key recent developments in aptamer selection methods, as well as other aspects of aptamer selection that have significant impact on the outcome. We discuss potential pitfalls and limitations in the selection process with an eye to aid researchers in the choice of a proper SELEX strategy, and we highlight areas where further developments and improvements are desired. We believe carefully designed multiplexed selection methods, when complemented with high-throughput downstream analysis and characterization assays, will yield numerous high-affinity aptamers to protein and small molecule targets, and thereby generate a vast array of reagents for probing basic biological mechanisms and implementing new diagnostic and therapeutic applications in the near future.
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Jiao F, Fan H, Yang G, Zhang F, He P. Directly investigating the interaction between aptamers and thrombin by atomic force microscopy. J Mol Recognit 2014; 26:672-8. [PMID: 24277612 DOI: 10.1002/jmr.2312] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2013] [Revised: 07/21/2013] [Accepted: 08/21/2013] [Indexed: 11/06/2022]
Abstract
Aptamers are single-stranded nucleic acid molecules that can be used for protein recognition, detection, and inhibition. Over the past decades, two thrombin-binding aptamers (15apt and 27apt) were reported by systemic evolution of ligands by exponential enrichment technique. Though many studies have been reported about the interactions between the aptamers and thrombin by atomic force microscopy, the thrombins in those studies were all immobilized by chemical agents. Recently, we developed a new method using atomic force microscopy to directly investigate the specific interactions between thrombin and its two aptamers without immobilizing the thrombin. Furthermore, the unbinding dynamics and dissociation energy landscapes of aptamer/thrombin were discussed. The results indicate that the underlying interaction mechanisms of thrombin with its two aptamers will be similar despite that the structures of 15apt and 27apt are different in buffer solution.
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Affiliation(s)
- Fang Jiao
- Department of Chemistry, East China Normal University, 500 Dongchuan Road, Shanghai, 200241, China
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Wang Q, Liu W, Xing Y, Yang X, Wang K, Jiang R, Wang P, Zhao Q. Screening of DNA aptamers against myoglobin using a positive and negative selection units integrated microfluidic chip and its biosensing application. Anal Chem 2014; 86:6572-9. [PMID: 24914856 DOI: 10.1021/ac501088q] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
An aptamer screening method using a positive and negative selection units integrated microfluidic chip was introduced. Here, myoglobin (Myo), one of the early markers to increase after acute myocardial infarction, was used as the model. After 7-round selection, the aptamers, which exhibited dissociation constants (K(d)) in the nanomolar range (from 4.93 to 6.38 nM), were successfully obtained using a positive and negative selection units integrated microfluidic chip. The aptamer with the highest affinity (K(d) = 4.93 nM) was then used for the fabrication of a label-free supersandwich electrochemical biosensor for Myo detection based on target-induced aptamer displacement. The detection limit of this aptamer-based electrochemical biosensor was 10 pM, which was significantly lower than that of those previous antibody-based biosensors for Myo detection. This work may not only develop a strategy for screening aptamer but also offer promising alternatives to the traditional analytical and immunological methods for Myo detection.
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Affiliation(s)
- Qing Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University , Changsha, Hunan 410082, China
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Yoshida W, Abe K, Ikebukuro K. Emerging techniques employed in aptamer-based diagnostic tests. Expert Rev Mol Diagn 2014; 14:143-51. [PMID: 24400930 DOI: 10.1586/14737159.2014.868307] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Since aptamers were reported in 1990, research into the applications of aptamers, particularly diagnostic applications, has been growing. Aptamers can act as recognition elements instead of antibodies. In this regard, aptamers have unique characteristics because they are composed of nucleic acids. Intra- and intermolecular interactions of nucleic acids can be easily tailored following straightforward hybridization rules. Nucleic acids can be enzymatically replicated and their sequences can be determined using high-throughput methods. Using these properties, ligand-induced structural change-based aptamer sensors for homogeneous assays, polymerase- and/or nuclease-combined aptamer sensors for ultrasensitive assays, and microarray/next-generation sequencing-based aptamer sensors for multiplexed assays have been developed. This article reviews these unique aptamer sensors, demonstrating their great potential for diagnostic applications.
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Affiliation(s)
- Wataru Yoshida
- Department of Biotechnology and Life Science, Tokyo University of Agriculture & Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
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Han L, Wang P, Zhao G, Wang H, Wang M, Chen J, Tong T. Upregulation of SIRT1 by 17β-estradiol depends on ubiquitin-proteasome degradation of PPAR-γ mediated by NEDD4-1. Protein Cell 2013; 4:310-21. [PMID: 23549616 DOI: 10.1007/s13238-013-2124-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
17β-estradiol (E2) treatment of cells results in an upregulation of SIRT1 and a down-regulation of PPARγ. The decrease in PPARγ expression is mediated by increased degradation of PPARγ. Here we report that PPARγ is ubiquitinated by HECT E3 ubiquitin ligase NEDD4-1 and degraded, along with PPARγ, in response to E2 stimulation. The PPARγ interacts with ubiquitin ligase NEDD4-1 through a conserved PPXY-WW binding motif. The WW3 domain in NEDD4-1 is critical for binding to PPARΓ. NEDD4-1 overexpression leads to PPARγ ubiquitination and reduced expression of PPARγ. Conversely, knockdown of NEDD4-1 by specific siRNAs abolishes PPARΓ ubiquitination. These data indicate that NEDD4-1 is the E3 ubiquitin ligase responsible for PPARγ ubiquitination. Here, we show that NEDD4-1 delays cellular senescence by degrading PPARΓ expression. Taken together, our data show that E2 could upregulate SIRT1 expression via promoting the PPARΓ ubiquitination-proteasome degradation pathway to delay the process of cell senescence.
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Affiliation(s)
- Limin Han
- Peking University Research Center on Aging, Peking University Health Science Center, Beijing 100191, China
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Park JW, Jin Lee S, Choi EJ, Kim J, Song JY, Bock Gu M. An ultra-sensitive detection of a whole virus using dual aptamers developed by immobilization-free screening. Biosens Bioelectron 2013; 51:324-9. [PMID: 23994614 DOI: 10.1016/j.bios.2013.07.052] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2013] [Revised: 07/26/2013] [Accepted: 07/26/2013] [Indexed: 12/27/2022]
Abstract
In this study, we successfully developed a ssDNA aptamer pairs by using an advanced immobilization-free SELEX method with affinity-based selection and counter-screening process at every round. By implementing this method, two different aptamers specifically binding to bovine viral diarrhea virus type 1(BVDV type 1) with high affinity were successfully screened. This aptamer pair was applied to ultrasensitive detection platform for BVDV type 1 in a sandwich manner. The ultrasensitive detection of BVDV type 1 using one of aptamers conjugated with gold nanoparticles was obtained in aptamer-aptamer sandwich type sensing format, with the limit of detection of 800 copies/ml, which is comparable to a real-time PCR method.
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Affiliation(s)
- Jee-Woong Park
- College of Life Sciences and Biotechnology, Korea University, Anam-dong, Seongbuk-gu, Seoul 136-713, South Korea
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Lou X, Zhang Y. Mechanism studies on nanoPCR and applications of gold nanoparticles in genetic analysis. ACS APPLIED MATERIALS & INTERFACES 2013; 5:6276-84. [PMID: 23734951 DOI: 10.1021/am4013209] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Recently, the applications of nanomaterial-assisted polymerase chain reaction (nanoPCR) have received considerable attention. Several potential mechanisms have been proposed, but mainly according to the results of PCR assays under specific conditions and lacking direct and general evidence. The mechanism of nanoPCR has not been elucidated yet. Here, taking gold nanoparticles (AuNPs) as an example, we report the three general effects of AuNPs: (1) AuNPs adsorb polymerase and modulate the amount of active polymerase in PCR, which was directly demonstrated by a simple and straightforward colorimetric assay and the dynamic light scattering measurements. (2) AuNPs adsorb primers and decrease the melting temperatures (Tm) of the duplexes formed with perfectly matched and mismatched primers and increase the Tm difference between them. (3) AuNPs adsorb PCR products and facilitate the dissociation of them in the denaturing step. All these effects were confirmed by addition of a rationally selected surface adsorbent, bovine thrombin, to highly efficiently modulate the surface adsorption of PCR components. These findings suggested that AuNPs should have multiple effects on PCR: (1) to regulate PCR in a case-by-case way via modulating the amount of active polymerase in PCR; (2) to improve PCR specificity in the annealing step via increasing the Tm difference between the perfectly matched and mismatched primers; (3) to improve PCR efficiency via speeding up the dissociation of the PCR products in the denaturing step. Taken together, we proposed the mechanism of nanoPCR is that the surface interaction of PCR components (polymerase, primers, and products) with AuNPs regulates nanoPCR. We further demonstrated that the applications of these findings improve the PCR of the amelogenin genes and Hepatitis B virus gene for genetic analysis. These findings could also provide helpful insight for the applications of other nanomaterials in nanoPCR.
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Affiliation(s)
- Xinhui Lou
- Department of Chemistry, Capital Normal University, Beijing, China.
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Wilson R, Cossins A, Nicolau DV, Missailidis S. The selection of DNA aptamers for two different epitopes of thrombin was not due to different partitioning methods. Nucleic Acid Ther 2012; 23:88-92. [PMID: 23216233 DOI: 10.1089/nat.2012.0386] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Nearly all aptamers identified so far for any given target molecule have been specific for the same binding site (epitope). The most notable exception to the 1 aptamer per target molecule rule is the pair of DNA aptamers that bind to different epitopes of thrombin. This communication refutes the suggestion that these aptamers exist because different partitioning methods were used when they were selected. The possibility that selection of these aptamers was biased by conflicting secondary structures was also investigated and found not to contribute. The preparation of protein-coated magnetic beads for systematic evolution of ligands by exponential enrichment (SELEX) and the different specificities of the thrombin aptamers for the α and β forms of thrombin are also reported.
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Affiliation(s)
- Robert Wilson
- Institute of Integrative Biology, Liverpool University, Liverpool, United Kingdom.
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Challenges and opportunities for small molecule aptamer development. J Nucleic Acids 2012; 2012:748913. [PMID: 23150810 PMCID: PMC3488411 DOI: 10.1155/2012/748913] [Citation(s) in RCA: 286] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2012] [Accepted: 09/08/2012] [Indexed: 12/14/2022] Open
Abstract
Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.
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Abstract
Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.
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Abstract
IMPORTANCE OF THE FIELD Therapeutic aptamers are synthetic, structured oligonucleotides that bind to a very broad range of targets with high affinity and specificity. They are an emerging class of targeting ligand that show great promise for treating a number of diseases. A series of aptamers currently in various stages of clinical development highlights the potential of aptamers for therapeutic applications. AREAS COVERED IN THIS REVIEW This review covers in vitro selection of oligonucleotide ligands, called aptamers, from a combinatorial library using the Systematic Evolution of Ligands by Exponential Enrichment process as well as the other known strategies for finding aptamers against various targets. WHAT THE READER WILL GAIN Readers will gain an understanding of the highly useful strategies for successful aptamer discovery. They may also be able to combine two or more of the presented strategies for their aptamer discovery projects. TAKE HOME MESSAGE Although many processes are available for discovering aptamers, it is not easy to discover an aptamer candidate that is ready to move toward pharmaceutical drug development. It is also apparent that there have been relatively few therapeutic advances and clinical trials undertaken due to the small number of companies that participate in aptamer development.
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Zhu Y, Chandra P, Ban C, Shim YB. Electrochemical Evaluation of Binding Affinity for Aptamer Selection Using the Microarray Chip. ELECTROANAL 2012. [DOI: 10.1002/elan.201100734] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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44
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Loakes D. Nucleotides and nucleic acids; oligo- and polynucleotides. ORGANOPHOSPHORUS CHEMISTRY 2012. [DOI: 10.1039/9781849734875-00169] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- David Loakes
- Medical Research Council Laboratory of Molecular Biology, Hills Road Cambridge CB2 2QH UK
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Marimuthu C, Tang TH, Tominaga J, Tan SC, Gopinath SCB. Single-stranded DNA (ssDNA) production in DNA aptamer generation. Analyst 2012; 137:1307-15. [PMID: 22314701 DOI: 10.1039/c2an15905h] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The discovery that synthetic short chain nucleic acids are capable of selective binding to biological targets has made them to be widely used as molecular recognition elements. These nucleic acids, called aptamers, are comprised of two types, DNA and RNA aptamers, where the DNA aptamer is preferred over the latter due to its stability, making it widely used in a number of applications. However, the success of the DNA selection process through Systematic Evolution of Ligands by Exponential Enrichment (SELEX) experiments is very much dependent on its most critical step, which is the conversion of the dsDNA to ssDNA. There is a plethora of methods available in generating ssDNA from the corresponding dsDNA. These include asymmetric PCR, biotin-streptavidin separation, lambda exonuclease digestion and size separation on denaturing-urea PAGE. Herein, different methods of ssDNA generation following the PCR amplification step in SELEX are reviewed.
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Affiliation(s)
- Citartan Marimuthu
- Infectious Disease Cluster, Advanced Medical & Dental Institute (AMDI), Universiti Sains Malaysia, 13200, Kepala Batas, Penang, Malaysia
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Neundlinger I, Poturnayova A, Karpisova I, Rankl C, Hinterdorfer P, Snejdarkova M, Hianik T, Ebner A. Characterization of enhanced monovalent and bivalent thrombin DNA aptamer binding using single molecule force spectroscopy. Biophys J 2012; 101:1781-7. [PMID: 21961605 DOI: 10.1016/j.bpj.2011.07.054] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Revised: 07/27/2011] [Accepted: 07/28/2011] [Indexed: 11/15/2022] Open
Abstract
Thrombin aptamer binding strength and stability is dependent on sterical parameters when used for atomic force microscopy sensing applications. Sterical improvements on the linker chemistry were developed for high-affinity binding. For this we applied single molecule force spectroscopy using two enhanced biotinylated thrombin aptamers, BFF and BFA immobilized on the atomic force microscopy tip via streptavidin. BFF is a dimer composed of two single-stranded aptamers (aptabody) connected to each other by a complementary sequence close to the biotinylated end. In contrast, BFA consists of a single DNA strand and a complementary strand in the supporting biotinylated part. By varying the pulling velocity in force-distance cycles the formed thrombin-aptamer complexes were ruptured at different force loadings allowing determination of the energy landscape. As a result, BFA aptamer showed a higher binding force at the investigated loading rates and a significantly lower dissociation rate constant, k(off), compared to BFF. Moreover, the potential of the aptabody BFF to form a bivalent complex could clearly be demonstrated.
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47
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Ge L, Jin G, Fang X. Investigation of the interaction between a bivalent aptamer and thrombin by AFM. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:707-713. [PMID: 22103891 DOI: 10.1021/la203954x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Aptamers are a new class of molecular probes for protein recognition, detection, and inhibition. Multivalent aptamer-protein binding through aptamer assembly has been currently developed as an effective way to achieve higher protein affinity and selectivity. In this study, the specific interaction between bivalent aptamer Bi-8S and thrombin has been measured directly and quantitatively by atomic force microscopy to investigate the unbinding dynamics and dissociation energy landscape of the multivalent interaction. Bivalent aptamer Bi-8S contains thrombin's two aptamers, 15apt and 27apt, which are linked by eight spacer phosphoramidites. The results revealed the sequential dissociation of the two aptamers. Moreover, the dynamic force spectroscopy data revealed that the 27apt's binding to the thrombin remains largely unaffected by the eight-spacer phosphoramidites within Bi-8S. In contrast, the eight-spacer phosphoramidites stabilized the 15apt-thrombin binding.
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Affiliation(s)
- Lin Ge
- Institute of Biophysics, Chinese Academy of Sciences, 15 Datun Road, Chaoyang District, 100101 Beijing, China
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48
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Challenges and opportunities for small molecule aptamer development. J Nucleic Acids 2012; 2012:748913. [PMID: 23150810 PMCID: PMC3488411 DOI: 10.1155/2012/748913;+10.1155/2012/748913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Abstract
Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.
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49
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Mascini M, Palchetti I, Tombelli S. Nucleic acid and peptide aptamers: fundamentals and bioanalytical aspects. Angew Chem Int Ed Engl 2011; 51:1316-32. [PMID: 22213382 DOI: 10.1002/anie.201006630] [Citation(s) in RCA: 244] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Indexed: 12/11/2022]
Abstract
In recent years new nucleic acid and protein-based combinatorial molecules have attracted the attention of researchers working in various areas of science, ranging from medicine to analytical chemistry. These molecules, called aptamers, have been proposed as alternatives to antibodies in many different applications. The aim of this Review is to illustrate the peculiarities of these combinatorial molecules which have initially been explored for their importance in molecular medicine, but have enormous potential in other biotechnological fields historically dominated by antibodies, such as bioassays. A description of these molecules is given, and the methods for their selection and production are also summarized. Moreover, critical aspects related to these molecules are discussed.
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Affiliation(s)
- Marco Mascini
- Dipartimento di Chimica Ugo Schiff, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
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50
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Mascini M, Palchetti I, Tombelli S. Nucleinsäure- und Peptidaptamere: Grundlagen und bioanalytische Aspekte. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006630] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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