1
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Hoffmann ES, De Pascali MC, Neu L, Domnick C, Soldà A, Kath-Schorr S. Reverse transcription as key step in RNA in vitro evolution with unnatural base pairs. RSC Chem Biol 2024; 5:556-566. [PMID: 38846072 PMCID: PMC11151862 DOI: 10.1039/d4cb00084f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 04/23/2024] [Indexed: 06/09/2024] Open
Abstract
Unnatural base pairs (UBPs) augment the chemical diversity of artificial nucleic acids and can thus enable the generation of new aptamers and catalytic nucleic acids by in vitro selection. However, owing to a lack of methodologies, the reverse transcription of UBPs, a key step in RNA aptamer selection, has not been sufficiently characterized. Here, we present a series of versatile assays to investigate the reverse transcription of the TPT3:NaM base pair as a representative for hydrophobic unnatural base pairs. We determine the fidelity and retention of the UBP for four different reverse transcriptases (RT) in the context of RNA in vitro evolution. The retention of the TPT3:NaM pair during the RNA in vitro selection process was investigated using a novel click-chemistry based electromobility shift assay. Real-time monitoring of reverse transcription kinetics revealed considerable differences in polymerase activity processing the TPT3:NaM base pair. Our findings identified SuperScript IV RT as the most efficient RT for processing the TPT3:NaM pair. Our approach can be applied universally to study newly developed UBPs, not only at the reverse transcription level, but also during PCR and in vitro transcription.
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Affiliation(s)
- Eva S Hoffmann
- Institute of Organic Chemistry, Department of Chemistry, University of Cologne Greinstrasse 4 50939 Cologne Germany
| | - Mareike C De Pascali
- Technical University of Munich, TUM School of Natural Sciences, Department of Bioscience Garching 85748 Germany
- Dynamic Biosensors GmbH Perchtinger Str. 8/10 Munich 81379 Germany
| | - Lukas Neu
- Institute of Organic Chemistry, Department of Chemistry, University of Cologne Greinstrasse 4 50939 Cologne Germany
| | - Christof Domnick
- Institute of Organic Chemistry, Department of Chemistry, University of Cologne Greinstrasse 4 50939 Cologne Germany
| | - Alice Soldà
- Dynamic Biosensors GmbH Perchtinger Str. 8/10 Munich 81379 Germany
| | - Stephanie Kath-Schorr
- Institute of Organic Chemistry, Department of Chemistry, University of Cologne Greinstrasse 4 50939 Cologne Germany
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2
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Gubu A, Ma Y, Yu S, Zhang H, Chen Z, Ni S, Abdullah R, Xiao H, Zhang Y, Dai H, Luo H, Yu Y, Wang L, Jiang H, Zhang N, Tian Y, Li H, Lu A, Zhang B, Zhang G. Unique quinoline orientations shape the modified aptamer to sclerostin for enhanced binding affinity and bone anabolic potential. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102146. [PMID: 38444701 PMCID: PMC10914587 DOI: 10.1016/j.omtn.2024.102146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 02/09/2024] [Indexed: 03/07/2024]
Abstract
Osteogenesis imperfecta (OI) is a rare genetic disease characterized by bone fragility and bone formation. Sclerostin could negatively regulate bone formation by antagonizing the Wnt signal pathway, whereas it imposes severe cardiac ischemic events in clinic. Our team has screened an aptamer that could promote bone anabolic potential without cardiovascular risk. However, the affinity of the aptamer is lower and needs to be improved. In the study, hydrophobic quinoline molecule with unique orientations (seven subtypes) were incorporated into key sites of a bone anabolic aptamer against sclerostin to form a modified aptamer library. Among all the quinoline modifications, 5-quinoline modification could shape the molecular recognition of modified aptamers to sclerostin to facilitate enhancing its binding to sclerostin toward the highest affinity by interacting with newly participated binding sites in sclerostin. Further, 5-quinoline modification could facilitate the modified aptamer attenuating the suppressed effect of the transfected sclerostin on both Wnt signaling and bone formation marker expression levels in vitro, promoting bone anabolism in OI mice (Col1a2+/G610C). The proposed quinoline-oriented modification strategy could shape the molecular recognition of modified aptamers to proteins to facilitate enhancing its binding affinity and therapeutic potency.
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Affiliation(s)
- Amu Gubu
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Yuan Ma
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Increasepharm & Hong Kong Baptist University Joint Centre for Nucleic Acid Drug Discovery, Hong Kong Science Park, New Territories, Hong Kong, China
| | - Sifan Yu
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
- Shenzhen Research Institute, The Chinese University of Hong Kong, School of Chinese Medicine, The Chinese University of Hong Kong, Shen Zhen 518063, China
| | - Huarui Zhang
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Zefeng Chen
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Increasepharm & Hong Kong Baptist University Joint Centre for Nucleic Acid Drug Discovery, Hong Kong Science Park, New Territories, Hong Kong, China
| | - Shuaijian Ni
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
| | - Razack Abdullah
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
| | - Huan Xiao
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Yihao Zhang
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Hong Dai
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
| | - Hang Luo
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Yuanyuan Yu
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Luyao Wang
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
| | - Hewen Jiang
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Ning Zhang
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Yuan Tian
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
| | - Haitian Li
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
- Institute of Integrated Bioinfomedicine and Translational Science, School of Chinese Medicine, Hong Kong Baptist University, Kowloon Tsai, Hong Kong 999077, China
| | - Aiping Lu
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
| | - Baoting Zhang
- School of Chinese Medicine, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR 999077, China
| | - Ge Zhang
- Guangdong-Hong Kong-Macao Greater Bay Area International Research Platform for Aptamer-based Translational Medicine and Drug Discovery, Hong Kong SAR 999077, China
- Law Sau Fai Institute for Advancing Translational Medicine in Bone & Joint Diseases, School of Chinese Medicine, Hong Kong Baptist University, Hong Kong SAR 999077, China
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3
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Ji C, Wei J, Zhang L, Hou X, Tan J, Yuan Q, Tan W. Aptamer-Protein Interactions: From Regulation to Biomolecular Detection. Chem Rev 2023; 123:12471-12506. [PMID: 37931070 DOI: 10.1021/acs.chemrev.3c00377] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.
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Affiliation(s)
- Cailing Ji
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Junyuan Wei
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Xinru Hou
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang 310022, China
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4
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Kimoto M, Tan HP, Matsunaga KI, Binte Mohd Mislan NA, Kawai G, Hirao I. Strict Interactions of Fifth Letters, Hydrophobic Unnatural Bases, in XenoAptamers with Target Proteins. J Am Chem Soc 2023; 145:20432-20441. [PMID: 37677157 PMCID: PMC10515488 DOI: 10.1021/jacs.3c06122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Indexed: 09/09/2023]
Abstract
XenoAptamers are DNA fragments containing additional letters (unnatural bases, UBs) that bind specifically to their target proteins with high affinities (sub-nanomolar KD values). One of the UBs is the highly hydrophobic 7-(2-thienyl)imidazo[4,5-b]pyridine (Ds), which significantly increases XenoAptamers' affinities to targets. Originally, Ds was developed as a third base pair with a complementary UB, 2-nitro-4-propynylpyrrole (Px), for replication, and thus it can be used for aptamer generation by an evolutional engineering method involving PCR amplification. However, it is unclear whether the Ds base is the best component as the hydrophobic fifth-letter ligand for interactions with target proteins. To optimize the ligand structure of the fifth letter, we prepared 13 Ds variants and examined the affinities of XenoAptamers containing these variants to target proteins. The results obtained using four XenoAptamers prepared by the replacement of Ds bases with variants indicated that subtle changes in the chemical structure of Ds significantly affect the XenoAptamer affinities. Among the variants, placing either 4-(2-thienyl)pyrrolo[2,3-b]pyridine (Ys) or 4-(2-thienyl)benzimidazole (Bs) at specific Ds positions in each original XenoAptamer greatly improved their affinities to targets. The Ys and Bs bases are variants derived by replacing only one nitrogen with a carbon in the Ds base. These results demonstrate the strict intramolecular interactions, which are not simple hydrophobic contacts between UBs and targets, thus providing a method to mature XenoAptamers' affinities to targets.
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Affiliation(s)
- Michiko Kimoto
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
| | - Hui Pen Tan
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
| | - Ken-ichiro Matsunaga
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
| | | | - Gota Kawai
- Chiba
Institute of Technology (CIT), Tsudanuma 2-17-1, Narashino, Chiba 275-0016, Japan
| | - Ichiro Hirao
- Xenolis
Pte. Ltd., 85 Science
Park Drive, #02-05B, The Cavendish, Singapore 118259, Singapore
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5
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Han J, Ma P, Khan IM, Zhang Y, Wang Z. Study of binding mechanism of aptamer to kanamycin and the development of fluorescent aptasensor in milk detection. Talanta 2023; 260:124530. [PMID: 37116356 DOI: 10.1016/j.talanta.2023.124530] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/28/2023] [Accepted: 04/04/2023] [Indexed: 04/30/2023]
Abstract
Aptasensors being versatile sensing platforms presented higher sensitivity toward target detection. However, lacking theoretical basis of recognition between most targets and their corresponding aptamers has impeded their applications. Herein, we conducted a study to explore the binding mechanism of aptamer to kanamycin (Kana) and developed rapid fluorescent aptasensing methods. Based on the fluorescence polarization results, base mutations were performed at different sites of the aptamer. The key binding nucleotides of Kana was identified as T7, T8, C13 and A15 by using isothermal titration calorimetry (ITC). The Kmut3 (2.18 μM) with lower dissociation constants (Kd), one-third of the native aptamer (6.91 μM), was also obtained. In addition, the lower K+ concentration and temperature were found to be conducive to Kana binding. Circular dichroism (CD) results revealed that the binding of Kana can trigger the change of base stacking force and helix force. On the aforementioned basis, a fluorescent sensor was designed with the native aptamer and Kmut3 as recognition elements. The comparison results proved that the Kmut3 presented a 3 times lower limit of detection of 59 nM compared to the native aptamer (148 nM). Notably, this developed aptasensor can be finished in 45 min and was convenient to operate.
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Affiliation(s)
- Jing Han
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Pengfei Ma
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China.
| | - Imran Mahmood Khan
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China
| | - Yin Zhang
- Key Laboratory of Meat Processing of Sichuan, Chengdu University, Chengdu, 610106, China
| | - Zhouping Wang
- State Key Laboratory of Food Science and Technology, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, 214122, China; International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China; School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang, 212004, China.
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6
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Kimoto M, Tan HP, Tan YS, Mislan NABM, Hirao I. Success probability of high-affinity DNA aptamer generation by genetic alphabet expansion. Philos Trans R Soc Lond B Biol Sci 2023; 378:20220031. [PMID: 36633272 PMCID: PMC9835594 DOI: 10.1098/rstb.2022.0031] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Nucleic acid aptamers as antibody alternatives bind specifically to target molecules. These aptamers are generated by isolating candidates from libraries with random sequence fragments, through an evolutionary engineering system. We recently reported a high-affinity DNA aptamer generation method that introduces unnatural bases (UBs) as a fifth letter into the library, by genetic alphabet expansion. By incorporating hydrophobic UBs, the affinities of DNA aptamers to target proteins are increased over 100-fold, as compared with those of conventional aptamers with only the natural four letters. However, there is still plenty of room for improvement of the methods for routinely generating high-affinity UB-containing DNA (UB-DNA) aptamers. The success probabilities of the high-affinity aptamer generation depend on the existence of the aptamer candidate sequences in the initial library. We estimated the success probabilities by analysing several UB-DNA aptamers that we generated, as examples. In addition, we investigated the possible improvement of conventional aptamer affinities by introducing one UB at specific positions. Our data revealed that UB-DNA aptamers adopt specific tertiary structures, in which many bases including UBs interact with target proteins for high affinity, suggesting the importance of the UB-DNA library design. This article is part of the theme issue 'Reactivity and mechanism in chemical and synthetic biology'.
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Affiliation(s)
- Michiko Kimoto
- Xenolis Pte Ltd, 79 Science Park Drive, #06-01/08, Cintech IV, Singapore 118264, Singapore,Institute of Bioengineering and Bioimaging, Agency for Science, Technologyand Research (A*STAR), 31 Biopolis Way, #07-01 Nanos, Singapore 138669, Singapore
| | - Hui Pen Tan
- Xenolis Pte Ltd, 79 Science Park Drive, #06-01/08, Cintech IV, Singapore 118264, Singapore,Institute of Bioengineering and Bioimaging, Agency for Science, Technologyand Research (A*STAR), 31 Biopolis Way, #07-01 Nanos, Singapore 138669, Singapore
| | - Yaw Sing Tan
- Xenolis Pte Ltd, 79 Science Park Drive, #06-01/08, Cintech IV, Singapore 118264, Singapore,Bioinformatics Institute, A*STAR, 30 Biopolis Street, #07-01 Matrix, Singapore 138671, Singapore
| | - Nur Afiqah Binte Mohd Mislan
- Xenolis Pte Ltd, 79 Science Park Drive, #06-01/08, Cintech IV, Singapore 118264, Singapore,Institute of Bioengineering and Bioimaging, Agency for Science, Technologyand Research (A*STAR), 31 Biopolis Way, #07-01 Nanos, Singapore 138669, Singapore
| | - Ichiro Hirao
- Xenolis Pte Ltd, 79 Science Park Drive, #06-01/08, Cintech IV, Singapore 118264, Singapore,Institute of Bioengineering and Bioimaging, Agency for Science, Technologyand Research (A*STAR), 31 Biopolis Way, #07-01 Nanos, Singapore 138669, Singapore
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7
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Tian T, Zhang T, Shi S, Gao Y, Cai X, Lin Y. A dynamic DNA tetrahedron framework for active targeting. Nat Protoc 2023; 18:1028-1055. [PMID: 36670289 DOI: 10.1038/s41596-022-00791-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 55.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 11/03/2022] [Indexed: 01/22/2023]
Abstract
An active targeting strategy-enabled DNA tetrahedron delivery vehicle could facilitate stable drug encapsulation and stimuli-responsive on-demand release, building a universal platform for different drug delivery requirements. Owing to the excellent biocompatible nature, programmability and remarkable cell and tissue permeability, the tetrahedral DNA nanostructure (TDN) has proven its value in the delivery of various bioactive molecules. We previously described this as a static multifunctional complex in our earlier protocol. However, static structures and passive targeting behavior might introduce off-target effects under complicated biological conditions. Therefore, in this Protocol Extension, we present a major update of the TDN delivery vehicle enabling an active targeting strategy to be used for stimuli-sensitive conformation changes and on-site cargo release, which could avoid drawbacks, including complex and time-consuming fabrication processes and undetermined cell penetration ability of other DNA-based delivery vehicles. Upon exquisite design of TDN size based on cargo type, one-pot annealing is applied to fabricate the Tiamat-designed TDN exoskeleton. Then the design of the dynamic DNA apparatus can be based on the target and environmental stimuli, including DNA strand hybridization-based and pH-sensitive DNA apparatus, and careful titration of strand lengths and mismatches is achieved using polyacrylamide and agarose gel electrophoresis, or fluorophore modifications. Finally, cargo loading strategies are designed, including site and stand titration and cargo encapsulation verification. The dynamic structures show promising targetability and effectiveness in antitumor and anti-inflammatory treatment in vitro and in vivo. Assembly and characterization in the lab takes ~5 d, and the timing for the verification of biostability and biological applications depends on the uses.
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Affiliation(s)
- Taoran Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Tao Zhang
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Sirong Shi
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Yang Gao
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Xiaoxiao Cai
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, P. R. China.
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8
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Cai R, Chen X, Zhang Y, Wang X, Zhou N. Systematic bio-fabrication of aptamers and their applications in engineering biology. SYSTEMS MICROBIOLOGY AND BIOMANUFACTURING 2022; 3:223-245. [PMID: 38013802 PMCID: PMC9550155 DOI: 10.1007/s43393-022-00140-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 10/27/2022]
Abstract
Aptamers are single-stranded DNA or RNA molecules that have high affinity and selectivity to bind to specific targets. Compared to antibodies, aptamers are easy to in vitro synthesize with low cost, and exhibit excellent thermal stability and programmability. With these features, aptamers have been widely used in biology and medicine-related fields. In the meantime, a variety of systematic evolution of ligands by exponential enrichment (SELEX) technologies have been developed to screen aptamers for various targets. According to the characteristics of targets, customizing appropriate SELEX technology and post-SELEX optimization helps to obtain ideal aptamers with high affinity and specificity. In this review, we first summarize the latest research on the systematic bio-fabrication of aptamers, including various SELEX technologies, post-SELEX optimization, and aptamer modification technology. These procedures not only help to gain the aptamer sequences but also provide insights into the relationship between structure and function of the aptamers. The latter provides a new perspective for the systems bio-fabrication of aptamers. Furthermore, on this basis, we review the applications of aptamers, particularly in the fields of engineering biology, including industrial biotechnology, medical and health engineering, and environmental and food safety monitoring. And the encountered challenges and prospects are discussed, providing an outlook for the future development of aptamers.
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Affiliation(s)
- Rongfeng Cai
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122 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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9
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Song M, Li Y, Gao R, Liu J, Huang Q. De novo design of DNA aptamers that target okadaic acid (OA) by docking-then-assembling of single nucleotides. Biosens Bioelectron 2022; 215:114562. [PMID: 35870338 DOI: 10.1016/j.bios.2022.114562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 06/24/2022] [Accepted: 07/07/2022] [Indexed: 11/15/2022]
Abstract
Okadaic acid (OA) is a diarrhetic shellfish poison widespread in ocean, so its detection is of great significance to seafood safety. Because of good sensitivity and low cost, biosensors using nucleic-acid aptamers as the recognition molecules are emerging as an important detection tool. However, the traditional SELEX screening method for acquiring OA high-affinity aptamers is time- and resource-intensive. Alternatively, here we developed a de novo design method based on the 3D structure of a target molecule, such as OA. Without experimental screening, this method designs OA aptamers by a computational approach of docking-then-assembling (DTA) of single nucleotides (A, C, G and T) as: (1) determining the high-affinity nucleotide binding sites of the target molecule via saturated molecular docking; (2) assembling the bound nucleotides into binding units to the target molecule; (3) constructing full-length aptamers by introducing stabilizing units to connect these binding units. In this way, five OA aptamers were designed, and microscale thermophoresis (MST) experiments verified that their Kd values are in the range of 100-600 nM; and one of them (named 9CGAT_4_a) could specifically bind to OA with low affinities for the other three marine biotoxins. Therefore, this study provides high-affinity and specific aptamers for the development of OA biosensors, and presents a promising de novo design method applicable to other target molecules.
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Affiliation(s)
- Menghua Song
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yuanyuan Li
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Ruihua Gao
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai, 200438, China
| | - Jianping Liu
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, MOE Engineering Research Center of Gene Technology, School of Life Sciences, Fudan University, Shanghai, 200438, China; Multiscale Research Institute of Complex Systems, Fudan University, Shanghai, 201203, China.
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10
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Tian T, Li Y, Lin Y. Prospects and challenges of dynamic DNA nanostructures in biomedical applications. Bone Res 2022; 10:40. [PMID: 35606345 PMCID: PMC9125017 DOI: 10.1038/s41413-022-00212-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/10/2022] [Accepted: 03/20/2022] [Indexed: 02/08/2023] Open
Abstract
The physicochemical nature of DNA allows the assembly of highly predictable structures via several fabrication strategies, which have been applied to make breakthroughs in various fields. Moreover, DNA nanostructures are regarded as materials with excellent editability and biocompatibility for biomedical applications. The ongoing maintenance and release of new DNA structure design tools ease the work and make large and arbitrary DNA structures feasible for different applications. However, the nature of DNA nanostructures endows them with several stimulus-responsive mechanisms capable of responding to biomolecules, such as nucleic acids and proteins, as well as biophysical environmental parameters, such as temperature and pH. Via these mechanisms, stimulus-responsive dynamic DNA nanostructures have been applied in several biomedical settings, including basic research, active drug delivery, biosensor development, and tissue engineering. These applications have shown the versatility of dynamic DNA nanostructures, with unignorable merits that exceed those of their traditional counterparts, such as polymers and metal particles. However, there are stability, yield, exogenous DNA, and ethical considerations regarding their clinical translation. In this review, we first introduce the recent efforts and discoveries in DNA nanotechnology, highlighting the uses of dynamic DNA nanostructures in biomedical applications. Then, several dynamic DNA nanostructures are presented, and their typical biomedical applications, including their use as DNA aptamers, ion concentration/pH-sensitive DNA molecules, DNA nanostructures capable of strand displacement reactions, and protein-based dynamic DNA nanostructures, are discussed. Finally, the challenges regarding the biomedical applications of dynamic DNA nanostructures are discussed.
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Affiliation(s)
- Taoran Tian
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China
| | - Yanjing Li
- Department of Prosthodontics, Tianjin Medical University School and Hospital of Stomatology, Tianjin, 300070, P. R. China
| | - Yunfeng Lin
- State Key Laboratory of Oral Diseases, National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, 610041, P. R. China.
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11
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Li Y, Song M, Gao R, Lu F, Liu J, Huang Q. Repurposing of thermally stable nucleic-acid aptamers for targeting tetrodotoxin (TTX). Comput Struct Biotechnol J 2022; 20:2134-2142. [PMID: 35832627 PMCID: PMC9092388 DOI: 10.1016/j.csbj.2022.04.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/23/2022] [Accepted: 04/23/2022] [Indexed: 01/03/2023] Open
Affiliation(s)
- Yuanyuan Li
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Centre of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Menghua Song
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Centre of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ruihua Gao
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200438, China
| | - Feng Lu
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Jianping Liu
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Centre of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
- Corresponding authors at: State Key Laboratory of Genetic Engineering, MOE Engineering Research Centre of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China (Q. Huang).
| | - Qiang Huang
- State Key Laboratory of Genetic Engineering, MOE Engineering Research Centre of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 201203, China
- Corresponding authors at: State Key Laboratory of Genetic Engineering, MOE Engineering Research Centre of Gene Technology, School of Life Sciences, Fudan University, Shanghai 200438, China (Q. Huang).
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12
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Qi S, Duan N, Khan IM, Dong X, Zhang Y, Wu S, Wang Z. Strategies to manipulate the performance of aptamers in SELEX, post-SELEX and microenvironment. Biotechnol Adv 2022; 55:107902. [DOI: 10.1016/j.biotechadv.2021.107902] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/21/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023]
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13
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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] [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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14
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Khanali J, Azangou-Khyavy M, Asaadi Y, Jamalkhah M, Kiani J. Nucleic Acid-Based Treatments Against COVID-19: Potential Efficacy of Aptamers and siRNAs. Front Microbiol 2021; 12:758948. [PMID: 34858370 PMCID: PMC8630580 DOI: 10.3389/fmicb.2021.758948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 10/19/2021] [Indexed: 01/10/2023] Open
Abstract
Despite significant efforts, there are currently no approved treatments for COVID-19. However, biotechnological approaches appear to be promising in the treatment of the disease. Accordingly, nucleic acid-based treatments including aptamers and siRNAs are candidates that might be effective in COVID-19 treatment. Aptamers can hamper entry and replication stages of the SARS-CoV-2 infection, while siRNAs can cleave the viral genomic and subgenomic RNAs to inhibit the viral life cycle and reduce viral loads. As a conjugated molecule, aptamer–siRNA chimeras have proven to be dual-functioning antiviral therapy, acting both as virus-neutralizing and replication-interfering agents as well as being a siRNA targeted delivery approach. Previous successful applications of these compounds against various stages of the pathogenesis of diseases and viral infections, besides their advantages over other alternatives, might provide sufficient rationale for the application of these nucleic acid-based drugs against the SARS-CoV-2. However, none of them are devoid of limitations. Here, the literature was reviewed to assess the plausibility of using aptamers, siRNAs, and aptamer–siRNA chimeras against the SARS-CoV-2 based on their previously established effectiveness, and discussing challenges lie in applying these molecules.
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Affiliation(s)
- Javad Khanali
- School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Yasaman Asaadi
- Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran
| | - Monire Jamalkhah
- Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, ON, Canada.,Ottawa Hospital Research Institute, Ottawa, ON, Canada
| | - Jafar Kiani
- Department of Molecular Medicine, School of Advanced Technologies in Medicine, Iran University of Medical Sciences, Tehran, Iran
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15
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Alamudi SH, Kimoto M, Hirao I. Uptake mechanisms of cell-internalizing nucleic acid aptamers for applications as pharmacological agents. RSC Med Chem 2021; 12:1640-1649. [PMID: 34778766 PMCID: PMC8528270 DOI: 10.1039/d1md00199j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 07/15/2021] [Indexed: 12/12/2022] Open
Abstract
Nucleic acid aptamers, also regarded as chemical antibodies, show potential as targeted therapeutic and delivery agents since they possess unique advantages over antibodies. Generated by an iterative selection and amplification process from oligonucleotide libraries using cultured cells, the aptamers bind to their target molecules expressed on the cell surface. Excitingly, most aptamers also demonstrate a cell-internalizing property in native living cells, allowing them to directly enter the cells via endocytosis depending on the target. In this review, we discuss selection methods in generating cell-internalizing aptamers via a cell-based selection process, along with their challenges and optimization strategies. We highlight the cellular uptake routes adopted by the aptamers and also their intracellular fate after the uptake, to give an overview of their mechanism of action for applications as promising pharmacological agents.
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Affiliation(s)
- Samira Husen Alamudi
- Institute of Bioengineering and Bioimaging (IBB), Agency for Science, Technology and Research (ASTAR) 31 Biopolis Way, Nanos #07-01 Singapore 138669 Singapore
| | - Michiko Kimoto
- Institute of Bioengineering and Bioimaging (IBB), Agency for Science, Technology and Research (ASTAR) 31 Biopolis Way, Nanos #07-01 Singapore 138669 Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Bioimaging (IBB), Agency for Science, Technology and Research (ASTAR) 31 Biopolis Way, Nanos #07-01 Singapore 138669 Singapore
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16
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Competitive ELISA for a serologic test to detect dengue serotype-specific anti-NS1 IgGs using high-affinity UB-DNA aptamers. Sci Rep 2021; 11:18000. [PMID: 34504185 PMCID: PMC8429655 DOI: 10.1038/s41598-021-97339-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Accepted: 08/24/2021] [Indexed: 02/08/2023] Open
Abstract
Serologic tests to detect specific IgGs to antigens related to viral infections are urgently needed for diagnostics and therapeutics. We present a diagnostic method for serotype-specific IgG identification of dengue infection by a competitive enzyme-linked immunosorbent assay (ELISA), using high-affinity unnatural-base-containing DNA (UB-DNA) aptamers that recognize the four categorized serotypes. Using UB-DNA aptamers specific to each serotype of dengue NS1 proteins (DEN-NS1), we developed our aptamer-antibody sandwich ELISA for dengue diagnostics. Furthermore, IgGs highly specific to DEN-NS1 inhibited the serotype-specific NS1 detection, inspiring us to develop the competitive ELISA format for dengue serotype-specific IgG detection. Blood samples from Singaporean patients with primary or secondary dengue infections confirmed the highly specific IgG detection of this format, and the IgG production initially reflected the serotype of the past infection, rather than the recent infection. Using this dengue competitive ELISA format, cross-reactivity tests of 21 plasma samples from Singaporean Zika virus-infected patients revealed two distinct patterns: 8 lacked cross-reactivity, and 13 were positive with unique dengue serotype specificities, indicating previous dengue infection. This antigen-detection ELISA and antibody-detection competitive ELISA combination using the UB-DNA aptamers identifies both past and current viral infections and will facilitate specific medical care and vaccine development for infectious diseases.
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17
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Matsunaga KI, Kimoto M, Lim VW, Tan HP, Wong YQ, Sun W, Vasoo S, Leo YS, Hirao I. High-affinity five/six-letter DNA aptamers with superior specificity enabling the detection of dengue NS1 protein variants beyond the serotype identification. Nucleic Acids Res 2021; 49:11407-11424. [PMID: 34169309 PMCID: PMC8599795 DOI: 10.1093/nar/gkab515] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 05/24/2021] [Accepted: 06/04/2021] [Indexed: 12/25/2022] Open
Abstract
Genetic alphabet expansion of DNA by introducing unnatural bases (UBs), as a fifth letter, dramatically augments the affinities of DNA aptamers that bind to target proteins. To determine whether UB-containing DNA (UB-DNA) aptamers obtained by affinity selection could spontaneously achieve high specificity, we have generated a series of UB-DNA aptamers (KD: 27-182 pM) targeting each of four dengue non-structural protein 1 (DEN-NS1) serotypes. The specificity of each aptamer is remarkably high, and the aptamers can recognize the subtle variants of DEN-NS1 with at least 96.9% amino acid sequence identity, beyond the capability of serotype identification (69-80% sequence identities). Our UB-DNA aptamers specifically identified two major variants of dengue serotype 1 with 10-amino acid differences in the DEN-NS1 protein (352 aa) in Singaporeans' clinical samples. These results suggest that the high-affinity UB-DNA aptamers generated by affinity selection also acquire high target specificity. Intriguingly, one of the aptamers contained two different UBs as fifth and sixth letters, which are essential for the tight binding to the target. These two types of unnatural bases with distinct physicochemical properties profoundly expand the potential of DNA aptamers. Detection methods incorporating the UB-DNA aptamers will facilitate precise diagnoses of viral infections and other diseases.
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Affiliation(s)
- Ken-Ichiro Matsunaga
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - Michiko Kimoto
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - Vanessa Weixun Lim
- National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore 308442, Singapore
| | - Hui Pen Tan
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - Yu Qian Wong
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - William Sun
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore.,Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117593, Singapore
| | - Shawn Vasoo
- National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore 308442, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore 308433, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Dr., Experimental Medicine Building, Singapore 636921, Singapore
| | - Yee Sin Leo
- National Centre for Infectious Diseases, 16 Jalan Tan Tock Seng, Singapore 308442, Singapore.,Department of Infectious Diseases, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore 308433, Singapore.,Lee Kong Chian School of Medicine, Nanyang Technological University, 59 Nanyang Dr., Experimental Medicine Building, Singapore 636921, Singapore.,Saw Swee Hock School of Public Health, National University of Singapore, 12 Science Drive 2, #10-01, Singapore 117549, Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Bioimaging, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
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18
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Berber B, Aydin C, Kocabas F, Guney-Esken G, Yilancioglu K, Karadag-Alpaslan M, Caliseki M, Yuce M, Demir S, Tastan C. Gene editing and RNAi approaches for COVID-19 diagnostics and therapeutics. Gene Ther 2021; 28:290-305. [PMID: 33318646 PMCID: PMC7734466 DOI: 10.1038/s41434-020-00209-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2020] [Revised: 10/20/2020] [Accepted: 10/27/2020] [Indexed: 01/29/2023]
Abstract
The novel coronavirus pneumonia (COVID-19) is a highly infectious acute respiratory disease caused by Severe Acute Respiratory Syndrome-Related Coronavirus (SARS-CoV-2) (Prec Clin Med 2020;3:9-13, Lancet 2020;395:497-506, N. Engl J Med 2020a;382:1199-207, Nature 2020;579:270-3). SARS-CoV-2 surveillance is essential to controlling widespread transmission. However, there are several challenges associated with the diagnostic of the COVID-19 during the current outbreak (Liu and Li (2019), Nature 2020;579:265-9, N. Engl J Med 2020;382:727-33). Firstly, the high number of cases overwhelms diagnostic test capacity and proposes the need for a rapid solution for sample processing (Science 2018;360:444-8). Secondly, SARS-CoV-2 is closely related to other important coronavirus species and subspecies, so detection assays can give false-positive results if they are not efficiently specific to SARS-CoV-2. Thirdly, patients with suspected SARS-CoV-2 infection sometimes have a different respiratory viral infection or co-infections with SARS-CoV-2 and other respiratory viruses (MedRxiv 2020a;1-18). Confirmation of the COVID-19 is performed mainly by virus isolation followed by RT-PCR and sequencing (N. Engl J Med 2020;382:727-33, MedRxiv 2020a, Turkish J Biol 2020;44:192-202). The emergence and outbreak of the novel coronavirus highlighted the urgent need for new therapeutic technologies that are fast, precise, stable, easy to manufacture, and target-specific for surveillance and treatment. Molecular biology tools that include gene-editing approaches such as CRISPR-Cas12/13-based SHERLOCK, DETECTR, CARVER and PAC-MAN, antisense oligonucleotides, antisense peptide nucleic acids, ribozymes, aptamers, and RNAi silencing approaches produced with cutting-edge scientific advances compared to conventional diagnostic or treatment methods could be vital in COVID-19 and other future outbreaks. Thus, in this review, we will discuss potent the molecular biology approaches that can revolutionize diagnostic of viral infections and therapies to fight COVID-19 in a highly specific, stable, and efficient way.
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Affiliation(s)
- Burak Berber
- Department of Biology, Faculty of Science, Eskisehir Technical University, Eskisehir, Turkey
| | - Cihan Aydin
- Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Istanbul Medeniyet University, Istanbul, Turkey
| | - Fatih Kocabas
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Gulen Guney-Esken
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Kaan Yilancioglu
- Institute of Addiction and Forensic Sciences, Uskudar University, Istanbul, Turkey
- Transgenic Cell Technologies and Epigenetics Application and Research Center (TRGENMER), Uskudar University, Istanbul, Turkey
| | - Medine Karadag-Alpaslan
- Department of Medical Genetics, Faculty of Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Mehmet Caliseki
- Department of Molecular Biology, Genetics and Bioengineering, Graduate School of Engineering and Natural Sciences, Sabanci University, Istanbul, Turkey
| | - Melek Yuce
- Center for Stem Cell Research, Ondokuz Mayis University, Samsun, Turkey
| | - Sevda Demir
- Department of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul, Turkey
| | - Cihan Tastan
- Transgenic Cell Technologies and Epigenetics Application and Research Center (TRGENMER), Uskudar University, Istanbul, Turkey.
- Acibadem Labcell Cellular Therapy Laboratory, Istanbul, Turkey.
- Faculty of Science and Letters, Department of Molecular Biology and Genetics, Istanbul Kultur University, Istanbul, Turkey.
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19
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Zhu M, Wang S. Functional Nucleic‐Acid‐Decorated Spherical Nanoparticles: Preparation Strategies and Current Applications in Cancer Therapy. SMALL SCIENCE 2021. [DOI: 10.1002/smsc.202000056] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Min Zhu
- Department of Pharmaceutical Engineering College of Chemistry and Chemical Engineering Central South University No. 932 South Lushan Rd Changsha Hunan 410083 P. R. China
| | - Shan Wang
- Department of Pharmaceutical Engineering College of Chemistry and Chemical Engineering Central South University No. 932 South Lushan Rd Changsha Hunan 410083 P. R. China
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20
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De Novo Nucleic Acids: A Review of Synthetic Alternatives to DNA and RNA That Could Act as Bio-Information Storage Molecules. Life (Basel) 2020; 10:life10120346. [PMID: 33322642 PMCID: PMC7764398 DOI: 10.3390/life10120346] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/04/2020] [Accepted: 12/09/2020] [Indexed: 01/30/2023] Open
Abstract
Modern terran life uses several essential biopolymers like nucleic acids, proteins and polysaccharides. The nucleic acids, DNA and RNA are arguably life’s most important, acting as the stores and translators of genetic information contained in their base sequences, which ultimately manifest themselves in the amino acid sequences of proteins. But just what is it about their structures; an aromatic heterocyclic base appended to a (five-atom ring) sugar-phosphate backbone that enables them to carry out these functions with such high fidelity? In the past three decades, leading chemists have created in their laboratories synthetic analogues of nucleic acids which differ from their natural counterparts in three key areas as follows: (a) replacement of the phosphate moiety with an uncharged analogue, (b) replacement of the pentose sugars ribose and deoxyribose with alternative acyclic, pentose and hexose derivatives and, finally, (c) replacement of the two heterocyclic base pairs adenine/thymine and guanine/cytosine with non-standard analogues that obey the Watson–Crick pairing rules. This manuscript will examine in detail the physical and chemical properties of these synthetic nucleic acid analogues, in particular on their abilities to serve as conveyors of genetic information. If life exists elsewhere in the universe, will it also use DNA and RNA?
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21
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Kimoto M, Hirao I. Genetic alphabet expansion technology by creating unnatural base pairs. Chem Soc Rev 2020; 49:7602-7626. [PMID: 33015699 DOI: 10.1039/d0cs00457j] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Recent advancements in the creation of artificial extra base pairs (unnatural base pairs, UBPs) are opening the door to a new research area, xenobiology, and genetic alphabet expansion technologies. UBPs that function as third base pairs in replication, transcription, and/or translation enable the site-specific incorporation of novel components into DNA, RNA, and proteins. Here, we describe the UBPs developed by three research teams and their application in PCR-based diagnostics, high-affinity DNA aptamer generation, site-specific labeling of RNAs, semi-synthetic organism creation, and unnatural-amino-acid-containing protein synthesis.
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Affiliation(s)
- Michiko Kimoto
- Institute of Bioengineering and Nanotechnology, A*STAR, Singapore.
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22
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Han J, Gao L, Wang J, Wang J. Application and development of aptamer in cancer: from clinical diagnosis to cancer therapy. J Cancer 2020; 11:6902-6915. [PMID: 33123281 PMCID: PMC7592013 DOI: 10.7150/jca.49532] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 09/20/2020] [Indexed: 01/04/2023] Open
Abstract
Traditional anticancer therapies can cause serious side effects in clinical treatment due to their nonspecific of tumor cells. Aptamers, also termed as 'chemical antibodies', are short DNA or RNA oligonucleotides selected from the synthetic large random single-strand oligonucleotide library by systematic evolution of ligands by exponential enrichment (SELEX) to bind to lots of different targets, such as proteins or nucleic acid structures. Aptamers have good affinities and high specificity with target molecules, thus may be able to act as drugs themselves to directly inhibit the proliferation of tumor cells, or own great potentialities in the targeted drug delivery systems which can be used in tumor diagnosis and target specific tumor cells, thereby minimizing the toxicity to normal cells. Here we review the unique properties of aptamer represents a great opportunity when applied to the rapidly developing fields of biotechnology and discuss the recent developments in the use of aptamers as powerful tools for analytic, diagnostic and therapeutic applications for cancer.
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Affiliation(s)
- Jing Han
- Department of Reproductive Medicine, Heping Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, 046000 China
| | - Liang Gao
- Department of Dermatology, Heji Hospital Affiliated to Changzhi Medical College, Changzhi, Shanxi, 046000 China
| | - Jinsheng Wang
- Department of Pathology, Changzhi Medical College, Changzhi, Shanxi, 046000 China
| | - Jia Wang
- Department of Immunology, Changzhi Medical College, Changzhi, Shanxi, 046000 China
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23
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Kimoto M, Hirao I. New Research Area, Xenobiology, by Integrating Chemistry and Biology. J SYN ORG CHEM JPN 2020. [DOI: 10.5059/yukigoseikyokaishi.78.465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Ichiro Hirao
- Institute of Bioengineering and Nanotechnology, A*STAR
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24
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Kimoto M, Soh SHG, Hirao I. Sanger Gap Sequencing for Genetic Alphabet Expansion of DNA. Chembiochem 2020; 21:2287-2296. [DOI: 10.1002/cbic.202000057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/19/2020] [Indexed: 01/03/2023]
Affiliation(s)
- Michiko Kimoto
- Institute of Bioengineering and Nanotechnology, A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
| | - Si Hui Gabriella Soh
- Institute of Bioengineering and Nanotechnology, A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
- Raffles Institution 1 Raffles Institution Lane Singapore 575954 Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Nanotechnology, A*STAR 31 Biopolis Way, The Nanos #07-01 Singapore 138669 Singapore
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25
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Xia X, Pollock N, Zhou J, Rossi J. Tissue-Specific Delivery of Oligonucleotides. Methods Mol Biol 2020; 2036:17-50. [PMID: 31410789 DOI: 10.1007/978-1-4939-9670-4_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
From the initial discovery of short-interfering RNA (siRNA) and antisense oligonucleotides for specific gene knockdown at the posttranscriptional level to the current CRISPR-Cas9 system offering gene editing at the genomic level, oligonucleotides, in addition to their biological functions in storing and conveying genetic information, provide the most prominent solutions to targeted gene therapies. Nonetheless, looking into the future of curing cancer and acute diseases, researchers are only cautiously optimistic as the cellular delivery of these polyanionic biomacromolecules is still the biggest hurdle for their therapeutic realization. To overcome the delivery obstacle, oligonucleotides have been encapsulated within or conjugated with delivery vehicles for enhanced membrane penetration, improved payload, and tissue-specific delivery. Such delivery systems include but not limited to virus-based vehicles, gold-nanoparticle vehicles, formulated liposomes, and synthetic polymers. In this chapter, delivery challenges imposed by biological barriers are briefly discussed; followed by recent advances in tissue-specific oligonucleotide delivery utilizing both viral and nonviral delivery vectors, discussing their advantages, and how judicious design and formulation could improve and expand their potential as delivery vehicles.
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Affiliation(s)
- Xin Xia
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Nicolette Pollock
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Jiehua Zhou
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - John Rossi
- Department of Molecular and Cellular Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA.
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Zhong Y, Zhao J, Li J, Liao X, Chen F. Advances of aptamers screened by Cell-SELEX in selection procedure, cancer diagnostics and therapeutics. Anal Biochem 2020; 598:113620. [PMID: 32087127 DOI: 10.1016/j.ab.2020.113620] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/10/2020] [Accepted: 02/10/2020] [Indexed: 12/23/2022]
Abstract
Aptamers are a class of short artificial single-stranded oligo(deoxy) nucleotides that can bind to different targets, which generated by Systematic Evolution of Ligands by Exponential Enrichment (SELEX). Due to excellent selectivity and high affinity to targets, aptamers hold considerable potential as molecular probe in diverse applications ranging from ensuring food safety, monitoring environment, disease diagnosis to therapy. This review highlights recent development and challenges about aptamers screened by Cell-SELEX, and its application about cancer diagnostics and therapeutics. Advances about some operation methods such as seperation method and culture method in aptamers selection procedure were summarized in this paper. Some common challenges and technological difficulties such as nonspecific binding and biostability were discussed. Up to now, the recent endeavors about cancer diagnostic and therapeutic applications of aptamers are summarized and expatiated. Most of aptamers screened by Cell-SELEX took tumor cells as target cells, and such aptamers have been assembled to various aptasensor for cancer diagnosis. Aptamers conjugated various drugs or nanomaterials are functioned for cancer target therapy to improve drugs delivery efficiency and reduce side effects. Furthermore, the duplexed aptamer is discussed to be applied for cancer cells detection and some conflicts of theories about duplexed aptamer designs are analyzed.
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Affiliation(s)
- Yi Zhong
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, China; National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jiayao Zhao
- Department of Clinical Laboratory, First Affiliated Hospital of Guangxi Medical University, Nanning, China; National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China
| | - Jiazhao Li
- Qionglai maternal&Child health care hospital, Chengdu, 611530, Sichuan, China
| | - Xin Liao
- School of laboratory medical and Life science, Wenzhou Medical University, Wenzhou, 325000, Fujian, China
| | - Fengling Chen
- National Center for International Research of Bio-targeting Theranostics, Guangxi Key Laboratory of Bio-targeting Theranostics, Collaborative Innovation Center for Targeting Tumor Diagnosis and Therapy, Guangxi Medical University, Nanning, 530021, Guangxi, China.
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Kimoto M, Shermane Lim YW, Hirao I. Molecular affinity rulers: systematic evaluation of DNA aptamers for their applicabilities in ELISA. Nucleic Acids Res 2019; 47:8362-8374. [PMID: 31392985 PMCID: PMC6895277 DOI: 10.1093/nar/gkz688] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/09/2019] [Accepted: 07/30/2019] [Indexed: 12/15/2022] Open
Abstract
Many nucleic acid aptamers that bind to target molecules have been reported as antibody alternatives. However, while the affinities of aptamers vary widely, little is known about the relationship between the affinities and their applicabilities for practical use. Here, we developed molecular affinity rulers: a series of DNA aptamers with different affinities that bind to the same area of target molecules, to measure the aptamer and its device applicabilities. For the ruler preparation, we used high-affinity DNA aptamers containing a hydrophobic unnatural base (Ds) as the fifth base. By replacing Ds bases with A bases in Ds-DNA aptamers targeting VEGF165 and interferon-γ, we prepared two sets of DNA aptamers with dissociation constants (KD) ranging from 10−12 to 10−8 M. Using these molecular affinity rulers, we evaluated the sensitivity of DNA aptamers in ELISA (enzyme-linked immunosorbent assay), which showed the clear relationship between aptamer affinities and their detection sensitivities. In sandwich-type ELISA using combinations of aptamers and antibodies, aptamers with KD values lower than ∼10−9 M were required for sufficient sensitivities (limit of detection (LOD) < 10 pM) and signal intensities, but optimizations improved the lower-affinity aptamers’ applicabilities. These aptamer affinity rulers could be useful for evaluating and improving aptamer applicabilities.
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Affiliation(s)
- Michiko Kimoto
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - Yun Wei Shermane Lim
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore.,NUS High School of Mathematics and Science, 20 Clementi Avenue 1, Singapore 129957, Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
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28
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Majerová T, Novotný P, Krýsová E, Konvalinka J. Exploiting the unique features of Zika and Dengue proteases for inhibitor design. Biochimie 2019; 166:132-141. [PMID: 31077760 DOI: 10.1016/j.biochi.2019.05.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/01/2019] [Indexed: 02/07/2023]
Abstract
Zika and Dengue viruses have attracted substantial attention from researchers in light of recent outbreaks of Dengue fever and increases in cases of congenital microcephaly in areas with Zika incidence. This review summarizes the current state of knowledge about Zika and Dengue proteases. These enzymes have several interesting features: 1) NS3 serine protease requires the activating co-factor NS2B, which is anchored in the membrane of the endoplasmic reticulum; 2) NS2B displays extensive conformational dynamics; 3) NS3 is a multidomain protein with proteolytic, NTPase, RNA 5' triphosphatase and helicase activity and has many protein-protein interaction partners; 4) NS3 is autoproteolytically released from its precursor. Attempts to design tight-binding and specific active-site inhibitors are complicated by the facts that the substrate pocket of the NS2B-NS3 protease is flat and the active-site ligands are charged. The ionic character of potential active-site inhibitors negatively influences their cell permeability. Possibilities to block cis-autoprocessing of the protease precursor have recently been considered. Additionally, potential allosteric sites on NS2B-NS3 proteases have been identified and allosteric compounds have been designed to impair substrate binding and/or block the NS2B-NS3 interaction. Such compounds could be specific to viral proteases, without off-target effects on host serine proteases, and could have favorable pharmacokinetic profiles. This review discusses various groups of inhibitors of these proteases according to their mechanisms of action and chemical structures.
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Affiliation(s)
- Taťána Majerová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic
| | - Pavel Novotný
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University in Prague, 12843, Prague, Czech Republic
| | - Eliška Krýsová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, 12843, Prague, Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University in Prague, 12843, Prague, Czech Republic.
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Antipova OM, Zavyalova EG, Golovin AV, Pavlova GV, Kopylov AM, Reshetnikov RV. Advances in the Application of Modified Nucleotides in SELEX Technology. BIOCHEMISTRY (MOSCOW) 2018; 83:1161-1172. [PMID: 30472954 DOI: 10.1134/s0006297918100024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aptamers are widely used as molecular recognition elements for detecting and blocking functional biological molecules. Since the common "alphabet" of DNA and RNA consists of only four letters, the chemical diversity of aptamers is less than the diversity of protein recognition elements built of 20 amino acids. Chemical modification of nucleotides enlarges the potential of DNA/RNA aptamers. This review describes the latest achievements in a variety of approaches to aptamers selection with an extended genetic alphabet.
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Affiliation(s)
- O M Antipova
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia. .,Apto-Pharm Ltd., Moscow, 115564, Russia
| | - E G Zavyalova
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.,Apto-Pharm Ltd., Moscow, 115564, Russia
| | - A V Golovin
- Apto-Pharm Ltd., Moscow, 115564, Russia.,Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119234, Russia.,Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, 119991, Russia
| | - G V Pavlova
- Apto-Pharm Ltd., Moscow, 115564, Russia.,Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, 119991, Russia.,Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia.,Burdenko National Scientific and Practical Center for Neurosurgery, Ministry of Healthcare of the Russian Federation, Moscow, 125047, Russia
| | - A M Kopylov
- Lomonosov Moscow State University, Faculty of Chemistry, Moscow, 119991, Russia.,Apto-Pharm Ltd., Moscow, 115564, Russia
| | - R V Reshetnikov
- Apto-Pharm Ltd., Moscow, 115564, Russia.,Lomonosov Moscow State University, Faculty of Bioengineering and Bioinformatics, Moscow, 119234, Russia.,Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Moscow, 119991, Russia.,Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia
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30
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Hamashima K, Kimoto M, Hirao I. Creation of unnatural base pairs for genetic alphabet expansion toward synthetic xenobiology. Curr Opin Chem Biol 2018; 46:108-114. [PMID: 30059833 DOI: 10.1016/j.cbpa.2018.07.017] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Revised: 05/02/2018] [Accepted: 07/13/2018] [Indexed: 01/10/2023]
Abstract
Artificial extra base pairs (unnatural base pairs, UBPs) expand the genetic alphabet of DNA, thus broadening entire biological systems in the central dogma. UBPs function as third base pairs in replication, transcription, and/or translation, and have created a new research area, synthetic xenobiology, providing genetic engineering tools to generate novel DNAs, RNAs, and proteins with increased functionalities. Several UBPs have been developed and applied to PCR technology, DNA aptamer generation, and semi-synthetic organism creation. Among them, we developed a series of UBPs and demonstrated unique quantitative PCR and high-affinity DNA aptamer generation methods.
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Affiliation(s)
- Kiyofumi Hamashima
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - Michiko Kimoto
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore
| | - Ichiro Hirao
- Institute of Bioengineering and Nanotechnology, 31 Biopolis Way, The Nanos, #07-01, Singapore 138669, Singapore.
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31
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Röthlisberger P, Gasse C, Hollenstein M. Nucleic Acid Aptamers: Emerging Applications in Medical Imaging, Nanotechnology, Neurosciences, and Drug Delivery. Int J Mol Sci 2017; 18:E2430. [PMID: 29144411 PMCID: PMC5713398 DOI: 10.3390/ijms18112430] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/08/2017] [Accepted: 11/09/2017] [Indexed: 12/25/2022] Open
Abstract
Recent progresses in organic chemistry and molecular biology have allowed the emergence of numerous new applications of nucleic acids that markedly deviate from their natural functions. Particularly, DNA and RNA molecules-coined aptamers-can be brought to bind to specific targets with high affinity and selectivity. While aptamers are mainly applied as biosensors, diagnostic agents, tools in proteomics and biotechnology, and as targeted therapeutics, these chemical antibodies slowly begin to be used in other fields. Herein, we review recent progress on the use of aptamers in the construction of smart DNA origami objects and MRI and PET imaging agents. We also describe advances in the use of aptamers in the field of neurosciences (with a particular emphasis on the treatment of neurodegenerative diseases) and as drug delivery systems. Lastly, the use of chemical modifications, modified nucleoside triphosphate particularly, to enhance the binding and stability of aptamers is highlighted.
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Affiliation(s)
- Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris CEDEX 15, France.
| | - Cécile Gasse
- Institute of Systems & Synthetic Biology, Xenome Team, 5 rue Henri Desbruères Genopole Campus 1, University of Evry, F-91030 Evry, France.
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris CEDEX 15, France.
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