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Yang G, Wang H, Jiang G, Zhao L, Qu F. Aptamer inhibitor selection of SpyCas9 through CE-SELEX. Talanta 2024; 273:125837. [PMID: 38479030 DOI: 10.1016/j.talanta.2024.125837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 04/09/2024]
Abstract
CRISPR/Cas9 is a natural immune system of archaea and bacteria, which has been widely used in gene editing. In order to better control and improve the accuracy and safety of the system, inhibitors for SpyCas9 as "switches" have been selected for several years. The available inhibitors currently are all natural polypeptides inhibitors derived from phages, except one small molecule inhibitor. These natural inhibitors are challenging to obtain and are available in limited quantities, and the small molecule inhibitor is cytotoxic. Herein, we discover aptamers against the SpyCas9 protein, by coupling CE-SELEX within one-round pressure controllable selection strategy. One of the identified aptamers, Apt2, shows high affinity at the nanomolar level and leads for effective SpyCas9 enzymatic inhibition in vitro. It is predicted that Apt2 interacts with the HNH and RuvC domains of SpyCas9, competitively inhibiting the binding of substrate DNA to SpyCas9. The proposed aptamer inhibitor is the oligonucleotide inhibitor of SpyCas9, which has the potential in construction of the universal, simple and precise CRISPR-Cas9 system activity control strategy. Meanwhile, these aptamers could also be valuable tools for study of the functions of CRISPR/Cas9 and the related functional mechanisms.
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Affiliation(s)
- Ge Yang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China; CAMS Key Laboratory of Antiviral Drug Research, Beijing Key Laboratory of Antimicrobial Agents, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Huimin Wang
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China
| | - Guangyu Jiang
- CAMS Key Laboratory of Antiviral Drug Research, Beijing Key Laboratory of Antimicrobial Agents, NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100050, China
| | - Liping Zhao
- Institute of Quality Standard and Testing Technology of BAAFS, Agricultural Product Quality and Safety Risk Assessment Laboratory of the Department of Agriculture, Beijing, 100097, China.
| | - Feng Qu
- Key Laboratory of Molecular Medicine and Biotherapy, School of Life Science, Beijing Institute of Technology, 5 South Zhongguancun Street, Beijing, 100081, China.
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2
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Zeng Z, Li W, Zhang J, Hu Z, Wu J, Ye G, Luo Y. Highly sensitive and specific graphene oxide-based FRET aptasensor for quantitative detection of human soluble growth stimulating gene protein 2. Talanta 2024; 271:125629. [PMID: 38245955 DOI: 10.1016/j.talanta.2024.125629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 12/31/2023] [Accepted: 01/04/2024] [Indexed: 01/23/2024]
Abstract
Soluble growth stimulation expressed gene 2 (sST2) is a new generation biomarker in the diagnosis and prognosis of heart failure (HF). Here, the sST2-specific aptamers were selected from a random ssDNA library with the full length of 88 nucleotides (nt) via target-immobilized magnetic beads (MB)-based systematic evolution of ligands by exponential enrichment (SELEX) technology. After eight rounds of selection, six aptamers with the most enrichment were selected. Among, the aptamer L1 showed the high-affinity binding to sST2 with the lowest Kd value (77.3 ± 0.05 nM), which was chosen as the optimal aptamer for further molecular docking. Then, the aptamer L1 was used to construct a graphene oxide (GO) - based fluorescence resonance energy transfer (FRET) biosensor for sST2, which exhibits a linear detection range of 0.1-100 μg/ml and a detection limit of 3.7 ng/ml. The aptasensor was applied to detect sST2 in real samples, with a good correlation and agreement with the traditional enzyme-linked immunosorbent assay (ELISA) when quantitative analyzing the sST2 concentration in serum samples from HF patients. The results show that not only an efficient strategy for screening the practicable aptamer, but also a rapid and sensitive detection platform for sST2 were established.
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Affiliation(s)
- Zhikun Zeng
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China
| | - Wenfeng Li
- The Second Clinical College of Wuhan University, Wuhan, 430071, Hubei, China
| | - Jixuan Zhang
- The Second Clinical College of Wuhan University, Wuhan, 430071, Hubei, China
| | - Zijian Hu
- The First Clinical College of Wuhan University, Wuhan, 430060, Hubei, China
| | - Junyi Wu
- The Second Clinical College of Wuhan University, Wuhan, 430071, Hubei, China
| | - Guangming Ye
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China.
| | - Yi Luo
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, China.
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Park SV, Kang B, Lee M, Yoo H, Jo H, Woo S, Oh SS. In vitro selection of a trans aptamer complex for target-responsive fluorescence activation. Anal Chim Acta 2024; 1301:342465. [PMID: 38553123 DOI: 10.1016/j.aca.2024.342465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/23/2024] [Accepted: 03/10/2024] [Indexed: 04/02/2024]
Abstract
BACKGROUND Most biological molecular complexes consist of multiple functional domains, yet rationally constructing such multifunctional complexes is challenging. Aptamers, the nucleic acid-based functional molecules, can perform multiple tasks including target recognition, conformational changes, and enzymatic activities, while being chemically synthesizable and tunable, and thus provide a basis for engineering enhanced functionalities through combination of multiple units. However, the conventional approach of simply combining aptamer units in a serial manner is susceptible to undesired crosstalk or interference between the aptamer units and to false interactions with non-target molecules; besides, the approach would require additional mechanisms to separate the units if they are desired to function independently. It is clearly a challenge to develop multi-aptamer complexes that preserve independent functions of each unit while avoiding undesired interference and non-specific interactions. RESULTS By directly in vitro selecting a 'trans' aptamer complex, we demonstrate that one aptamer unit ('utility module') can remain hidden or 'inactive' until a target analyte triggers the other unit ('sensing module') and separates the two aptamers. Since the operation of the utility module occurs free from the sensing module, unnecessary crosstalk between the two units can be avoided. Because the utility module is kept inactive until separated from the complex, non-specific interactions of the hidden module with noncognate targets can be naturally prevented. In our demonstration, the sensing module was selected to detect serotonin, a clinically important neurotransmitter, and the target-binding-induced structure-switching of the sensing module reveals and activates the utility module that turns on a fluorescence signal. The aptamer complex exhibited a moderately high affinity and an excellent specificity for serotonin with ∼16-fold discrimination against common neurotransmitter molecules, and displayed strong robustness to perturbations in the design, disallowing nonspecific reactions against various challenges. SIGNIFICANCE This work represents the first example of a trans aptamer complex that was in vitro selected de novo. The trans aptamer complex selected by our strategy does not require chemical modifications or immediate optimization processes to function, because the complex is directly selected to perform desired functions. This strategy should be applicable to a wide range of functional nucleic acid moieties, which will open up diverse applications in biosensing and molecular therapeutics.
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Affiliation(s)
- Soyeon V Park
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Byunghwa Kang
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Minjong Lee
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Hyebin Yoo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Hyesung Jo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea
| | - Sungwook Woo
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea.
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), 77 Cheongam-Ro, Nam-Gu, Pohang, Gyeongbuk 37673, South Korea.
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Cunha PDS, de Miranda MC, de Melo MIA, Ferreira ADF, Barbosa JL, Oliveira JADC, Goes TDS, Gomes DA, de Goes AM. Selection of internalizing RNA aptamers into human breast cancer cells derived from primary sites. J Cell Biochem 2024; 125:e30540. [PMID: 38372191 DOI: 10.1002/jcb.30540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 01/30/2024] [Accepted: 02/06/2024] [Indexed: 02/20/2024]
Abstract
Breast cancer is the most common cancer in women. Although chemotherapy is still broadly used in its treatment, adverse effects remain a challenge. In this scenario, aptamers emerge as a promising alternative for theranostic applications. Studies using breast cancer cell lines provide useful information in laboratory and preclinical investigations, most of which use cell lines established from metastatic sites. However, these cell lines correspond to cell populations of the late stage of tumor progression. On the other hand, studies using breast cancer cells established from primary sites make it possible to search for new theranostic approaches in the early stages of the disease. Therefore, this work aimed to select RNA aptamers internalized by MGSO-3 cells, a human breast cancer cell line, derived from a primary site previously established in our laboratory. Using the Cell-Internalization SELEX method, we have selected two candidate aptamers (ApBC1 and ApBC2). We evaluated their internalization efficiencies, specificities, cellular localization by Reverse Transcription-qPCR (RT-qPCR) and confocal microscopy assays. The results suggest that both aptamers were efficiently internalized by human breast cancer cells, MACL-1, MDA-MB-231, and especially by MGSO-3 cells. Furthermore, both aptamers could effectively distinguish human breast cancer cells derived from normal human mammary cell (MCF 10A) and prostate cancer cell (PC3) lines. Therefore, ApBC1 and ApBC2 could be promising candidate molecules for theranostic applications, even in the early stages of tumor progression.
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Affiliation(s)
- Pricila da Silva Cunha
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Marcelo Coutinho de Miranda
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Mariane Izabella Abreu de Melo
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Andrea da Fonseca Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Joana Lobato Barbosa
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | | | - Tércio de Souza Goes
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Dawidson Assis Gomes
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Alfredo Miranda de Goes
- Departamento de Patologia Geral, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
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Li J, Xu T, Zheng Y, Liu D, Zhang C, Li J, Wang ZA, Du Y. In Silico Study on a Binding Mechanism of ssDNA Aptamers Targeting Glycosidic Bond-Containing Small Molecules. Anal Chem 2024; 96:5056-5064. [PMID: 38497564 DOI: 10.1021/acs.analchem.4c00927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Aptamer-based detection targeting glycoconjugates has attracted significant attention for its remarkable potential in identifying structural changes in saccharides in different stages of various diseases. However, the challenges in screening aptamers for small carbohydrates or glycoconjugates, which contain highly flexible and diverse glycosidic bonds, have hindered their application and commercialization. In this study, we investigated the binding conformations between three glycosidic bond-containing small molecules (GlySMs; glucose, N-acetylneuraminic acid, and neomycin) and their corresponding aptamers in silico, and analyzed factors contributing to their binding affinities. Based on the findings, a novel binding mechanism was proposed, highlighting the central role of the stem structure of the aptamer in binding and recognizing GlySMs and the auxiliary role of the mismatched bases in the adjacent loop. Guided by this binding mechanism, an aptamer with a higher 6'-sialyllactose binding affinity was designed, achieving a KD value of 4.54 ± 0.64 μM in vitro through a single shear and one mutation. The binding mechanism offers crucial guidance for designing high-affinity aptamers, enhancing the virtual screening efficiency for GlySMs. This streamlined workflow filters out ineffective binding sites, accelerating aptamer development and providing novel insights into glycan-nucleic acid interactions.
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Affiliation(s)
- Jiaqing Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Tong Xu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- School of Chemical Engineering, University of Chinese Academy of Sciences, No.19A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yalan Zheng
- Key Laboratory for Animal Disease-Resistant Nutrition of the Ministry of Education of China, Institute of Animal Nutrition, Sichuan Agricultural University, Chengdu, Sichuan 611130, China
| | - Dongdong Liu
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
| | - Chen Zhang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
| | - Jianjun Li
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
| | - Zhuo A Wang
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
| | - Yuguang Du
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
- Key Laboratory of Biopharmaceutical Preparation and Delivery, Chinese Academy of Sciences, 1 North second Street, Zhongguancun, Haidian District, Beijing 100190, China
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Chen L, Yu Z, Wu Z, Zhou M, Wang Y, Yu X, Li W, Liu G, Tang Y. AptaDB: a comprehensive database integrating aptamer-target interactions. RNA 2024; 30:189-199. [PMID: 38164624 PMCID: PMC10870366 DOI: 10.1261/rna.079784.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/12/2023] [Indexed: 01/03/2024]
Abstract
Aptamers have emerged as research hotspots of the next generation due to excellent performance benefits and application potentials in pharmacology, medicine, and analytical chemistry. Despite the numerous aptamer investigations, the lack of comprehensive data integration has hindered the development of computational methods for aptamers and the reuse of aptamers. A public access database named AptaDB, derived from experimentally validated data manually collected from the literature, was hence developed, integrating comprehensive aptamer-related data, which include six key components: (i) experimentally validated aptamer-target interaction information, (ii) aptamer property information, (iii) structure information of aptamer, (iv) target information, (v) experimental activity information, and (vi) algorithmically calculated similar aptamers. AptaDB currently contains 1350 experimentally validated aptamer-target interactions, 1230 binding affinity constants, 1293 aptamer sequences, and more. Compared to other aptamer databases, it contains twice the number of entries found in available databases. The collection and integration of the above information categories is unique among available aptamer databases and provides a user-friendly interface. AptaDB will also be continuously updated as aptamer research evolves. We expect that AptaDB will become a powerful source for aptamer rational design and a valuable tool for aptamer screening in the future. For access to AptaDB, please visit http://lmmd.ecust.edu.cn/aptadb/.
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Affiliation(s)
- Long Chen
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zhuohang Yu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Zengrui Wu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Moran Zhou
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yimeng Wang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Xinxin Yu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Guixia Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
| | - Yun Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
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7
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Pitolli M, Cela M, Paulus C, Rudinger-Thirion J, Frugier M. RNA aptamers developed against tRip: A preliminary approach targeting tRNA entry in Plasmodium. Biochimie 2024; 217:106-115. [PMID: 37414209 DOI: 10.1016/j.biochi.2023.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 05/26/2023] [Accepted: 06/24/2023] [Indexed: 07/08/2023]
Abstract
Malaria is caused by Plasmodium parasites that multiply inside host cells and can be lethal when P. falciparum is involved. We identified tRip as a membrane protein that facilitates the import of exogenous transfer RNA (tRNA) into the parasite. tRip encompasses a tRNA binding domain exposed on the parasite surface. We used the SELEX approach to isolate high-affinity and specific tRip-binding RNA motifs from a library of random 25 nucleotide-long sequences. In five rounds of combined negative and positive selections, an enriched pool of aptamers was obtained; sequencing revealed that they were all different in their primary sequence; only by comparing their structure predictions did most of the selected aptamers reveal a conserved 5-nucleotide motif sequence. We showed that the integral motif is essential for tRip-binding while the rest of the molecule can be significantly reduced or mutated as long as the motif is presented in a single-stranded region. Such RNA aptamers bind in place of the original tRNA substrate and act as an efficient competitor, suggesting that they can block tRip function and slow parasite development.
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Affiliation(s)
- Martina Pitolli
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67084, Strasbourg, France
| | - Marta Cela
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67084, Strasbourg, France
| | - Caroline Paulus
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67084, Strasbourg, France
| | - Joëlle Rudinger-Thirion
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67084, Strasbourg, France
| | - Magali Frugier
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67084, Strasbourg, France.
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8
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Chen Z, Sun Q, Yang Y, Nie X, Xiang W, Ren Y, Le T. Aptamer-based diagnostic and therapeutic approaches for animal viruses: A review. Int J Biol Macromol 2024; 257:128677. [PMID: 38072350 DOI: 10.1016/j.ijbiomac.2023.128677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/28/2023] [Accepted: 12/06/2023] [Indexed: 01/27/2024]
Abstract
Animal diseases often have significant consequences due to the unclear and time-consuming diagnosis process. Furthermore, the emergence of new viral infections and drug-resistant pathogens has further complicated the diagnosis and treatment of viral diseases. Aptamers, which are obtained through systematic evolution of ligands by exponential enrichment (SELEX) technology, provide a promising solution as they enable specific identification and binding to targets, facilitating pathogen detection and the development of novel therapeutics. This review presented an overview of aptasensors for animal virus detection, discussed the antiviral activity and mechanisms of aptamers, and highlighted advancements in aptamer-based antiviral research following the COVID-19 pandemic. Additionally, the challenges and prospects of aptamer-based virus diagnosis and treatment research were explored. Although this review was not exhaustive, it offered valuable insights into the progress of aptamer-based antiviral drug research, target mechanisms, as well as the development of novel antiviral drugs and biosensors.
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Affiliation(s)
- Zhuoer Chen
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Qi Sun
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Ying Yang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Xunqing Nie
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Wenyu Xiang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Yueyang Ren
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Tao Le
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China.
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9
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Requena MD, Yan A, Llanga T, Sullenger BA. Reversible Aptamer Staining, Sorting, and Cleaning of Cells (Clean FACS) with Antidote Oligonucleotide or Nuclease Yields Fully Responsive Cells. Nucleic Acid Ther 2024; 34:12-17. [PMID: 38285522 DOI: 10.1089/nat.2023.0050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024] Open
Abstract
The ability to reverse the binding of aptamers to their target proteins has received considerable attention for developing controllable therapeutic agents. Recently, use of aptamers as reversible cell-sorting ligands has also sparked interest. Antibodies are currently utilized for isolating cells expressing a particular cell surface receptor. The inability to remove antibodies from isolated cells following sorting greatly limits their utility for many applications. Previously, we described how a particular aptamer-antidote oligonucleotide pair can isolate cells and clean them. Here, we demonstrate that this approach is generalizable; aptamers can simultaneously recognize more than one cell type during fluorescent activated cell sorting (FACS). Moreover, we describe a novel approach to reverse aptamer binding following cell sorting using a nuclease. This alternative strategy represents a cleaning approach that does not require the generation of antidote oligonucleotides for each aptamer and will greatly reduce the cost and expand the utility of Clean FACS.
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Affiliation(s)
- Martin D Requena
- Department of Surgery, Duke University, Durham, North Carolina, USA
- University Program in Genetics and Genomics, and Duke University, Durham, North Carolina, USA
| | - Amy Yan
- Department of Surgery, Duke University, Durham, North Carolina, USA
| | - Telmo Llanga
- Department of Surgery, Duke University, Durham, North Carolina, USA
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA
| | - Bruce A Sullenger
- Department of Surgery, Duke University, Durham, North Carolina, USA
- University Program in Genetics and Genomics, and Duke University, Durham, North Carolina, USA
- Department of Pharmacology and Cancer Biology, Duke University, Durham, North Carolina, USA
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Kim J, Baek S, Nam J, Park J, Kim K, Kang J, Yeom G. Simultaneous Detection of Infectious Diseases Using Aptamer-Conjugated Gold Nanoparticles in the Lateral Flow Immunoassay-Based Signal Amplification Platform. Anal Chem 2024; 96:1725-1732. [PMID: 38240676 DOI: 10.1021/acs.analchem.3c04870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
Abstract
Various platforms for the accurate diagnosis of infectious diseases have been studied because of the emergence of coronavirus disease (COVID-19) in 2019. Recently, it has become difficult to distinguish viruses with similar symptoms due to the continuous mutation of viruses, and there is an increasing need for a diagnostic method to detect them simultaneously. Therefore, we developed a paper-based rapid antigen diagnostic test using DNA aptamers for the simultaneous detection of influenza A, influenza B, and COVID-19. Aptamers specific for each target viral antigen were selected and attached to AuNPs for application in a rapid antigen diagnosis kit using our company's heterogeneous sandwich-type aptamer screening method (H-SELEX). We confirmed that the three viruses could be detected on the same membrane without cross-reactivity based on the high stability, specificity, and binding affinity of the selected aptamers. Further, the limit of detection was 2.89 pg·mL-1 when applied to develop signal amplification technology; each virus antigen was detected successfully in diluted nasopharyngeal samples. We believe that the developed simultaneous diagnostic kit, based on such high accuracy, can distinguish various infectious diseases, thereby increasing the therapeutic effect and contributing to the clinical field.
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Affiliation(s)
- Jinwoo Kim
- SB BIOSCIENCE Inc., Room 120, Venture Building, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sowon Baek
- SB BIOSCIENCE Inc., Room 120, Venture Building, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jungmin Nam
- SB BIOSCIENCE Inc., Room 120, Venture Building, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Jeongeun Park
- SB BIOSCIENCE Inc., Room 120, Venture Building, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Kihyeun Kim
- Advanced Photonics Research Institute (APRI), Gwangju Institute of Science and Technology (GIST), 123 Cheomdan-gwagiro, Buk-gu, Gwangju 61005, Republic of Korea
| | - Juyoung Kang
- SB BIOSCIENCE Inc., Room 120, Venture Building, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Gyuho Yeom
- SB BIOSCIENCE Inc., Room 120, Venture Building, 125 Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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11
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Kramat J, Kraus L, Gunawan VJ, Smyej E, Froehlich P, Weber TE, Spiehl D, Koeppl H, Blaeser A, Suess B. Sensing Levofloxacin with an RNA Aptamer as a Bioreceptor. Biosensors (Basel) 2024; 14:56. [PMID: 38275309 PMCID: PMC10813692 DOI: 10.3390/bios14010056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 01/27/2024]
Abstract
To combat the growing threat of antibiotic resistance, environmental testing for antibiotic contamination is gaining an increasing role. This study aims to develop an easy-to-use assay for the detection of the fluoroquinolone antibiotic levofloxacin. Levofloxacin is used in human and veterinary medicine and has been detected in wastewater and river water. An RNA aptamer against levofloxacin was selected using RNA Capture-SELEX. The 73 nt long aptamer folds into three stems with a central three-way junction. It binds levofloxacin with a Kd of 6 µM and discriminates the closely related compound ciprofloxacin. Furthermore, the selection process was analyzed using a next-generation sequencing approach to better understand the sequence evolution throughout the selection. The aptamer was used as a bioreceptor for the development of a lateral flow assay. The biosensor exploited the innate characteristic of RNA Capture-SELEX to select aptamers that displace a complementary DNA oligonucleotide upon ligand binding. The lateral flow assay achieved a limit of visual detection of 100 µM. While the sensitivity of this assay constrains its immediate use in environmental testing, the present study can serve as a template for the selection of RNA aptamer-based biosensors.
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Affiliation(s)
- Janice Kramat
- Synthetic RNA Biology, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Leon Kraus
- Synthetic RNA Biology, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Vincent J. Gunawan
- Synthetic RNA Biology, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Elias Smyej
- Synthetic RNA Biology, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
| | - Philipp Froehlich
- Self-Organizing Systems, Department of Electrical Engineering and Information Technology, Technical University of Darmstadt, 64283 Darmstadt, Germany
| | - Tim E. Weber
- Institute for BioMedical Printing Technologies, Technical University of Darmstadt, 64289 Darmstadt, Germany
| | - Dieter Spiehl
- Institute for BioMedical Printing Technologies, Technical University of Darmstadt, 64289 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, 64289 Darmstadt, Germany
| | - Heinz Koeppl
- Self-Organizing Systems, Department of Electrical Engineering and Information Technology, Technical University of Darmstadt, 64283 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, 64289 Darmstadt, Germany
| | - Andreas Blaeser
- Institute for BioMedical Printing Technologies, Technical University of Darmstadt, 64289 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, 64289 Darmstadt, Germany
| | - Beatrix Suess
- Synthetic RNA Biology, Department of Biology, Technical University of Darmstadt, 64287 Darmstadt, Germany
- Centre for Synthetic Biology, Technical University of Darmstadt, 64289 Darmstadt, Germany
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12
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Córdova-Espinoza MG, González-Vázquez R, Barron-Fattel RR, Gónzalez-Vázquez R, Vargas-Hernández MA, Albores-Méndez EM, Esquivel-Campos AL, Mendoza-Pérez F, Mayorga-Reyes L, Gutiérrez-Nava MA, Medina-Quero K, Escamilla-Gutiérrez A. Aptamers: A Cutting-Edge Approach for Gram-Negative Bacterial Pathogen Identification. Int J Mol Sci 2024; 25:1257. [PMID: 38279257 PMCID: PMC10817072 DOI: 10.3390/ijms25021257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 01/04/2024] [Accepted: 01/15/2024] [Indexed: 01/28/2024] Open
Abstract
Early and accurate diagnoses of pathogenic microorganisms is essential to correctly identify diseases, treating infections, and tracking disease outbreaks associated with microbial infections, to develop precautionary measures that allow a fast and effective response in epidemics and pandemics, thus improving public health. Aptamers are a class of synthetic nucleic acid molecules with the potential to be used for medical purposes, since they can be directed towards any target molecule. Currently, the use of aptamers has increased because they are a useful tool in the detection of specific targets. We present a brief review of the use of aptamers to detect and identify bacteria or even some toxins with clinical importance. This work describes the advances in the technology of aptamers, with the purpose of providing knowledge to develop new aptamers for diagnoses and treatment of different diseases caused by infectious microorganisms.
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Affiliation(s)
- María Guadalupe Córdova-Espinoza
- Immunology Laboratory, Escuela Militar de Graduados de Sanidad, SEDENA, Mexico City 11200, Mexico;
- National School of Biological Sciences, National Polytechnic Institute, Laboratory of Medical Bacteriology, Mexico City 11350, Mexico; (R.G.-V.); (R.R.B.-F.)
- Mexican Social Security Institute, Unidad Medica de Alta Especialidad, Hospital de Especialidades, “Dr. Antonio Fraga Mouret”, National Medical Center La Raza, Mexico City 02990, Mexico
| | - Rosa González-Vázquez
- National School of Biological Sciences, National Polytechnic Institute, Laboratory of Medical Bacteriology, Mexico City 11350, Mexico; (R.G.-V.); (R.R.B.-F.)
- Mexican Social Security Institute, Unidad Medica de Alta Especialidad, Hospital de Especialidades, “Dr. Antonio Fraga Mouret”, National Medical Center La Raza, Mexico City 02990, Mexico
| | - Rolando Rafik Barron-Fattel
- National School of Biological Sciences, National Polytechnic Institute, Laboratory of Medical Bacteriology, Mexico City 11350, Mexico; (R.G.-V.); (R.R.B.-F.)
| | - Raquel Gónzalez-Vázquez
- Laboratory of Biotechnology, Department of Biological Systems, Metropolitana Campus Xochimilco, CONAHCYT—Universidad Autonoma, Calzada del Hueso 1100, Col. Villa Quietud, Alcaldia Coyoacan, Mexico City 04960, Mexico;
| | - Marco Antonio Vargas-Hernández
- Research Department, Escuela Militar de Graduados de Sanidad, SEDENA, Mexico City 11200, Mexico; (M.A.V.-H.); (E.M.A.-M.)
| | - Exsal Manuel Albores-Méndez
- Research Department, Escuela Militar de Graduados de Sanidad, SEDENA, Mexico City 11200, Mexico; (M.A.V.-H.); (E.M.A.-M.)
| | - Ana Laura Esquivel-Campos
- Laboratory of Biotechnology, Department of Biological Systems, Universidad Autonoma Metropolitana, Campus Xochimilco, Calzada del Hueso 1100, Col. Villa Quietud, Alcaldia Coyoacan, Mexico City 04960, Mexico; (A.L.E.-C.); (F.M.-P.); (L.M.-R.)
| | - Felipe Mendoza-Pérez
- Laboratory of Biotechnology, Department of Biological Systems, Universidad Autonoma Metropolitana, Campus Xochimilco, Calzada del Hueso 1100, Col. Villa Quietud, Alcaldia Coyoacan, Mexico City 04960, Mexico; (A.L.E.-C.); (F.M.-P.); (L.M.-R.)
| | - Lino Mayorga-Reyes
- Laboratory of Biotechnology, Department of Biological Systems, Universidad Autonoma Metropolitana, Campus Xochimilco, Calzada del Hueso 1100, Col. Villa Quietud, Alcaldia Coyoacan, Mexico City 04960, Mexico; (A.L.E.-C.); (F.M.-P.); (L.M.-R.)
| | - María Angélica Gutiérrez-Nava
- Laboratory of Microbial Ecology, Department of Biological Systems, Universidad Autonoma Metropolitana, Campus Xochimilco, Calzada del Hueso 1100, Col. Villa Quietud, Coyoacan, Mexico City 04960, Mexico;
| | - Karen Medina-Quero
- Immunology Laboratory, Escuela Militar de Graduados de Sanidad, SEDENA, Mexico City 11200, Mexico;
| | - Alejandro Escamilla-Gutiérrez
- National School of Biological Sciences, National Polytechnic Institute, Laboratory of Medical Bacteriology, Mexico City 11350, Mexico; (R.G.-V.); (R.R.B.-F.)
- Mexican Social Security Institute, Unidad Medica de Alta Especialidad, Microbiology Laboratory, Hospital General “Dr. Gaudencio González Garza”, National Medical Center La Raza, Mexico City 02990, Mexico
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13
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Liu Y, Lu X, Chen M, Wei Z, Peng G, Yang J, Tang C, Yu P. Advances in screening, synthesis, modification, and biomedical applications of peptides and peptide aptamers. Biofactors 2024; 50:33-57. [PMID: 37646383 DOI: 10.1002/biof.2001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
Peptides and peptide aptamers have emerged as promising molecules for a wide range of biomedical applications due to their unique properties and versatile functionalities. The screening strategies for identifying peptides and peptide aptamers with desired properties are discussed, including high-throughput screening, display screening technology, and in silico design approaches. The synthesis methods for the efficient production of peptides and peptide aptamers, such as solid-phase peptide synthesis and biosynthesis technology, are described, along with their advantages and limitations. Moreover, various modification techniques are explored to enhance the stability, specificity, and pharmacokinetic properties of peptides and peptide aptamers. This includes chemical modifications, enzymatic modifications, biomodifications, genetic engineering modifications, and physical modifications. Furthermore, the review highlights the diverse biomedical applications of peptides and peptide aptamers, including targeted drug delivery, diagnostics, and therapeutic. This review provides valuable insights into the advancements in screening, synthesis, modification, and biomedical applications of peptides and peptide aptamers. A comprehensive understanding of these aspects will aid researchers in the development of novel peptide-based therapeutics and diagnostic tools for various biomedical challenges.
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Affiliation(s)
- Yijie Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Xiaoling Lu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Meilun Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Zheng Wei
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Guangnan Peng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Jie Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Chunhua Tang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Peng Yu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
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14
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Rossi JJ. Aptamer selection in a porous hydrogel. Cell Rep Methods 2023; 3:100667. [PMID: 38065094 PMCID: PMC10753376 DOI: 10.1016/j.crmeth.2023.100667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 12/21/2023]
Abstract
The process of nucleic acid aptamer selection can be quite laborious and fraught with artifacts. In a work published in Nature Biotechnology, Singh et al. describe an approach that should allow more facile aptamer selection.
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Affiliation(s)
- John J Rossi
- Center for RNA Biology and Therapeutics, City of Hope, Beckman Research Institute, Duarte, CA 91010, USA.
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15
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Kumar S, Singh P, Verma SK. Selection of Highly Specific DNA Aptamer for the Development of QCM-Based Arsenic Sensor. Chembiochem 2023; 24:e202300585. [PMID: 37792297 DOI: 10.1002/cbic.202300585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/03/2023] [Indexed: 10/05/2023]
Abstract
Heavy metal arsenic is a water pollutant that affects millions of lives worldwide. A novel aptamer candidate for specific and sensitive arsenic detection was identified using Graphene Oxide-SELEX (GO-SELEX). Eleven rounds of GO-SELEX were performed to screen As(III) specific sequences. The selected aptamer sequences were evaluated for their binding affinity. The dissociation constant of the best aptamer candidate, As-06 was estimated by fluorescence recovery upon target addition, and it was found to be 8.15 nM. A QCM-based biosensing platform was designed based on the target-triggered release of aptamer from the QCM electrode. An rGO-SWCNT nanocomposite was adsorbed on the gold surface, and the single-stranded probe was stacked on the rGO-CNT layer. Upon addition of the target to the solution, a concentration-dependent release of the ssDNA probe was observed and recorded as the change in the electrode frequency. The developed QCM sensor showed a dynamic linear range from 10 nM to 100 nM and a low detection limit of 8.6 nM. The sensor exhibited excellent selectivity when challenged with common interfering anions and cations.
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Affiliation(s)
- Sandeep Kumar
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, Pilani, Rajasthan, 333031, India
| | - Poonam Singh
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, Pilani, Rajasthan, 333031, India
| | - Sanjay Kumar Verma
- Department of Biological Sciences, Birla Institute of Technology & Science Pilani, Pilani, Rajasthan, 333031, India
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16
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Wang Z, Chang D, Sargent EH, Kelley SO. Apta FastZ: An Algorithm for the Rapid Identification of Aptamers with Defined Binding Affinities. Anal Chem 2023; 95:17438-17443. [PMID: 37991715 DOI: 10.1021/acs.analchem.3c02881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Real-time biomolecular monitoring requires biosensors based on affinity reagents, such as aptamers, with moderate to low affinities for the best binding dynamics and signal gain. We recently reported Pro-SELEX, an approach that utilizes parallelized SELEX and high-content bioinformatics for the selection of aptamers with predefined binding affinities. The Pro-SELEX pipeline relies on an algorithm, termed AptaZ, that can predict the binding affinities of selected aptamers. The original AptaZ algorithm is computationally complex and slows the overall throughput of Pro-SELEX. Here, we present Apta FastZ, a rapid equivalent of AptaZ. The Apta FastZ algorithm considers the spare nature of the sequences from SELEX and is coded to avoid unnecessary comparison between sequences. As a result, Apta FastZ achieved a 10 to 40-fold faster computing speed compared to the original AptaZ algorithm while maintaining identical outcomes, allowing the bioinformatics to be completed within 1-10 h for large-scale data sets. We further validated the affinity of myeloperoxidase aptamers predicted by Apta FastZ by experiments and observed a high level of linear correlation between predicted scores and measured affinities. Taken together, the implementation of Apta FastZ could greatly accelerate the current Pro-SELEX workflow, allowing customized aptamers to be discovered within 3 days using preselected DNA libraries.
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Affiliation(s)
- Zongjie Wang
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, Illinois 60208, United States
| | - Dingran Chang
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
| | - Edward H Sargent
- Department of Chemistry, Weinberg College of Arts & Sciences, Northwestern University, Evanston, Illinois 60208, United States
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
- Department of Electrical and Computer Engineering, McCormick School of Engineering, Northwestern University, Evanston, Illinois 60208, United States
- The Edward S. Rogers Sr. Department of Electrical & Computer Engineering, University of Toronto, Toronto M5S 3G4, Canada
| | - Shana O Kelley
- Department of Biomedical Engineering, McCormick School of Engineering, Northwestern University, Evanston, Illinois 60208, United States
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto M5S 3M2, Canada
- Department of Chemistry, Weinberg College of Arts & Sciences, Northwestern University, Evanston, Illinois 60208, United States
- International Institute for Nanotechnology, Northwestern University, Evanston, Illinois 60208, United States
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois 60611, United States
- Simpson Querrey Institute, Northwestern University, Chicago, Illinois 60611, United States
- Chan Zuckerberg Biohub Chicago, Chicago, Illinois 60607, United States
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17
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Lozoya-Colinas A, Yu Y, Chaput JC. Functionally Enhanced XNA Aptamers Discovered by Parallelized Library Screening. J Am Chem Soc 2023; 145:25789-25796. [PMID: 37962593 PMCID: PMC10690791 DOI: 10.1021/jacs.3c09497] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023]
Abstract
In vitro evolution strategies have been used for >30 years to generate nucleic acid aptamers against therapeutic targets of interest, including disease-associated proteins. However, this process requires many iterative cycles of selection and amplification, which severely restricts the number of target and library design combinations that can be explored in parallel. Here, we describe a single-round screening approach to aptamer discovery that relies on function-enhancing chemotypes to increase the distribution of high-affinity sequences in a random-sequence library. We demonstrate the success of de novo discovery by affinity selection of threomers against the receptor binding domain of the S1 protein from SARS-CoV-2. Detailed biochemical characterization of the enriched population identified threomers with binding affinity values that are comparable to aptamers produced by conventional SELEX. This work establishes a highly parallelizable path for querying diverse chemical repertoires and may offer a viable route for accelerating the discovery of therapeutic aptamers.
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Affiliation(s)
- Adriana Lozoya-Colinas
- Department
of Pharmaceutical Sciences, University of
California, Irvine, Irvine, California 92697-3958, United States
| | - Yutong Yu
- Department
of Pharmaceutical Sciences, University of
California, Irvine, Irvine, California 92697-3958, United States
| | - John C. Chaput
- Department
of Pharmaceutical Sciences, University of
California, Irvine, Irvine, California 92697-3958, United States
- Department
of Chemistry, University of California,
Irvine, Irvine, California 92697-3958, United States
- Department
of Molecular Biology and Biochemistry, University
of California, Irvine, Irvine, California 92697-3958, United States
- Department
of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697-3958, United States
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18
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Zhou J, Li H, Li J, Liu X, Zhao J, Wang N, Wang Y, Zhang Y, Zhang X, Xin Y, Li X, Wang Z, Shao N, Lou X. Selection of regioselective DNA aptamer for detection of homocysteine in nondeproteinized human plasma. Biosens Bioelectron 2023; 237:115528. [PMID: 37480786 DOI: 10.1016/j.bios.2023.115528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 07/24/2023]
Abstract
Small molecule-binding aptamers often suffer from high cross reactivity to structure analogues in biological samples, limiting their value for clinical diagnosis. Herein, we present a method to overcome this issue, by performing binding-inhibited organic reaction-based regioselective selection of aptamers against homocysteine (Hcy), which is a marker for diagnosing many disorders including stroke and Alzheimer's. This approach has led to isolation of a DNA aptamer that binds to the alkane thiol chain of Hcy with exceptional specificity against cysteine. It also binds with oxidized Hcy at weaker affinity. Using this new aptamer, we produced a reusable fluorescent optical fiber aptasensor for direct and validated detection of both free and total Hcy in nondeproteinized patient plasma in the diagnostic concentration range. The binding site-specific aptamer selection and optical-fiber-sensing strategy can expand the practical utility of aptamers in clinical diagnosis.
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Affiliation(s)
- Jianshuo Zhou
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China
| | - Hui Li
- Beijing Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Jinming Li
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China
| | - Xuemei Liu
- Beijing Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Jiaxing Zhao
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China
| | - Nan Wang
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China
| | - Yuxiao Wang
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China
| | - Yu Zhang
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China
| | - Xin Zhang
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China
| | - Yucen Xin
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China
| | - Xiaoqi Li
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China
| | - Zheng Wang
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China
| | - Ningsheng Shao
- Beijing Institute of Basic Medical Sciences, Beijing, 100850, China.
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Xisanhuan North Road. 105, Beijing, 100048, China.
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19
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Zhang W, Xiao L, Luo J, Wu M, Zhu Y, Cong F. Application of aptamer-based viral detection in animals. Pol J Vet Sci 2023; 26:521-529. [PMID: 37727988 DOI: 10.24425/pjvs.2023.145056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/21/2023]
Abstract
Viral infections are common causes of diseases in animals and appropriate methods are increasingly being required to detect viral pathogens in animals. In this regard, similar to antigen- -antibody interactions, aptamers have high affinity and specificity for their respective target molecules, and can be selected using the Systematic Evolution of Ligands by EXponential enrichment (SELEX) technique. Recently, significant progress has been made in the development of aptamer selection and aptamer-based sensors for viral detection, and here we review some of the recent advances in aptamer-based detection of viral infections in animals. This review will serve as a comprehensive resource for aptamer-based strategies in viral diagnostics.
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Affiliation(s)
- W Zhang
- Guangdong Eco-Engineering Polytechnic, 297# Guangshan 1st Road, Guangzhou 510520, Guangdong, China
| | - L Xiao
- Guangdong Laboratory Animals Monitoring institute and Guangdong Provincial Key Laboratory of Laboratory Animals, 11# Fengxin Road, Guangzhou 510033, Guangdong, China
| | - J Luo
- Guangdong Eco-Engineering Polytechnic, 297# Guangshan 1st Road, Guangzhou 510520, Guangdong, China
| | - M Wu
- Guangdong Laboratory Animals Monitoring institute and Guangdong Provincial Key Laboratory of Laboratory Animals, 11# Fengxin Road, Guangzhou 510033, Guangdong, China
| | - Y Zhu
- Guangdong Laboratory Animals Monitoring institute and Guangdong Provincial Key Laboratory of Laboratory Animals, 11# Fengxin Road, Guangzhou 510033, Guangdong, China
| | - F Cong
- Guangdong Laboratory Animals Monitoring institute and Guangdong Provincial Key Laboratory of Laboratory Animals, 11# Fengxin Road, Guangzhou 510033, Guangdong, China
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20
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Schofield P, Taylor AI, Rihon J, Peña Martinez CD, Zinn S, Mattelaer CA, Jackson J, Dhaliwal G, Schepers G, Herdewijn P, Lescrinier E, Christ D, Holliger P. Characterization of an HNA aptamer suggests a non-canonical G-quadruplex motif. Nucleic Acids Res 2023; 51:7736-7748. [PMID: 37439359 PMCID: PMC10450178 DOI: 10.1093/nar/gkad592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/09/2023] [Accepted: 07/05/2023] [Indexed: 07/14/2023] Open
Abstract
Nucleic acids not only form the basis of heredity, but are increasingly a source of novel nano-structures, -devices and drugs. This has spurred the development of chemically modified alternatives (xeno nucleic acids (XNAs)) comprising chemical configurations not found in nature to extend their chemical and functional scope. XNAs can be evolved into ligands (XNA aptamers) that bind their targets with high affinity and specificity. However, detailed investigations into structural and functional aspects of XNA aptamers have been limited. Here we describe a detailed structure-function analysis of LYS-S8-19, a 1',5'-anhydrohexitol nucleic acid (HNA) aptamer to hen egg-white lysozyme (HEL). Mapping of the aptamer interaction interface with its cognate HEL target antigen revealed interaction epitopes, affinities, kinetics and hot-spots of binding energy similar to protein ligands such as anti-HEL-nanobodies. Truncation analysis and molecular dynamics (MD) simulations suggest that the HNA aptamer core motif folds into a novel and not previously observed HNA tertiary structure, comprising non-canonical hT-hA-hT/hT-hT-hT triplet and hG4-quadruplex structures, consistent with its recognition by two different G4-specific antibodies.
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Affiliation(s)
- Peter Schofield
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW 2010, Australia
| | - Alexander I Taylor
- MRC Laboratory of Molecular Biology, Cambridge CB2 2QH, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge CB2 0AW, UK
| | - Jérôme Rihon
- Rega Institute, Laboratory of Medicinal Chemistry, Katholieke Universiteit Leuven, Herestraat 49, B 3000, Leuven, Belgium
| | - Cristian D Peña Martinez
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW 2010, Australia
| | - Sacha Zinn
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW 2010, Australia
| | - Charles-Alexandre Mattelaer
- Rega Institute, Laboratory of Medicinal Chemistry, Katholieke Universiteit Leuven, Herestraat 49, B 3000, Leuven, Belgium
| | - Jennifer Jackson
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
| | - Gurpreet Dhaliwal
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Cambridge CB2 0AW, UK
| | - Guy Schepers
- Rega Institute, Laboratory of Medicinal Chemistry, Katholieke Universiteit Leuven, Herestraat 49, B 3000, Leuven, Belgium
| | - Piet Herdewijn
- Rega Institute, Laboratory of Medicinal Chemistry, Katholieke Universiteit Leuven, Herestraat 49, B 3000, Leuven, Belgium
| | - Eveline Lescrinier
- Rega Institute, Laboratory of Medicinal Chemistry, Katholieke Universiteit Leuven, Herestraat 49, B 3000, Leuven, Belgium
| | - Daniel Christ
- Garvan Institute of Medical Research, Darlinghurst, Sydney, NSW 2010, Australia
- St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Kensington, Sydney, NSW 2010, Australia
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21
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Albright S, Cacace M, Tivon Y, Deiters A. Cell Surface Labeling and Detection of Protein Tyrosine Kinase 7 via Covalent Aptamers. J Am Chem Soc 2023; 145:16458-16463. [PMID: 37473438 PMCID: PMC10401710 DOI: 10.1021/jacs.3c02752] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Indexed: 07/22/2023]
Abstract
Covalent aptamers are novel biochemical tools for fast and selective transfer of labels to target proteins. Equipped with cleavable electrophiles, these nucleic acid probes enable the installation of functional handles onto native proteins. The high affinity and specificity with which aptamers bind their selected targets allows for quick, covalent labeling that can compete with nuclease-mediated degradation. Here, we introduce the first application of covalent aptamers to modify a specific cell surface protein through proximity-driven label transfer. We targeted protein tyrosine kinase 7 (PTK7), a prominent cancer marker, and demonstrated aptamer-mediated biotin transfer to specific lysine residues on the extracellular domain of the protein. This allowed for tracking of PTK7 expression, localization, and cellular internalization. These studies validate the programmability of covalent aptamers and highlight their applicability in a cellular context, including protein and small molecule delivery.
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Affiliation(s)
| | | | - Yaniv Tivon
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Alexander Deiters
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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22
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Wen X, Yan X, Zheng X, Kou Q, Yang L, Tang J, Chen X, Xie Y, Le T. Selection and truncation of aptamers as fluorescence sensing platforms for selective and sensitive detection of nitrofurazone. Anal Chim Acta 2023; 1252:341044. [PMID: 36935137 DOI: 10.1016/j.aca.2023.341044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 02/02/2023] [Accepted: 03/02/2023] [Indexed: 03/13/2023]
Abstract
Nitrofurazone (NFZ) is an antibiotic banned in many countries, as its residue seriously harms the human body. Herein, anti-NFZ aptamers were selected and identified based on the magnetic bead SELEX technique using a ssDNA library with a full length of 90 nucleotides (nt). Five full sequence candidate aptamers (NFZ8, NFZ24, NFZ28, NFZ34, and NFZ70) were obtained by secondary structure analysis. We optimized the entire sequence to obtain a truncated aptamer, a 16 nt sequence (NFZ8-1:5'-GTTCTATTGAAAAAAC-3') that showed the highest affinity for NFZ (Kd = 76.11 nM). The binding site of NFZ and aptamer NFZ8-1 was found to be "GAA" by molecular docking. In addition, utilizing the most special truncated aptamer NFZ8-1 as the identification probe, a graphene oxide fluorescent aptasensor is an innovative for the detection of NFZ residue that showed a wide linear reach from 1.25 to 160 ng/mL and a low limit of detection of 1.13 ng/mL. In the actual water environment sample detection, the recovery rate ranged from 95.21 to 113.66%, and the coefficient of variation ranged from 3.53 to 11.24%. These results demonstrate that the NFZ-truncated aptamer applied to the aptasensor provides a novel methodology for recognizing NFZ residues.
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Affiliation(s)
- Xu Wen
- College of Life Science, Chongqing Normal University, Chongqing, 401331, PR China
| | - Xueling Yan
- College of Life Science, Chongqing Normal University, Chongqing, 401331, PR China
| | - Xiaoling Zheng
- College of Life Science, Chongqing Normal University, Chongqing, 401331, PR China
| | - Qiming Kou
- College of Life Science, Chongqing Normal University, Chongqing, 401331, PR China
| | - Lulan Yang
- College of Life Science, Chongqing Normal University, Chongqing, 401331, PR China
| | - Jiaming Tang
- College of Life Science, Chongqing Normal University, Chongqing, 401331, PR China
| | - Xingyue Chen
- College of Life Science, Chongqing Normal University, Chongqing, 401331, PR China
| | - Yong Xie
- Bioassay 3D Reconstruction Laboratory, Chongqing College of Electronic Engineering, Chongqing, 401331, PR China
| | - Tao Le
- College of Life Science, Chongqing Normal University, Chongqing, 401331, PR China.
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23
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Chen J, Chen X, Zhang Y, Wang X, Zhou N. Screening of a Sialyllactose-Specific Aptamer and Engineering a Pair of Recognition Elements with Unique Fluorescent Characteristics for Sensitive Detection of Sialyllactose. J Agric Food Chem 2023; 71:2628-2636. [PMID: 36700646 DOI: 10.1021/acs.jafc.2c07784] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
A single-stranded DNA (ssDNA) aptamer specific for 6'-sialyllactose (6'-SL) was screened through magnetic separation-based SELEX and post-SELEX truncation and used to construct unique aptamer bio-dots for sensitive detection of 6'-SL. Eighteen rounds of screening were conducted during the SELEX process. The ssDNA aptamer Apt9 (Kd = 152.3 nM) with a length of 79 nucleotides (nt) was demonstrated as the optimal aptamer candidate after affinity and specificity evaluation. Then, Apt9 was truncated and optimized according to secondary structure and molecular docking. A 35 nt truncated aptamer Apt9-1 (Kd = 91.75 nM) with higher affinity than Apt9 was finally obtained. Furthermore, Apt9-1 was used to synthesize bio-dots as a new recognition element of 6'-SL, and the aminobenzene boric acid functionalized carbon dots were employed as the other recognition element. With the respective fluorescent characteristics, the two quantum dots (QDs) were made a pair to construct a 6'-SL fluorescent biosensor. The linear detection range of the biosensor is 10 μM to 5 mM, and the detection limit is 0.9 μM. With the advantages of time-saving, high efficiency, and simplicity in the actual sample detection, the screened aptamer and dual-QD-based biosensor have broad application prospects in 6'-SL detection.
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Affiliation(s)
- Jinri Chen
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Jiangsu Key Laboratory of Marine Bioresources and Environment, Jiangsu Ocean University, 59 Cangwu Road, Haizhou 222005, China
| | - Xin Chen
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Yuting Zhang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xiaoli Wang
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Nandi Zhou
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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24
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Liu Y, Yang J, Chen M, Lu X, Wei Z, Tang C, Yu P. Recent Advances in Computer-aided Virtual Screening and Docking Optimization for Aptamer. Curr Top Med Chem 2023; 23:1985-2000. [PMID: 37357516 DOI: 10.2174/1568026623666230623145802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 05/21/2023] [Accepted: 05/30/2023] [Indexed: 06/27/2023]
Abstract
Aptamers, as artificially synthesized short nucleotide sequences, have been widely used in protein analysis, gene engineering, and molecular diagnostics. Currently, the screening process of aptamers still relies on the traditional SELEX process, which is cumbersome and complex. Moreover, the success rate of aptamer screening through the SELEX process is not high, which has become a major challenge. In recent years, the development of computers has facilitated virtual screening, which can greatly accelerate the screening process of aptamers through computer-assisted screening. However, the accuracy and precision of current virtual screening software on the market vary. Therefore, this work summarizes the docking characteristics of four mainstream molecular docking software programs, including Auto dock, Auto dock Vina, MOE, and hex Dock, in recent years. Moreover, the accuracy and prediction performance of these four molecular docking software programs for aptamer docking based on experimental data is also evaluated. This will guide researchers in the selection of molecular docking software. Additionally, this review provides a detailed overview of the application of computer-aided virtual screening in aptamer screening, thus providing a direction for future development in this field.
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Affiliation(s)
- Yijie Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Jie Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Meilun Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Xiaoling Lu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Zheng Wei
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Chunhua Tang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Peng Yu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
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25
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Abstract
The systematic evolution of ligands by exponential enrichment (SELEX) enables the identification of ssDNA or RNA sequences binding to different target molecules, highly specific and with high affinity. In this chapter, we describe a selection strategy with ssDNA for a histidine-tagged protein that could be either performed hands-on manually or fully automated by an appropriate robotic selection platform.
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Affiliation(s)
- Stefan Breuers
- Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
- Center of Aptamer Research and Development, University of Bonn, Bonn, Germany
| | - Günter Mayer
- Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany.
- Center of Aptamer Research and Development, University of Bonn, Bonn, Germany.
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26
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Abstract
RNA aptamers are structured RNAs that can bind to diverse ligands, including proteins, metabolites, and other small molecules. RNA aptamers are widely used as in vitro affinity reagents. However, RNA aptamers have not been highly successful as bioactive intracellular molecules that can bind target molecules and influence cellular processes. We describe how poor RNA aptamer expression and especially poor RNA aptamer folding have limited the use of RNA aptamers in RNA synthetic biology applications. We discuss innovative new approaches that promote RNA aptamer folding in living cells and how these approaches have improved the function of aptamers in mammalian cells. These new approaches are making RNA aptamer-based synthetic biology and RNA aptamer therapeutic applications much more achievable.
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Affiliation(s)
- Qian Hou
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, The Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
| | - Samie R. Jaffrey
- Tri-Institutional PhD Program in Chemical Biology, Weill Cornell Medicine, The Rockefeller University, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Department of Pharmacology, Weill Cornell Medical College, Cornell University, New York, NY, USA
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27
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Piwko AT, Han X, Kabza AM, Dey S, Sczepanski JT. Inverse In Vitro Selection Enables Comprehensive Analysis of Cross-Chiral L-Aptamer Interactions. Chembiochem 2022; 23:e202200520. [PMID: 36282114 PMCID: PMC9798143 DOI: 10.1002/cbic.202200520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/25/2022] [Indexed: 01/25/2023]
Abstract
Aptamers composed of mirror-image L-(deoxy)ribose nucleic acids, referred to as L-aptamers, are a promising class of RNA-binding reagents. Yet, the selectivity of cross-chiral interactions between L-aptamers and their RNA targets remain poorly characterized, limiting the potential utility of this approach for applications in biological systems. Herein, we carried out the first comprehensive analysis of cross-chiral L-aptamer selectivity using a newly developed "inverse" in vitro selection approach that exploits the genetic nature of the D-RNA ligand. By employing a library of more than a million target-derived sequences, we determined the RNA sequence and structural preference of a model L-aptamer and revealed previously unidentified and potentially broad off-target RNA binding behaviors. These results provide valuable information for assessing the likelihood and consequences of potential off-target interactions and reveal strategies to mitigate these effects. Thus, inverse in vitro selection provides several opportunities to advance L-aptamer technology.
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Affiliation(s)
- Alexander T Piwko
- Department of Chemistry, Texas A&M University, College Station, 77843 TX, USA
- Current address: Department of Chemistry and Biochemistry, Florida State University, 32304, Tallahassee, FL, USA
| | - Xuan Han
- Department of Chemistry, Texas A&M University, College Station, 77843 TX, USA
| | - Adam M Kabza
- Department of Chemistry, Texas A&M University, College Station, 77843 TX, USA
- Current address: Avidity Biosciences, 92121, San Diego, CA, USA
| | - Sougata Dey
- Department of Chemistry, Texas A&M University, College Station, 77843 TX, USA
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28
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Liu M, Wang Z, Li S, Deng Y, He N. Identification of PHB2 as a Potential Biomarker of Luminal A Breast Cancer Cells Using a Cell-Specific Aptamer. ACS Appl Mater Interfaces 2022; 14:51593-51601. [PMID: 36346944 DOI: 10.1021/acsami.2c12291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Precise diagnosis of breast cancer molecular subtypes remains a great challenge in clinics. The present molecular biomarkers are not specific enough to classify breast cancer subtypes precisely, which requests for more accurate and specific molecular biomarkers to be discovered. Aptamers evolved by the cell-systematic evolution of ligands by exponential enrichment (SELEX) method show great potential in the discovery and identification of cell membrane targets via aptamer-based cell membrane protein pull-down, which has been regarded as a novel and powerful weapon for the discovery and identification of new molecular biomarkers. Herein, a cell membrane protein PHB2 was identified as a potential molecular biomarker specifically expressed in the cell membranes of MCF-7 breast cancer cells using a DNA aptamer MF3Ec. Further experiments demonstrated that the PHB2 protein is differentially expressed in the cell membranes of MCF-7, SK-BR-3, and MDA-MB-231 breast cancer cells and MCF-10A cells, and the binding molecular domains of aptamer MF3Ec and anti-PHB2 antibodies to the PHB2 protein are different due to there being no obvious competitions between aptamer MF3Ec and anti-PHB2 antibodies in the binding to the cell membranes of target MCF-7 cells. Due to those four cells belonging to luminal A, HER2-positive, and triple-negative breast cancer cell subtypes and human normal mammary epithelial cells, respectively, the PHB2 protein in the cell membrane may be a potential biomarker for precise diagnosis of the luminal A breast cancer cell subtype, which is endowed with the ability to differentiate the luminal A breast cancer cell subtype from HER2-positive and triple-negative breast cancer cell subtypes and human normal mammary epithelial cells, providing a new molecular biomarker and therapeutic target for the accurate and precise classification and diagnostics and personalized therapy of breast cancer.
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Affiliation(s)
- Mei Liu
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education (Southeast University), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, P. R. China
- Key Laboratory of Basic and Translational Research on Immune-Mediated Skin Diseases, Chinese Academy of Medical Sciences, Nanjing 210042, P. R. China
- Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College, Nanjing 210042, P. R. China
| | - Zhifei Wang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, P. R. China
| | - Song Li
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Yan Deng
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, National Demonstration Center for Experimental Biomedical Engineering Education (Southeast University), School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, P. R. China
- Economical Forest Cultivation and Utilization of 2011 Collaborative Innovation Center in Hunan Province, Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, P. R. China
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29
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Gholikhani T, Kumar S, Valizadeh H, Mahdinloo S, Adibkia K, Zakeri-Milani P, Barzegar-Jalali M, Jimenez B. Advances in Aptamers-Based Applications in Breast Cancer: Drug Delivery, Therapeutics, and Diagnostics. Int J Mol Sci 2022; 23:ijms232214475. [PMID: 36430951 PMCID: PMC9695968 DOI: 10.3390/ijms232214475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 11/03/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
Aptamers are synthetic single-stranded oligonucleotides (such as RNA and DNA) evolved in vitro using Systematic Evolution of Ligands through Exponential enrichment (SELEX) techniques. Aptamers are evolved to have high affinity and specificity to targets; hence, they have a great potential for use in therapeutics as delivery agents and/or in treatment strategies. Aptamers can be chemically synthesized and modified in a cost-effective manner and are easy to hybridize to a variety of nano-particles and other agents which has paved a way for targeted therapy and diagnostics applications such as in breast tumors. In this review, we systematically explain different aptamer adoption approaches to therapeutic or diagnostic uses when addressing breast tumors. We summarize the current therapeutic techniques to address breast tumors including aptamer-base approaches. We discuss the next aptamer-based therapeutic and diagnostic approaches targeting breast tumors. Finally, we provide a perspective on the future of aptamer-based sensors for breast therapeutics and diagnostics. In this section, the therapeutic applications of aptamers will be discussed for the targeting therapy of breast cancer.
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Affiliation(s)
- Tooba Gholikhani
- Student Research Committee, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
- NanoRa Pharmaceuticals Ltd., Tabriz 5166-15731, Iran
| | - Shalen Kumar
- IQ Science Limited, Wellington 5010, New Zealand
| | - Hadi Valizadeh
- Drug Applied Research Centre, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
| | - Somayeh Mahdinloo
- Student Research Committee, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
| | - Khosro Adibkia
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
| | - Parvin Zakeri-Milani
- Liver and Gastrointestinal Diseases Research Center, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
| | - Mohammad Barzegar-Jalali
- Pharmaceutical Analysis Research Center, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz 5166-15731, Iran
| | - Balam Jimenez
- School of Biological Sciences, Victoria University of Wellington, Wellington 6012, New Zealand
- Correspondence:
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30
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Guo H, Deng B, Zhao L, Gao Y, Zhang X, Yang C, Zou B, Chen H, Sun M, Wang L, Jiao B. Programmed Aptamer Screening, Characterization, and Rapid Detection for α-Conotoxin MI. Toxins (Basel) 2022; 14:toxins14100706. [PMID: 36287974 PMCID: PMC9606946 DOI: 10.3390/toxins14100706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/23/2022] Open
Abstract
Conotoxins (CTXs) are a variety of mixed polypeptide toxins, among which α-conotoxin MI (CTX-MI) is the most toxic. Serious toxic symptoms, a lack of counteracting drugs, and cumbersome detection processes have made CTX-MI a hidden danger for humans. One of the obstacles to resolving this problem is the absence of specific recognition elements. Aptamers have shown great advantages in the fields of molecule detection, drug development, etc. In this study, we screened and characterized aptamers for CTX-MI through a programmed process. MBMI-01c, the isolated aptamer, showed great affinity, with an affinity constant (K<sub>D</sub>) of 0.524 μM, and it formed an antiparallel G-quadruplet (GQ) structure for the specific recognition of CTX-MI. Additionally, an aptasensor based on the biolayer interferometry (BLI) platform was developed and displayed high precision, specificity, and repeatability with a limit of detection (LOD) of 0.26 μM. This aptasensor provides a potential tool for the rapid detection of CTX-MI in 10 min. The aptamer can be further developed for the enrichment, detoxification, and biological studies of CTX-MI. Additionally, the programmed process is applicable to screening and characterizing aptamers for other CTXs.
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31
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Kissmann AK, Wolf D, Krämer M, Müller F, Amann V, Xing H, Gottschalk KE, Weil T, Eichmann R, Schäfer P, Rosenau F. Polyclonal Aptamer Libraries from a FluRoot-SELEX for the Specific Labeling of the Apical and Elongation/Differentiation Zones of Arabidopsis thaliana Roots. Int J Mol Sci 2022; 23:ijms232012220. [PMID: 36293073 PMCID: PMC9602526 DOI: 10.3390/ijms232012220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/10/2022] [Accepted: 10/12/2022] [Indexed: 11/16/2022] Open
Abstract
In more than 30 years of aptamer research, it has become widely accepted that aptamers are fascinating binding molecules for a vast variety of applications. However, the majority of targets have been proteins, although special variants of the so-called SELEX process for the molecular evolution of specific aptamers have also been developed, allowing for the targeting of small molecules as well as larger structures such as cells and even cellular networks of human (tumor) tissues. Although the provocative thesis is widely accepted in the field, that is, in principle, any level of complexity for SELEX targets is possible, the number of studies on whole organs or at least parts of them is limited. To pioneer this thesis, and based on our FluCell-SELEX process, here, we have developed polyclonal aptamer libraries against apices and the elongation/differentiation zones of plant roots as examples of organs. We show that dedicated libraries can specifically label the respective parts of the root, allowing us to distinguish them in fluorescence microscopy. We consider this achievement to be an initial but important evidence for the robustness of this SELEX variant. These libraries may be valuable tools for plant research and a promising starting point for the isolation of more specific individual aptamers directed against root-specific epitopes.
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Affiliation(s)
- Ann-Kathrin Kissmann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
- Max-Planck-Institute for Polymer Research Mainz, Ackermannweg 10, 55128 Mainz, Germany
| | - Dennis Wolf
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Markus Krämer
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Franziska Müller
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Valerie Amann
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Hu Xing
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Kay-Eberhard Gottschalk
- Institute of Experimental Physics, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
| | - Tanja Weil
- Max-Planck-Institute for Polymer Research Mainz, Ackermannweg 10, 55128 Mainz, Germany
| | - Ruth Eichmann
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392 Giessen, Germany
| | - Patrick Schäfer
- Institute of Phytopathology, Research Centre for BioSystems, Land Use and Nutrition, Justus Liebig University, 35392 Giessen, Germany
| | - Frank Rosenau
- Institute of Pharmaceutical Biotechnology, Ulm University, Albert-Einstein-Allee 11, 89081 Ulm, Germany
- Max-Planck-Institute for Polymer Research Mainz, Ackermannweg 10, 55128 Mainz, Germany
- Correspondence:
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32
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Abstract
In both biomedical research and clinical cell therapy manufacturing, there is a need for cell isolation systems that recover purified cells in the absence of any selection agent. Reported traceless cell isolation methods using engineered antigen-binding fragments or aptamers have been limited to processing a single cell type at a time. There remains an unmet need for cell isolation processes that rapidly sort multiple target cell types. Here, we utilized two aptamers along with their designated complementary strands (reversal agents) to tracelessly isolate two cell types from a mixed cell population with one aptamer-labeling step and two sequential cell elution steps with reversal agents. We engineered a CD71-binding aptamer (rvCD71apt) and a reversal agent pair to be used simultaneously with our previously reported traceless purification approach using the CD8 aptamer (rvCD8apt) and its reversal agent. We verified the compatibility of the two aptamer displacement mechanisms by flow cytometry and the feasibility of incorporating rvCD71apt with a magnetic solid state. We then combined rvCD71apt with rvCD8apt to isolate activated CD4+ T cells and resting CD8+ cells by eluting these target cells into separate fractions with orthogonal strand displacements. This is the first demonstration of isolating different cell types using two aptamers and reversal agents at the same time. Potentially, different or more aptamers can be included in this traceless multiplexed isolation system for diverse applications with a shortened operation time and a lower production cost.
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Affiliation(s)
- Emmeline L Cheng
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Nataly Kacherovsky
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
| | - Suzie H Pun
- Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, United States
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Xu R, Yang C, Huang L, Lv W, Yang W, Wu Y, Fu F. Broad-Specificity Aptamer of Sulfonamides: Isolation and Its Application in Simultaneous Detection of Multiple Sulfonamides in Fish Sample. J Agric Food Chem 2022; 70:11804-11812. [PMID: 36070569 DOI: 10.1021/acs.jafc.2c03423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Sulfonamide antibiotics (SAs) are widely used in animal husbandry and aquaculture, and the excess residues of SAs in animal-derived foods will harm the health of consumers. In reality, various SAs were alternately used in animal husbandry and aquaculture, and thus, it is urgent need to develop simple and high-throughput methods for simultaneously detecting multiple SAs or groups of SAs in order to realize rapid screening of total SAs residues in animal-derived foods. We herein isolated a broad-specificity aptamer for SAs by using a multi-SAs systematic evolution of ligands by exponential enrichment (SELEX) strategy. The isolated broad-specificity aptamer has a higher binding affinity to five different SAs including sulfaquinoxaline (SQ), sulfamethoxypyridazine (SMPZ), sulfametoxydiazine (SMD), sulfachloropyridazine (SCP), and sulfapyridine (SPD) and, thus, can be used as a bioreceptor for developing various high-throughput methods for the simultaneous detection or rapid screening of above five SAs. Based on the isolated broad-specificity aptamer and Cy7 (diethylthiatricarbocyanine) displacement strategy, a colorimetric aptasensor was developed for the simultaneous detection of SQ, SMPZ, SMD, SCP, and SPD with a visual detection limit of 2.0-5.0 μM and a spectrometry detection limit of 0.2-0.5 μM. The colorimetric aptasensor was successfully used to detect SQ, SMPZ, SMD, SCP, and SPD in fish muscle with a recovery of 82%-92% and a RSD (n = 5) < 7%. The success of this study provided a promising bioreceptor for developing various high-throughput methods for on-site rapid screening of multiple SAs residues, as well as a simple method for the rapid and cost-effective screening of total SQ, SMPZ, SMD, SCP, and SPD in seafood.
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Affiliation(s)
- Ruyi Xu
- Key Laboratory for Analytical Science of Food Safety and Biology of MOE, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Chen Yang
- Key Laboratory for Analytical Science of Food Safety and Biology of MOE, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Lin Huang
- Key Laboratory for Analytical Science of Food Safety and Biology of MOE, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Wenchao Lv
- Key Laboratory for Analytical Science of Food Safety and Biology of MOE, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, China
| | - Weijuan Yang
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yongning Wu
- NHC Key Lab of Food Safety Risk Assessment, Food Safety Research Unit (2019RU014) of China Academy of Medical Science, China National Center for Food Safety Risk Assessment, Beijing 100021, China
| | - FengFu Fu
- Key Laboratory for Analytical Science of Food Safety and Biology of MOE, College of Chemistry, Fuzhou University, Fuzhou, Fujian 350108, China
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Williams NB, Batool S, Zumrut HE, Patel R, Sosa G, Jamal M, Mallikaratchy P. An In Vitro Selection Platform to Identify Multiple Aptamers against Multiple Cell-Surface Markers Using Ligand-Guided Selection. Biochemistry 2022; 61:1600-1613. [PMID: 35829681 PMCID: PMC10117398 DOI: 10.1021/acs.biochem.2c00105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aptamer ligand discovery against multiple molecules expressed on whole cells is an essential component in molecular tool development. However, owing to their intrinsic structural characteristics, cell-surface receptors have proven to be challenging targets in ligand discovery. Several variants to systematic evolution of ligands by exponential enrichment (SELEX) have been introduced to address the ″target problem″ for aptamer screening. To this end, we introduced a variant of SELEX, termed ligand-guided selection (LIGS), to identify highly specific aptamers against complex cell-surface markers in their native state. So far, the application of LIGS has been aimed at identifying aptamers against the most dominant receptors on the cell surface. Here, we report that LIGS can be expanded to identify two receptors on the same cell surface, paving the way to generate a multiplexed ligand discovery platform based on SELEX-targeting membrane receptors in their native functional state. Using CD19 and CD20 expressed on Toledo cells as a model system, multiple aptamer families were evolved against Toledo cells. We then utilized two monoclonal antibodies (mAbs) against CD20 and CD19 to selectively partition specific aptamers against CD19 and CD20. Following biochemical characterization, we introduce two specific aptamers against CD19 and two specific aptamers against CD20 with high affinity. Multi-target LIGS, as reported here, demonstrates a successful combinatorial approach for nucleic acid library screening to generate multiple artificial nucleic acid ligands against multiple receptors expressed on a single cell.
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Affiliation(s)
- Nicole B Williams
- Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, The City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Sana Batool
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd., West Bronx, New York, New York 10468, United States
| | - Hasan E Zumrut
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, The City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - Rutika Patel
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, The City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
| | - German Sosa
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd., West Bronx, New York, New York 10468, United States
| | - Mohammad Jamal
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd., West Bronx, New York, New York 10468, United States
| | - Prabodhika Mallikaratchy
- Department of Chemistry, Lehman College, The City University of New York, 250 Bedford Park Blvd., West Bronx, New York, New York 10468, United States
- Ph.D. Programs in Chemistry and Biochemistry, CUNY Graduate Center, The City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
- Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, The City University of New York, 365 Fifth Avenue, New York, New York 10016, United States
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Mukherjee M, Appaiah P, Sistla S, Bk B, Bhatt P. Bio-Layer Interferometry-Based SELEX and Label-Free Detection of Patulin Using Generated Aptamer. J Agric Food Chem 2022; 70:6239-6246. [PMID: 35546052 DOI: 10.1021/acs.jafc.2c01591] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This study reports a novel bio-layer interferometry (BLI)-based SELEX for generation of high affinity aptamers against patulin. Unlike conventional SELEX, the present method enabled real-time monitoring of increasing affinity of the oligonucleotides to the toxin. After seven rounds of selection cycles, the enriched pool of aptamers was characterized by cloning and sequencing and clustered into two families based on similarity. Two sequences, PAT C3 and PAT C4, each belonging to different clades, were further evaluated for their binding affinity. SPR studies determined the dissociation constants (KD) of 8.2 × 10-8 and 1.9 × 10-7 M for aptamer PAT C3 and PAT C4, respectively. The highest affinity PAT C3 aptamer was used to develop a patulin BLI aptasensor, which indicated a linear detection range from 0.045 to 100 ng/mL [limit of detection (LOD) = 0.173 ng/mL; limit of quantification (LOQ) = 0.526 ng/mL]. The aptasensor displayed no cross-reactivity with its structural analogue isopatulin or any of the other mycotoxin groups tested. Spiking studies in simulated apple juice samples showed recoveries in the range of 82.11 to 100.23%, indicating good sensor performance. The study is the first report of BLI-based SELEX for a non-protein toxin, which resulted in the generation of high affinity aptamers and development of an aptasensor which can have wide application in the food industry for high throughput screening of samples for patulin contamination within a short span of time.
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Affiliation(s)
- Monali Mukherjee
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute (CFTRI), Mysuru 570020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Prakruthi Appaiah
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute (CFTRI), Mysuru 570020, India
| | - Srinivas Sistla
- Department of Microbiology & Immunology, Stonybrook University, New York, New York 11794, United States
| | - Bettadaiah Bk
- Spices and Flavour Sciences Department, CSIR-Central Food Technological Research Institute (CFTRI), Mysuru 570020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
| | - Praveena Bhatt
- Microbiology & Fermentation Technology Department, CSIR-Central Food Technological Research Institute (CFTRI), Mysuru 570020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India
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36
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Hoetzel J, Suess B. Structural changes in aptamers are essential for synthetic riboswitch engineering. J Mol Biol 2022; 434:167631. [PMID: 35595164 DOI: 10.1016/j.jmb.2022.167631] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 05/05/2022] [Accepted: 05/07/2022] [Indexed: 11/19/2022]
Abstract
Synthetic riboswitches are powerful tools in synthetic biology in which sensing and execution are consolidated in a single RNA molecule. By using SELEX to select aptamers in vitro, synthetic riboswitches can in theory be engineered against any ligand of choice. Surprisingly, very few in vitro selected aptamers have been used for the engineering of synthetic riboswitches. In-depth studies of these aptamers suggest that the key characteristics of such regulatory active RNAs are their structural switching abilities and their binding dynamics. Conventional SELEX approaches seem to be inadequate to select for these characteristics, which may explain the lack of in vitro selected aptamers suited for engineering of synthetic riboswitches. In this review, we explore the functional principles of synthetic riboswitches, identify key characteristics of regulatory active in vitro selected aptamers and integrate these findings in context with available in vitro selection methods. Based on these insights, we propose to use a combination of capture-SELEX and subsequent functional screening for a more successful in vitro selection of aptamers that can be applied for the engineering of synthetic riboswitches.
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Affiliation(s)
- Janis Hoetzel
- Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany. https://www.twitter.com/J_Hoetzel
| | - Beatrix Suess
- Department of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, D-64287 Darmstadt, Germany; Center for Synthetic Biology, Technical University of Darmstadt, Germany.
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37
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Liu M, Yue F, Kong Q, Liu Z, Guo Y, Sun X. Aptamers against Pathogenic Bacteria: Selection Strategies and Apta-assay/Aptasensor Application for Food Safety. J Agric Food Chem 2022; 70:5477-5498. [PMID: 35471004 DOI: 10.1021/acs.jafc.2c01547] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Pathogenic bacteria are primarily kinds of detrimental agents that cause mankind illness via contaminated food with traits of multiple types, universality, and low content. In view of the detection demands for rapidity, aptamer recognition factors emerged as a substitution for antibodies, which are short single strands of nucleic acid selected via in vitro. They display certain superiorities over antibodies, such as preferable stability, liable modification, and cost-efficiency. Taking advantage of the situation, numerous aptamers against pathogenic bacteria have been successfully selected and applied, yet there are still restrictions on commercial availability. In this review, the strategies/approaches to key sections in pathogen aptamers SELEX and post-SELEX are summarized and sorted out. Recently, optical, electrochemical, and piezoelectric aptamer-based assays or sensors dedicated to pathogen detection have been critically reviewed. Ultimately, the existing challenges and future trends in this field are proposed to further promote development prospects.
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Affiliation(s)
- Mengyue Liu
- School of Agricultural Engineering and Food Science, Shandong University of Technology, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
| | - Fengling Yue
- School of Agricultural Engineering and Food Science, Shandong University of Technology, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
| | - Qianqian Kong
- School of Agricultural Engineering and Food Science, Shandong University of Technology, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
| | - Zhanli Liu
- School of Agricultural Engineering and Food Science, Shandong University of Technology, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
| | - Yemin Guo
- School of Agricultural Engineering and Food Science, Shandong University of Technology, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
| | - Xia Sun
- School of Agricultural Engineering and Food Science, Shandong University of Technology, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Shandong Provincial Engineering Research Center of Vegetable Safety and Quality Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
- Zibo City Key Laboratory of Agricultural Product Safety Traceability, 266 Xincun Xilu, Zibo, Shandong 255049, People's Republic of China
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38
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Huang Y, Nguyen MK, Nguyen VH, Loo J, Lehtonen AJ, Kuzyk A. Characterizing Aptamers with Reconfigurable Chiral Plasmonic Assemblies. Langmuir 2022; 38:2954-2960. [PMID: 35212547 PMCID: PMC8908738 DOI: 10.1021/acs.langmuir.1c03434] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 02/15/2022] [Indexed: 06/14/2023]
Abstract
Aptamers have emerged as versatile affinity ligands and as promising alternatives to protein antibodies. However, the inconsistency in the reported affinities and specificities of aptamers has greatly hindered the development of aptamer-based applications. Herein, we present a strategy to characterize aptamers by using DNA origami-based chiral plasmonic assemblies as reporters and establishing a competitive hybridization reaction-based thermodynamic model. We demonstrate the characterization of several DNA aptamers, including aptamers for small molecules and macromolecules, as well as aptamers with high and low affinities. The presented characterization scheme can be readily adapted to a wide selection of aptamers. We anticipate that our approach will advance the development of aptamer-based applications by enabling reliable and reproducible characterization of aptamers.
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Affiliation(s)
- Yike Huang
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Minh-Kha Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
- Faculty
of Chemical Engineering, Ho Chi Minh City
University of Technology (HCMUT), 268 Ly Thuong Kiet Street, Dist. 10, 700000 Ho Chi Minh City, Vietnam
- Vietnam
National University Ho Chi Minh City,
Linh Trung Ward, Thu Duc District, 700000 Ho Chi Minh City, Vietnam
| | - Vu Hoang Nguyen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Jacky Loo
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
| | - Arttu J. Lehtonen
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
- Department
of Electrical Engineering and Automation, School of Electrical Engineering, Aalto University, FI-00076 Aalto, Finland
| | - Anton Kuzyk
- Department
of Neuroscience and Biomedical Engineering, School of Science, Aalto University, FI-00076 Aalto, Finland
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Mironov V, Shchugoreva IA, Artyushenko PV, Morozov D, Borbone N, Oliviero G, Zamay TN, Moryachkov RV, Kolovskaya OS, Lukyanenko KA, Song Y, Merkuleva IA, Zabluda VN, Peters G, Koroleva LS, Veprintsev DV, Glazyrin YE, Volosnikova EA, Belenkaya SV, Esina TI, Isaeva AA, Nesmeyanova VS, Shanshin DV, Berlina AN, Komova NS, Svetlichnyi VA, Silnikov VN, Shcherbakov DN, Zamay GS, Zamay SS, Smolyarova T, Tikhonova EP, Chen KH, Jeng U, Condorelli G, de Franciscis V, Groenhof G, Yang C, Moskovsky AA, Fedorov DG, Tomilin FN, Tan W, Alexeev Y, Berezovski MV, Kichkailo AS. Structure- and Interaction-Based Design of Anti-SARS-CoV-2 Aptamers. Chemistry 2022; 28:e202104481. [PMID: 35025110 PMCID: PMC9015568 DOI: 10.1002/chem.202104481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Indexed: 11/10/2022]
Abstract
Aptamer selection against novel infections is a complicated and time-consuming approach. Synergy can be achieved by using computational methods together with experimental procedures. This study aims to develop a reliable methodology for a rational aptamer in silico et vitro design. The new approach combines multiple steps: (1) Molecular design, based on screening in a DNA aptamer library and directed mutagenesis to fit the protein tertiary structure; (2) 3D molecular modeling of the target; (3) Molecular docking of an aptamer with the protein; (4) Molecular dynamics (MD) simulations of the complexes; (5) Quantum-mechanical (QM) evaluation of the interactions between aptamer and target with further analysis; (6) Experimental verification at each cycle for structure and binding affinity by using small-angle X-ray scattering, cytometry, and fluorescence polarization. By using a new iterative design procedure, structure- and interaction-based drug design (SIBDD), a highly specific aptamer to the receptor-binding domain of the SARS-CoV-2 spike protein, was developed and validated. The SIBDD approach enhances speed of the high-affinity aptamers development from scratch, using a target protein structure. The method could be used to improve existing aptamers for stronger binding. This approach brings to an advanced level the development of novel affinity probes, functional nucleic acids. It offers a blueprint for the straightforward design of targeting molecules for new pathogen agents and emerging variants.
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40
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Cheng H, Yang Q, Wang R, Luo R, Zhu S, Li M, Li W, Chen C, Zou Y, Huang Z, Xie T, Wang S, Zhang H, Tian Q. Emerging Advances of Detection Strategies for Tumor-Derived Exosomes. Int J Mol Sci 2022; 23:ijms23020868. [PMID: 35055057 PMCID: PMC8775838 DOI: 10.3390/ijms23020868] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/06/2022] [Accepted: 01/11/2022] [Indexed: 12/12/2022] Open
Abstract
Exosomes derived from tumor cells contain various molecular components, such as proteins, RNA, DNA, lipids, and carbohydrates. These components play a crucial role in all stages of tumorigenesis and development. Moreover, they reflect the physiological and pathological status of parental tumor cells. Recently, tumor-derived exosomes have become popular biomarkers for non-invasive liquid biopsy and the diagnosis of numerous cancers. The interdisciplinary significance of exosomes research has also attracted growing enthusiasm. However, the intrinsic nature of tumor-derived exosomes requires advanced methods to detect and evaluate the complex biofluid. This review analyzes the relationship between exosomes and tumors. It also summarizes the exosomal biological origin, composition, and application of molecular markers in clinical cancer diagnosis. Remarkably, this paper constitutes a comprehensive summary of the innovative research on numerous detection strategies for tumor-derived exosomes with the intent of providing a theoretical basis and reference for early diagnosis and clinical treatment of cancer.
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Affiliation(s)
- Huijuan Cheng
- College of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (H.C.); (Q.Y.); (R.W.); (R.L.); (M.L.); (W.L.); (C.C.); (Y.Z.); (Z.H.); (T.X.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Qian Yang
- College of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (H.C.); (Q.Y.); (R.W.); (R.L.); (M.L.); (W.L.); (C.C.); (Y.Z.); (Z.H.); (T.X.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Rongrong Wang
- College of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (H.C.); (Q.Y.); (R.W.); (R.L.); (M.L.); (W.L.); (C.C.); (Y.Z.); (Z.H.); (T.X.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Ruhua Luo
- College of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (H.C.); (Q.Y.); (R.W.); (R.L.); (M.L.); (W.L.); (C.C.); (Y.Z.); (Z.H.); (T.X.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Shanshan Zhu
- Public Health Institutes, Hangzhou Normal University, Hangzhou 311121, China;
| | - Minhui Li
- College of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (H.C.); (Q.Y.); (R.W.); (R.L.); (M.L.); (W.L.); (C.C.); (Y.Z.); (Z.H.); (T.X.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Wenqi Li
- College of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (H.C.); (Q.Y.); (R.W.); (R.L.); (M.L.); (W.L.); (C.C.); (Y.Z.); (Z.H.); (T.X.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Cheng Chen
- College of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (H.C.); (Q.Y.); (R.W.); (R.L.); (M.L.); (W.L.); (C.C.); (Y.Z.); (Z.H.); (T.X.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Yuqing Zou
- College of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (H.C.); (Q.Y.); (R.W.); (R.L.); (M.L.); (W.L.); (C.C.); (Y.Z.); (Z.H.); (T.X.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Zhihua Huang
- College of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (H.C.); (Q.Y.); (R.W.); (R.L.); (M.L.); (W.L.); (C.C.); (Y.Z.); (Z.H.); (T.X.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Tian Xie
- College of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (H.C.); (Q.Y.); (R.W.); (R.L.); (M.L.); (W.L.); (C.C.); (Y.Z.); (Z.H.); (T.X.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Shuling Wang
- College of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (H.C.); (Q.Y.); (R.W.); (R.L.); (M.L.); (W.L.); (C.C.); (Y.Z.); (Z.H.); (T.X.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
- Correspondence: (S.W.); (H.Z.); (Q.T.)
| | - Honghua Zhang
- College of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (H.C.); (Q.Y.); (R.W.); (R.L.); (M.L.); (W.L.); (C.C.); (Y.Z.); (Z.H.); (T.X.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
- Correspondence: (S.W.); (H.Z.); (Q.T.)
| | - Qingchang Tian
- College of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (H.C.); (Q.Y.); (R.W.); (R.L.); (M.L.); (W.L.); (C.C.); (Y.Z.); (Z.H.); (T.X.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Hangzhou Normal University, Hangzhou 311121, China
- Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
- Correspondence: (S.W.); (H.Z.); (Q.T.)
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Yang C, Zhao H, Sun Y, Wang C, Geng X, Wang R, Tang L, Han D, Liu J, Tan W. OUP accepted manuscript. Nucleic Acids Res 2022; 50:3083-3095. [PMID: 35293579 PMCID: PMC8989545 DOI: 10.1093/nar/gkac156] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 01/24/2022] [Accepted: 02/19/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
| | | | | | - Cheng Wang
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Xinyao Geng
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Ruowen Wang
- To whom correspondence should be addressed. Tel: +86 02168385698; Fax:+86 02168385698;
| | - Lumin Tang
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Da Han
- Institute of Molecular Medicine (IMM), Department of Nuclear Medicine, Institute of Clinical Nuclear Medicine, State Key Laboratory of Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Jianjun Liu
- Correspondence may also be addressed to Jianjun Liu.
| | - Weihong Tan
- Correspondence may also be addressed to Weihong Tan.
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Valero J, Civit L, Dupont DM, Selnihhin D, Reinert LS, Idorn M, Israels BA, Bednarz AM, Bus C, Asbach B, Peterhoff D, Pedersen FS, Birkedal V, Wagner R, Paludan SR, Kjems J. A serum-stable RNA aptamer specific for SARS-CoV-2 neutralizes viral entry. Proc Natl Acad Sci U S A 2021; 118:e2112942118. [PMID: 34876524 PMCID: PMC8685691 DOI: 10.1073/pnas.2112942118] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/11/2021] [Indexed: 12/23/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has created an urgent need for new technologies to treat COVID-19. Here we report a 2'-fluoro protected RNA aptamer that binds with high affinity to the receptor binding domain (RBD) of SARS-CoV-2 spike protein, thereby preventing its interaction with the host receptor ACE2. A trimerized version of the RNA aptamer matching the three RBDs in each spike complex enhances binding affinity down to the low picomolar range. Binding mode and specificity for the aptamer-spike interaction is supported by biolayer interferometry, single-molecule fluorescence microscopy, and flow-induced dispersion analysis in vitro. Cell culture experiments using virus-like particles and live SARS-CoV-2 show that the aptamer and, to a larger extent, the trimeric aptamer can efficiently block viral infection at low concentration. Finally, the aptamer maintains its high binding affinity to spike from other circulating SARS-CoV-2 strains, suggesting that it could find widespread use for the detection and treatment of SARS-CoV-2 and emerging variants.
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Affiliation(s)
- Julián Valero
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark;
- Centre for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus DK-8000, Denmark
| | - Laia Civit
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark
| | - Daniel M Dupont
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark
| | - Denis Selnihhin
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Line S Reinert
- Department of Biomedicine, Aarhus University DK-8000 Aarhus, Denmark
| | - Manja Idorn
- Department of Biomedicine, Aarhus University DK-8000 Aarhus, Denmark
| | - Brett A Israels
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark
- Department of Chemistry, Aarhus University, DK-8000, Aarhus, Denmark
| | - Aleksandra M Bednarz
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark
- Department of Chemistry, Aarhus University, DK-8000, Aarhus, Denmark
| | - Claus Bus
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark
| | - Benedikt Asbach
- Institute of Medical Microbiology and Hygiene/Molecular Microbiology (Virology), Regensburg University 93053 Regensburg, Germany
| | - David Peterhoff
- Institute of Medical Microbiology and Hygiene/Molecular Microbiology (Virology), Regensburg University 93053 Regensburg, Germany
| | - Finn S Pedersen
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
| | - Victoria Birkedal
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark
- Department of Chemistry, Aarhus University, DK-8000, Aarhus, Denmark
| | - Ralf Wagner
- Institute of Medical Microbiology and Hygiene/Molecular Microbiology (Virology), Regensburg University 93053 Regensburg, Germany
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg 93053, Germany
| | - Søren R Paludan
- Department of Biomedicine, Aarhus University DK-8000 Aarhus, Denmark
| | - Jørgen Kjems
- Interdisciplinary Nanoscience Center, Aarhus University DK-8000 Aarhus, Denmark;
- Centre for Cellular Signal Patterns (CellPAT), Aarhus University, Aarhus DK-8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, DK-8000 Aarhus, Denmark
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43
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Duan N, Song M, Mi W, Wang Z, Wu S. Effectively Selecting Aptamers for Targeting Aromatic Biogenic Amines and Their Application in Aptasensing Establishment. J Agric Food Chem 2021; 69:14671-14679. [PMID: 34809428 DOI: 10.1021/acs.jafc.1c05934] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
It is necessary to detect the biogenic amine (BA) content in food due to their toxicological effects and their role as an index of freshness for protein-rich foods. Aptamer-based techniques have the potential to provide alternative methods for sensitive and efficient monitoring of BAs. Herein, we described the selection and characterization of DNA aptamers for tyramine (TYR) and β-phenethylamine (PHE) using a one-pot coupled with separate selection strategy. During the selection process, melting curve analysis was developed to monitor the enrichment of the aptamer species, and a saturation of the selection was found at the 14th round. Based on the fluorescence assay, aptamers TYR-2 and PHE-2 showed high affinity to TYR and PHE with the dissociation constant values of 64.28 ± 10.4 and 71.64 ± 11.47 nM, respectively. The circular dichromatic and molecular docking technologies were employed for the preliminary binding mechanism analysis. The obtained aptamers TYR-2 and PHE-2 were used in a fluorescence method for the TYR and PHE determination with limits of detection of 0.34 and 0.39 ng/mL, respectively. In addition, the developed aptasensor was further applied to the TYR and PHE detection in pork and beer samples, and the recovery rate was between 95.6 and 104.2%. It was demonstrated that the selected aptamers had enormous potential as a molecular probe for the identification and determination of BAs.
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Affiliation(s)
- Nuo Duan
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Mingqian Song
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Weiyu Mi
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
| | - Shijia Wu
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, International Joint Laboratory on Food Safety, Jiangnan University, Wuxi 214122, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
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Zhang L, Zhou L, Zhang H, Zhang Y, Li L, Xie T, Chen Y, Li X, Ling N, Dai J, Sun X, Liu J, Zhao J, Peng T, Ye M. Development of a DNA Aptamer against Multidrug-Resistant Hepatocellular Carcinoma for In Vivo Imaging. ACS Appl Mater Interfaces 2021; 13:54656-54664. [PMID: 34779207 DOI: 10.1021/acsami.1c12391] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Hepatocellular carcinoma (HCC) is a type of cancer that has high rates of recurrence and mortality. One of the most important factors that lead to treatment failure of HCC is the acquisition of multidrug resistance (MDR). Development of specific ligands for multidrug-resistant HCC will provide useful molecular tools for precise diagnosis and targeted theranostics. Herein, a multidrug-resistant HCC cell (HepG2/MDR)-specific aptamer was developed through Cell-SELEX (systematic evolution of ligands by exponential enrichment) technology. With dissociation constants lying in the nanomolar range, the molecularly designed PS-ZL-7c aptamer showed great selectivity to drug-resistant cancer cells. The in vivo imaging results illustrated that the PS-ZL-7c specifically accumulated in the drug-resistant tumors but not in drug-sensitive tumors and normal tissues, indicating that the PS-ZL-7c aptamer possessed excellent potential as a targeting ligand for precise diagnosis and target theranostics of multidrug-resistant HCC.
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MESH Headings
- Animals
- Antineoplastic Agents/chemical synthesis
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacology
- Aptamers, Nucleotide/chemical synthesis
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/pharmacology
- Carcinoma, Hepatocellular/diagnostic imaging
- Carcinoma, Hepatocellular/drug therapy
- Cell Proliferation/drug effects
- Cell Survival/drug effects
- Drug Development
- Drug Resistance, Neoplasm/drug effects
- Drug Screening Assays, Antitumor
- Hep G2 Cells
- Humans
- Liver Neoplasms/diagnostic imaging
- Liver Neoplasms/drug therapy
- Liver Neoplasms, Experimental/drug therapy
- Liver Neoplasms, Experimental/pathology
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Optical Imaging
- SELEX Aptamer Technique
- Tumor Cells, Cultured
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Affiliation(s)
- Lin Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Lingli Zhou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Hui Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yibin Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Ling Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Tiantian Xie
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Yinglei Chen
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Xiaodong Li
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Neng Ling
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Jing Dai
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Xing Sun
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Jing Liu
- Molecular Biology Research Center & Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan 410078, China
| | - Jinfeng Zhao
- Key Laboratory of Nanobiological Technology of Chinese Ministry of Health, Xiangya Hospital, Central South University, Changsha, Hunan 410008, China
| | - Tianhuan Peng
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
| | - Mao Ye
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan 410082, China
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45
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Ren X, Gelinas AD, Linehan M, Iwasaki A, Wang W, Janjic N, Pyle AM. Evolving A RIG-I Antagonist: A Modified DNA Aptamer Mimics Viral RNA. J Mol Biol 2021; 433:167227. [PMID: 34487794 DOI: 10.1016/j.jmb.2021.167227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/09/2021] [Accepted: 08/26/2021] [Indexed: 12/25/2022]
Abstract
Vertebrate organisms express a diversity of protein receptors that recognize and respond to the presence of pathogenic molecules, functioning as an early warning system for infection. As a result of mutation or dysregulated metabolism, these same innate immune receptors can be inappropriately activated, leading to inflammation and disease. One of the most important receptors for detection and response to RNA viruses is called RIG-I, and dysregulation of this protein is linked with a variety of disease states. Despite its central role in inflammatory responses, antagonists for RIG-I are underdeveloped. In this study, we use invitro selection from a pool of modified DNA aptamers to create a high affinity RIG-I antagonist. A high resolution crystal structure of the complex reveals molecular mimicry between the aptamer and the 5'-triphosphate terminus of viral ligands, which bind to the same amino acids within the CTD recognition platform of the RIG-I receptor. Our study suggests a powerful, generalizable strategy for generating immunomodulatory drugs and mechanistic tool compounds.
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MESH Headings
- Antigens, Viral/chemistry
- Antigens, Viral/metabolism
- Aptamers, Nucleotide/chemistry
- Aptamers, Nucleotide/metabolism
- Binding Sites
- Cloning, Molecular
- Crystallography, X-Ray
- DEAD Box Protein 58/chemistry
- DEAD Box Protein 58/genetics
- DEAD Box Protein 58/metabolism
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Gene Expression
- Genetic Vectors/chemistry
- Genetic Vectors/metabolism
- Humans
- Immunologic Factors/chemistry
- Immunologic Factors/metabolism
- Kinetics
- Models, Molecular
- Molecular Mimicry
- Mutation
- Nucleic Acid Conformation
- Protein Binding
- Protein Conformation, alpha-Helical
- Protein Conformation, beta-Strand
- Protein Interaction Domains and Motifs
- RNA, Viral/chemistry
- RNA, Viral/metabolism
- Receptors, Immunologic/chemistry
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Recombinant Proteins/chemistry
- Recombinant Proteins/genetics
- Recombinant Proteins/metabolism
- SELEX Aptamer Technique
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Affiliation(s)
- Xiaoming Ren
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA
| | - Amy D Gelinas
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA
| | - Melissa Linehan
- Department of Immunobiology, Yale University, New Haven, CT 06519, USA
| | - Akiko Iwasaki
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA; Department of Immunobiology, Yale University, New Haven, CT 06519, USA
| | - Wenshuai Wang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA
| | - Nebojsa Janjic
- SomaLogic, Inc., 2945 Wilderness Place, Boulder, CO 80301, USA.
| | - Anna Marie Pyle
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Yale University, New Haven, CT 06520, USA.
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46
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Hedayati N, Taghdisi SM, Yazdian-Robati R, Mansouri A, Abnous K, Ahmad Mohajeri S. Selection of DNA aptamers for tramadol through the systematic evolution of ligands by exponential enrichment method for fabrication of a sensitive fluorescent aptasensor based on graphene oxide. Spectrochim Acta A Mol Biomol Spectrosc 2021; 259:119840. [PMID: 33965888 DOI: 10.1016/j.saa.2021.119840] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/10/2021] [Accepted: 04/12/2021] [Indexed: 06/12/2023]
Abstract
Tramadol hydrochloride (TH), as an atypical opioid and a 4-phenyl-piperidine analogue of codeine, is mainly used for treating moderate to severe pains. Due to its extensive application, the consequent need for its analysis in various samples is essential. The current study focuses on the introduction of a rapid fluorescent assay using graphene oxide (GO) and aptamer for determination of tramadol in serum samples. Specific ssDNA aptamers for TH were developed by SELEX (Systematic Evolution of Ligands by EXponential Enrichment) technique using GO as a fluorescence quencher. After 10 rounds, two aptamers (Apt19 and Apt39) were selected from various families. Then, the binding constants of aptamers were measured using fluorometric assay and finally Apt39 (labeled with ATTO 647N) was chosen for development of a fluorescent aptasensor because this aptamer bound to TH with high affinity (Kd = 178.4 nM) and specificity. The current analytical system showed detection limits of 1.04 nM and 2.56 nM in serum sample and phosphate buffer saline (10 mM PBS), respectively.
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Affiliation(s)
- Narges Hedayati
- Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Seyed Mohammad Taghdisi
- Targeted Drug Delivery Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rezvan Yazdian-Robati
- Molecular and Cell Biology Research Center, Faculty of Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Atena Mansouri
- Cellular & Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran; Biotechnology Research Centre, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Medicinal Chemistry, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Seyed Ahmad Mohajeri
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran; Department of Pharmacodynamics and Toxicology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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47
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Pei Y, Wang C, Chen Z, Li S, Chen H, Wang Z, He N. AutoCell Systematic Evolution of Ligands by Exponential Enrichment: The Software Designed and Developed for the Automated Screening System of Nucleic Acid Aptamers. J Nanosci Nanotechnol 2021; 21:5363-5369. [PMID: 33875130 DOI: 10.1166/jnn.2021.19342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Aptamers are a new kind of nano-probes for bioassays and drug delivery, etc. In this paper, software has been developed as an automatic control center for the automated aptamer selecting system which realized the high integration of aptamer selection, data acquisition and processing. This software, applied in windows system, is developed by C# with the Microsoft Visual Studio 2015 integrated developing environment and the database used in this software is implemented using open source relational database MYSQL. According to the requirement analysis, this software realized various important necessary functions including feasible experiment design, auto-control of the hardware, real time process monitoring and efficient data management which perfectly satisfies the users' demands. During the actual experiment operation, this software worked smoothly and assumed stable serial port communication between it and the hardware, meanwhile, the interaction between the software and MYSQL remained good stability. As a consequence, it is practical and reasonable to apply this software to the automated aptamer selecting system for research.
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Affiliation(s)
- Yuhong Pei
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Chao Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Zhu Chen
- Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou 412007, PR China
| | - Song Li
- Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou 412007, PR China
| | - Hui Chen
- Hunan Key Laboratory of Green Chemistry and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou 412007, PR China
| | - Zunliang Wang
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
| | - Nongyue He
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, National Demonstration Center for Experimental Biomedical Engineering Education, Southeast University, Nanjing 210096, China
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Mahajan UM, Li Q, Alnatsha A, Maas J, Orth M, Maier SH, Peterhansl J, Regel I, Sendler M, Wagh PR, Mishra N, Xue Y, Allawadhi P, Beyer G, Kühn JP, Marshall T, Appel B, Lämmerhirt F, Belka C, Müller S, Weiss FU, Lauber K, Lerch MM, Mayerle J. Tumor-Specific Delivery of 5-Fluorouracil-Incorporated Epidermal Growth Factor Receptor-Targeted Aptamers as an Efficient Treatment in Pancreatic Ductal Adenocarcinoma Models. Gastroenterology 2021; 161:996-1010.e1. [PMID: 34097885 DOI: 10.1053/j.gastro.2021.05.055] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 04/19/2021] [Accepted: 05/20/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUNDS & AIMS Fluoropyrimidine c (5-fluorouracil [5FU]) increasingly represents the chemotherapeutic backbone for neoadjuvant, adjuvant, and palliative treatment of pancreatic ductal adenocarcinoma (PDAC). Even in combination with other agents, 5FU efficacy remains transient and limited. One explanation for the inadequate response is insufficient and nonspecific delivery of 5FU to the tumor. METHODS We designed, generated, and characterized 5FU-incorporated systematic evolution of ligands by exponential enrichment (SELEX)-selected epidermal growth factor receptor (EGFR)-targeted aptamers for tumor-specific delivery of 5FU to PDAC cells and tested their therapeutic efficacy in vitro and in vivo. RESULTS 5FU-EGFR aptamers reduced proliferation in a concentration-dependent manner in mouse and human pancreatic cancer cell lines. Time-lapsed live imaging showed EGFR-specific uptake of aptamers via clathrin-dependent endocytosis. The 5FU-aptamer treatment was equally effective in 5FU-sensitive and 5FU-refractory PDAC cell lines. Biweekly treatment with 5FU-EGFR aptamers reduced tumor burden in a syngeneic orthotopic transplantation model of PDAC, in an autochthonously growing genetically engineered PDAC model (LSL-KrasG12D/+;LSL-Trp53flox/+;Ptf1a-Cre [KPC]), in an orthotopic cell line-derived xenograft model using human PDAC cells in athymic mice (CDX; Crl:NU-Foxn1nu), and in patient-derived organoids. Tumor growth was significantly attenuated during 5FU-EGFR aptamer treatment in the course of follow-up. CONCLUSIONS Tumor-specific targeted delivery of 5FU using EGFR aptamers as the carrier achieved high target specificity; overcame 5FU resistance; and proved to be effective in a syngeneic orthotopic transplantation model, in KPC mice, in a CDX model, and in patient-derived organoids and, therefore, represents a promising backbone for pancreatic cancer chemotherapy in patients. Furthermore, our approach has the potential to target virtually any cancer entity sensitive to 5FU treatment by incorporating 5FU into cancer cell-targeting aptamers as the delivery platform.
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MESH Headings
- Animals
- Antimetabolites, Antineoplastic/administration & dosage
- Antimetabolites, Antineoplastic/metabolism
- Aptamers, Nucleotide/administration & dosage
- Aptamers, Nucleotide/metabolism
- Carcinoma, Pancreatic Ductal/drug therapy
- Carcinoma, Pancreatic Ductal/metabolism
- Carcinoma, Pancreatic Ductal/pathology
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Drug Delivery Systems
- Drug Resistance, Neoplasm
- Endocytosis
- ErbB Receptors/genetics
- ErbB Receptors/metabolism
- Female
- Fluorouracil/administration & dosage
- Fluorouracil/metabolism
- Humans
- Male
- Mice, Inbred C57BL
- Mice, Transgenic
- Organoids
- Pancreatic Neoplasms/drug therapy
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/metabolism
- Pancreatic Neoplasms/pathology
- SELEX Aptamer Technique
- Tumor Burden/drug effects
- Tumor Cells, Cultured
- Xenograft Model Antitumor Assays
- Mice
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Affiliation(s)
- Ujjwal M Mahajan
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Qi Li
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Ahmed Alnatsha
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Jessica Maas
- Department of Radiation Oncology, Hospital of Ludwig-Maximilians-University, Munich, Germany
| | - Michael Orth
- Department of Radiation Oncology, Hospital of Ludwig-Maximilians-University, Munich, Germany
| | | | - Julian Peterhansl
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Ivonne Regel
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Matthias Sendler
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Preshit R Wagh
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Neha Mishra
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Yonggan Xue
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Prince Allawadhi
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Georg Beyer
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany
| | - Jens-Peter Kühn
- Institute and Policlinic of Diagnostic and Interventional Radiology, Medical University, Carl-Gustav-Carus, Dresden, Germany
| | - Thomas Marshall
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Bettina Appel
- Institute of Biochemistry, University Greifswald, Germany
| | - Felix Lämmerhirt
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Claus Belka
- Department of Radiation Oncology, Hospital of Ludwig-Maximilians-University, Munich, Germany
| | - Sabine Müller
- Institute of Biochemistry, University Greifswald, Germany
| | - Frank-Ulrich Weiss
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany
| | - Kirsten Lauber
- Department of Radiation Oncology, Hospital of Ludwig-Maximilians-University, Munich, Germany
| | - Markus M Lerch
- Department of Medicine A, University Medicine Greifswald, Greifswald, Germany; LMU Klinikum, Munich, Germany
| | - Julia Mayerle
- Department of Medicine II, University Hospital, LMU Munich, Munich, Germany; Department of Medicine A, University Medicine Greifswald, Greifswald, Germany.
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Abstract
During an epidemic or pandemic, the primary task is to rapidly develop precise diagnostic approaches and effective therapeutics. Oligonucleotide aptamer-based pathogen detection assays and control therapeutics are promising, as aptamers that specifically recognize and block pathogens can be quickly developed and produced through simple chemical synthesis. This work reviews common aptamer-based diagnostic techniques for communicable diseases and summarizes currently available aptamers that target various pathogens, including the SARS-CoV-2 virus. Moreover, this review discusses how oligonucleotide aptamers might be leveraged to control pathogen propagation and improve host immune system responses. This review offers a comprehensive data source to the further develop aptamer-based diagnostics and therapeutics specific for infectious diseases.
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Affiliation(s)
| | | | - Youli Zu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, Houston, TX 77030, USA
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Abstract
The Competition-Enhanced Ligand Selection (CompELS) approach was used to identify aptamer candidates for spherical gold nanoparticles (AuNPs). This approach differs from conventional Systematic Evolution of Ligands by EXponential enrichment (SELEX)-based aptamer screening by eliminating repeated elution and polymerase chain reaction (PCR) amplification steps of bound candidate sequences between each selection round to continually enrich the candidate aptamer pool with oligonucleotides remaining from an earlier SELEX selection round. Instead, a new pool of unenriched oligonucleotides is added during each CompELS selection round to compete with existing target-bound oligonucleotides species for target binding sites. In this study, 24 aptamer candidates for AuNPs were identified using the CompELS approach and then compared to reveal similarities in their primary structures and their predicted secondary structures. No strong patterns in individual base identities (position-dependent) nor in segments of consecutive bases (independent of position) prevailed among the identified sequences. Motifs in predicted secondary structures, on the other hand, were shared among otherwise unrelated aptamer sequences. These motifs were revealed using a systematic classification and enumeration of distinct secondary structure elements, namely, hairpins, duplexes, single-stranded segments, interior loops, bulges, and multibranched loops.
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Affiliation(s)
| | - Patrick Dennis
- Materials & Manufacturing Directorate, Soft Matter Materials Branch, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Rajesh R Naik
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
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