1
|
Zhu C, Feng Z, Qin H, Chen L, Yan M, Li L, Qu F. Recent progress of SELEX methods for screening nucleic acid aptamers. Talanta 2024; 266:124998. [PMID: 37527564 DOI: 10.1016/j.talanta.2023.124998] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 07/04/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023]
Abstract
Nucleic acid aptamers are oligonucleotide sequences screened by an in vitro methodology called Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Known as "chemical antibodies", aptamers can achieve specific recognition towards the targets through conformational changes with high affinity, and possess multiple attractive features including, but not limited to, easy and inexpensive to prepare by chemical synthesis, relatively stable and low batch-to-batch variability, easy modification and signal amplification, and low immunogenicity. Now, aptamers are attracting researchers' attentions from more than 25 disciplines, and have showed great potential for application and economic benefits in disease diagnosis, environmental detection, food security, drug delivery and discovery. Although some aptamers exist naturally as the ligand-binding elements of riboswitches, SELEX is a recognized method for aptamers screening. After thirty-two years of development, a series of SELEX methods have been investigated and developed, as well as have shown unique advantages to improve sequence performances or to explore screening mechanisms. This review would mainly focus on the novel or improved SELEX methods that are available in the past five years. Firstly, we present a clear overview of the aptamer's history, features, and SELEX development. Then, we highlight the specific examples to emphasize the recent progress of SELEX methods in terms of carrier materials, technical improvements, real sample-improved screening, post-SELEX and other methods, as well as their respects of screening strategies, implementation features, screening parameters. Finally, we discuss the remaining challenges that have the potential to hinder the success of SELEX and aptamers in practical applications, and provide the suggestions and future directions for developing more convenient, efficient, and stable SELEX methods in the future.
Collapse
Affiliation(s)
- Chao Zhu
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Ziru Feng
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Hongwei Qin
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China
| | - Lu Chen
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China.
| | - Mengmeng Yan
- Institute of Quality Standard and Testing Technology for Agro-products, Shandong Academy of Agricultural Sciences, Jinan, 250100, China; Shandong Provincial Key Laboratory Test Technology on Food Quality and Safety, Jinan, 250100, China.
| | - Linsen Li
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Feng Qu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| |
Collapse
|
2
|
Ji C, Wei J, Zhang L, Hou X, Tan J, Yuan Q, Tan W. Aptamer-Protein Interactions: From Regulation to Biomolecular Detection. Chem Rev 2023; 123:12471-12506. [PMID: 37931070 DOI: 10.1021/acs.chemrev.3c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.
Collapse
Affiliation(s)
- Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xinru Hou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
| |
Collapse
|
3
|
Aljohani MM, Cialla-May D, Popp J, Chinnappan R, Al-Kattan K, Zourob M. Aptamers: Potential Diagnostic and Therapeutic Agents for Blood Diseases. Molecules 2022; 27:383. [PMID: 35056696 PMCID: PMC8778139 DOI: 10.3390/molecules27020383] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/15/2021] [Accepted: 01/04/2022] [Indexed: 02/07/2023] Open
Abstract
Aptamers are RNA/DNA oligonucleotide molecules that specifically bind to a targeted complementary molecule. As potential recognition elements with promising diagnostic and therapeutic applications, aptamers, such as monoclonal antibodies, could provide many treatment and diagnostic options for blood diseases. Aptamers present several superior features over antibodies, including a simple in vitro selection and production, ease of modification and conjugation, high stability, and low immunogenicity. Emerging as promising alternatives to antibodies, aptamers could overcome the present limitations of monoclonal antibody therapy to provide novel diagnostic, therapeutic, and preventive treatments for blood diseases. Researchers in several biomedical areas, such as biomarker detection, diagnosis, imaging, and targeted therapy, have widely investigated aptamers, and several aptamers have been developed over the past two decades. One of these is the pegaptanib sodium injection, an aptamer-based therapeutic that functions as an anti-angiogenic medicine, and it is the first aptamer approved by the U.S. Food and Drug Administration (FDA) for therapeutic use. Several other aptamers are now in clinical trials. In this review, we highlight the current state of aptamers in the clinical trial program and introduce some promising aptamers currently in pre-clinical development for blood diseases.
Collapse
Affiliation(s)
- Maher M. Aljohani
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany; (D.C.-M.); (J.P.)
- Department of Pathology, College of Medicine, Taibah University, Madinah 42353, Saudi Arabia
| | - Dana Cialla-May
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany; (D.C.-M.); (J.P.)
- Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, 07745 Jena, Germany
| | - Jürgen Popp
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Helmholtzweg 4, 07743 Jena, Germany; (D.C.-M.); (J.P.)
- Leibniz Institute of Photonic Technology, Albert-Einstein-Str. 9, 07745 Jena, Germany
- Center for Applied Research, InfectoGnostics Research Campus Jena, University of Jena, Philosophenweg 7, 07743 Jena, Germany
| | - Raja Chinnappan
- Department of Chemistry, Alfaisal University, Riyadh 11533, Saudi Arabia;
| | - Khaled Al-Kattan
- College of Medicine, Alfaisal University, Al Zahrawi Street, Al Maather, Al Takhassusi Rd, Riyadh 11533, Saudi Arabia;
| | - Mohammed Zourob
- Department of Chemistry, Alfaisal University, Riyadh 11533, Saudi Arabia;
| |
Collapse
|
4
|
Ren HX, Zhong Q, Miao YB, Wen XW, Wu GY, Wang HL, Zhang Y. A label-free reusable aptasensor for Alzheimer's disease. Mikrochim Acta 2020; 187:515. [PMID: 32839875 DOI: 10.1007/s00604-020-04518-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 08/18/2020] [Indexed: 11/29/2022]
Abstract
To early effectively detect amyloid-beta (Aβ) oligomers, a label-free reusable aptasensor was designed. This aptasensor based on a luminescent nanoscale lanthanum-based metal-organic framework (L-MOF)-armored single-stranded DNA antibody (MOF-armored-anti-DNA antibody) as signal tags and aptamer bound to magnetic beads (Apt-MB) as capture probe. The reusable aptasensor combines signal tag and capture probe with antigen-antibody interaction. When the reusable aptasensor is formed, the strong fluorescence intensity of L-MOF will "turn off" by photo-induced electron transfer from excited states to an unfilled d shell of iron cations on the nanoparticle surface. Upon the presence of Aβ oligomers in serum samples, they can be especially distinguished with the Aβ oligomers aptamer in capture probes and then signal tags are released into the solution for developing the fluorescence aptasensor under excitation/emission 365 nm/430 nm. Meanwhile, the aptamer was recovered from the complex of Aβ oligomers/Apt-MB by heat treatment. When the temperature returns to room temperature, the recovered aptamer in the capture probe can once again bound to the MOF-armored-anti-DNA antibody for reuse. The label-free reusable aptasensor system detection has high sensitivity and selectivity toward Aβ oligomers (LOD = 0.4 pg/mL) and an excellent linear range (0.001-100 ng/mL). This strategy is a fruitful step for the development of reusable aptasensor and may turn on new avenues for the applications of Aβ oligomer detection in clinical diagnosis.Graphical abstract.
Collapse
Affiliation(s)
- Hong-Xia Ren
- School of Chemistry and Chemical Engineering, Zunyi Normal College, Zunyi, 563000, Guizhou, China.
| | | | - Yang-Bao Miao
- Department of Chemical Engineering, National Tsing Hua University, Hsinchu, Taiwan, 30013
| | - Xiao-Wei Wen
- School of Chemistry and Chemical Engineering, Zunyi Normal College, Zunyi, 563000, Guizhou, China
| | - Gui-Yan Wu
- School of Chemistry and Chemical Engineering, Zunyi Normal College, Zunyi, 563000, Guizhou, China
| | - Hui-Ling Wang
- School of Chemistry and Chemical Engineering, Zunyi Normal College, Zunyi, 563000, Guizhou, China
| | - Ying Zhang
- School of Chemistry and Chemical Engineering, Zunyi Normal College, Zunyi, 563000, Guizhou, China
| |
Collapse
|
5
|
Eissa S, Alkhaldi S, Chinnappan R, Siddiqua A, Abduljabbar M, Abdel Rahman AM, Dasouki M, Zourob M. Selection, characterization, and electrochemical biosensing application of DNA aptamers for sepiapterin. Talanta 2020; 216:120951. [PMID: 32456943 DOI: 10.1016/j.talanta.2020.120951] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/15/2020] [Accepted: 03/17/2020] [Indexed: 12/22/2022]
Abstract
Sepiapterin reductase deficiency (SR) is a rare inborn disorder of neurotransmitter metabolism. The early diagnosis of SR disease should be achieved through the determination of the sepiapterin level in body fluids of suspected patients. Here, we report the selection, identification, and characterization of DNA aptamers against sepiapterin. The aptamer selection was achieved via the systematic evolution of ligand by the exponential enrichment technique. After ten rounds of selection, high-affinity aptamers were identified. The binding affinities of the selected aptamers were evaluated using fluorescence binding assays showing dissociation constants ranging from 37.3 to 79.0 nM. The highest affinity aptamer was then integrated into a competitive electrochemical biosensor. The biosensor achieved outstanding sensitivity with a detection limit of 0.8 pg/ml which was much lower than the reported chromatographic method for sepiapterin quantification. The aptasensor has also shown a high degree of selectivity against the closely-related compound. The aptasensor was then challenged by detecting the sepiapterin in spiked serum samples where a good recovery percentage was achieved.
Collapse
Affiliation(s)
- Shimaa Eissa
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, AlTakhassusi Rd, Riyadh, 11533, Saudi Arabia
| | - Shahad Alkhaldi
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, AlTakhassusi Rd, Riyadh, 11533, Saudi Arabia
| | - Raja Chinnappan
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, AlTakhassusi Rd, Riyadh, 11533, Saudi Arabia
| | - Ayesha Siddiqua
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, AlTakhassusi Rd, Riyadh, 11533, Saudi Arabia
| | - Mai Abduljabbar
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Zahrawi Street, Al Maather, Riyadh, 11211, Saudi Arabia
| | - Anas M Abdel Rahman
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Zahrawi Street, Al Maather, Riyadh, 11211, Saudi Arabia; College of Medicine, Alfaisal University, Riyadh, Saudi Arabia; Department of Chemistry, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Majed Dasouki
- Department of Genetics, King Faisal Specialist Hospital and Research Center, Zahrawi Street, Al Maather, Riyadh, 11211, Saudi Arabia
| | - Mohammed Zourob
- Department of Chemistry, Alfaisal University, Al Zahrawi Street, Al Maather, AlTakhassusi Rd, Riyadh, 11533, Saudi Arabia; Department of Genetics, King Faisal Specialist Hospital and Research Center, Zahrawi Street, Al Maather, Riyadh, 11211, Saudi Arabia.
| |
Collapse
|