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Xu C, Tan Y, Zhang LY, Luo XJ, Wu JF, Ma L, Deng F. The Application of Aptamer and Research Progress in Liver Disease. Mol Biotechnol 2024; 66:1000-1018. [PMID: 38305844 PMCID: PMC11087326 DOI: 10.1007/s12033-023-01030-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/15/2023] [Indexed: 02/03/2024]
Abstract
Aptamers, as a kind of small-molecule nucleic acid, have attracted much attention since their discovery. Compared with biological reagents such as antibodies, aptamers have the advantages of small molecular weight, low immunogenicity, low cost, and easy modification. At present, aptamers are mainly used in disease biomarker discovery, disease diagnosis, treatment, and targeted drug delivery vectors. In the process of screening and optimizing aptamers, it is found that there are still many problems need to be solved such as the design of the library, optimization of screening conditions, the truncation of screened aptamer, and the stability and toxicity of the aptamer. In recent years, the incidence of liver-related diseases is increasing year by year and the treatment measures are relatively lacking, which has attracted the people's attention in the application of aptamers in liver diseases. This article mainly summarizes the research status of aptamers in disease diagnosis and treatment, especially focusing on the application of aptamers in liver diseases, showing the crucial significance of aptamers in the diagnosis and treatment of liver diseases, and the use of Discovery Studio software to find the binding target and sequence of aptamers, and explore their possible interaction sites.
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Affiliation(s)
- Cheng Xu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, 443002, Hubei, China
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China
| | - Yong Tan
- Hubei Selenium and Human Health Institute, The Central Hospital of Enshi Tujia and Miao Autonomous Prefecture, Enshi, Hubei, China
| | - Li-Ye Zhang
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, 443002, Hubei, China
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China
| | - Xiao-Jie Luo
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, 443002, Hubei, China
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China
| | - Jiang-Feng Wu
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
- College of Basic Medical Science, China Three Gorges University, Yichang, 443002, Hubei, China
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China
| | - Lan Ma
- Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China.
- College of Basic Medical Science, China Three Gorges University, Yichang, 443002, Hubei, China.
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, Yichang, China.
| | - Fei Deng
- Department of Oncology, The Second People's Hospital of China Three Gorges University, Yichang, 443000, China.
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Ou X, Wan Z, Xiong Y, Huang K, Wei Z, Nuermaimaiti Z, Chen Y, Yiliya D, Lin H, Dai Z, Li Y, Chen P. Homogeneous Dual Fluorescence Count of CD4 in Clinical HIV-Positive Samples via Parallel Catalytic Hairpin Assembly and Multiple Recognitions. ACS APPLIED MATERIALS & INTERFACES 2023; 15:38285-38293. [PMID: 37526600 DOI: 10.1021/acsami.3c06742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Regularly measuring the level of CD4+ cells is necessary for monitoring progression and predicting prognosis in patients suffering from an infection with the human immunodeficiency virus (HIV). However, the current flow cytometry standard detection method is expensive and complicated. A parallel catalytic hairpin assembly (CHA)-assisted fluorescent aptasensor is reported for homogeneous CD4 count by targeting the CD4 protein expressed on the membrane of CD4+ cells. Detection was achieved using CdTe quantum dots (QDs) and methylene blue (MB) as signal reporters. CdTe QDs distinguished CHA-assisted release of Ag+ and C-Ag+-C and MB that has differentiated cytosine (C)-rich single-stranded DNA (ssDNA) and C-Ag+-C, generating changes in fluorescence intensity. With the assistance of the CHA strategy and luminescent nanomaterials, this method reached limits of detection of 0.03 fg/mL for the CD4 protein and 0.3 cells/mL for CD4+ cells with linear ranges of 0.1 to 100 fg/mL and 1 to 1000 cells/mL, respectively. The method was validated in 50 clinical whole blood samples consisting of 30 HIV-positive patients, 10 healthy volunteers, and 10 patients with cancer or other chronic infections. The findings from this method were in good agreement with the data from clinical flow cytometry. Due to its sensitivity, affordability, and ease of operation, the current method has demonstrated great potential for routine CD4 counts for the management of HIV, especially in communities and remote areas.
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Affiliation(s)
- Xiaoqi Ou
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zhengli Wan
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ying Xiong
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Ke Huang
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu, Sichuan 610068, China
| | - Zeliang Wei
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zulimire Nuermaimaiti
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yanting Chen
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Duerdanna Yiliya
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Hongyin Lin
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Zhenjie Dai
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yi Li
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Piaopiao Chen
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Department of Urology, National Clinical Research Center for Geriatrics, Core Facilities of West China Hospital, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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3
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Hu X, Zhang D, Zeng Z, Huang L, Lin X, Hong S. Aptamer-Based Probes for Cancer Diagnostics and Treatment. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111937. [PMID: 36431072 PMCID: PMC9695321 DOI: 10.3390/life12111937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/23/2022] [Accepted: 11/12/2022] [Indexed: 11/22/2022]
Abstract
Aptamers are single-stranded DNA or RNA oligomers that have the ability to generate unique and diverse tertiary structures that bind to cognate molecules with high specificity. In recent years, aptamer researches have witnessed a huge surge, owing to its unique properties, such as high specificity and binding affinity, low immunogenicity and toxicity, and simplicity of synthesis with negligible batch-to-batch variation. Aptamers may bind to targets, such as various cancer biomarkers, making them applicable for a wide range of cancer diagnosis and treatment. In cancer diagnostic applications, aptamers are used as molecular probes instead of antibodies. They have the potential to detect various cancer-associated biomarkers. For cancer therapeutic purposes, aptamers can serve as therapeutic or delivery agents. The chemical stabilization and modification strategies for aptamers may expand their serum half-life and shelf life. However, aptamer-based probes for cancer diagnosis and therapy still face several challenges for successful clinical translation. A deeper understanding of nucleic acid chemistry, tissue distribution, and pharmacokinetics is required in the development of aptamer-based probes. This review summarizes their application in cancer diagnostics and treatments based on different localization of target biomarkers, as well as current challenges and future prospects.
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Ullah S, Zahra QUA, Mansoorianfar M, Hussain Z, Ullah I, Li W, Kamya E, Mehmood S, Pei R, Wang J. Heavy Metal Ions Detection Using Nanomaterials-Based Aptasensors. Crit Rev Anal Chem 2022:1-17. [PMID: 36018260 DOI: 10.1080/10408347.2022.2115287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022]
Abstract
Heavy metals ions as metallic pollutants are a growing global issue due to their adverse effects on the aquatic ecosystem, and human health. Unfortunately, conventional detection methods such as atomic absorption spectrometry exhibit a relatively low limit of detection and hold numerous disadvantages, and therefore, the development of an efficient method for in-situ and real-time detection of heavy metal residues is of great importance. The aptamer-based sensors offer distinct advantages over antibodies and emerged as a robust sensing platform against various heavy metals due to their high sensitivity, ease of production, simple operations, excellent specificity, better stability, low immunogenicity, and cost-effectiveness. The nucleic acid aptamers in conjugation with nanomaterials can bind to the metal ions with good specificity/selectivity and can be used for on-site monitoring of metal ion residues. This review aimed to provide background information about nanomaterials-based aptasensor, recent advancements in aptamer conjunction on nanomaterials surface, the role of nanomaterials in improving signal transduction, recent progress of nanomaterials-based aptasening procedures (from 2010 to 2022), and future perspectives toward the practical applications of nanomaterials-based aptasensors against hazardous metal ions for food safety and environmental monitoring.
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Affiliation(s)
- Salim Ullah
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), Chinese Academy of Sciences, Suzhou, Jiangsu, PR China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China (USTC), Hefei, Anhui, PR China
| | - Qurat Ul Ain Zahra
- Biomedical Imaging Center, University of Science and Technology of China (USTC), Hefei, Anhui, PR China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, PR China
| | - Mojtaba Mansoorianfar
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), Chinese Academy of Sciences, Suzhou, Jiangsu, PR China
| | - Zahid Hussain
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), Chinese Academy of Sciences, Suzhou, Jiangsu, PR China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China (USTC), Hefei, Anhui, PR China
| | - Ismat Ullah
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), Chinese Academy of Sciences, Suzhou, Jiangsu, PR China
| | - Wenjing Li
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), Chinese Academy of Sciences, Suzhou, Jiangsu, PR China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China (USTC), Hefei, Anhui, PR China
| | - Edward Kamya
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), Chinese Academy of Sciences, Suzhou, Jiangsu, PR China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China (USTC), Hefei, Anhui, PR China
| | - Shah Mehmood
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), Chinese Academy of Sciences, Suzhou, Jiangsu, PR China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China (USTC), Hefei, Anhui, PR China
| | - Renjun Pei
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), Chinese Academy of Sciences, Suzhou, Jiangsu, PR China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China (USTC), Hefei, Anhui, PR China
| | - Jine Wang
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics (SINANO), Chinese Academy of Sciences, Suzhou, Jiangsu, PR China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China (USTC), Hefei, Anhui, PR China
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Serumula W, Fernandez G, Gonzalez VM, Parboosing R. Anti-HIV Aptamers: Challenges and Prospects. Curr HIV Res 2022; 20:7-19. [PMID: 34503417 DOI: 10.2174/1570162x19666210908114825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 08/06/2021] [Accepted: 08/11/2021] [Indexed: 02/08/2023]
Abstract
Human Immunodeficiency Virus (HIV) infection continues to be a significant health burden in many countries around the world. Current HIV treatment through a combination of different antiretroviral drugs (cART) effectively suppresses viral replication, but drug resistance and crossresistance are significant challenges. This has prompted the search for novel targets and agents, such as nucleic acid aptamers. Nucleic acid aptamers are oligonucleotides that attach to the target sites with high affinity and specificity. This review provides a target-by-target account of research into anti-HIV aptamers and summarises the challenges and prospects of this therapeutic strategy, specifically in the unique context of HIV infection.
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Affiliation(s)
- William Serumula
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, c/o Inkosi Albert Luthuli Central Hospital, 5th Floor Laboratory Building, 800 Bellair Road, Mayville, Durban 4091, South Africa
| | - Geronimo Fernandez
- Departamento de Bioquímica-Investigación, Aptus Biotech SL, Avda. Cardenal Herrera Oria, 298-28035 Madrid. Spain
| | - Victor M Gonzalez
- Departamento de Bioquímica-Investigación, Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS)-Hospital Ramón y Cajal, 28034 Madrid, Spain
| | - Raveen Parboosing
- Department of Virology, National Health Laboratory Service, University of KwaZulu-Natal, c/o Inkosi Albert Luthuli Central Hospital, 5th Floor Laboratory Building, 800 Bellair Road, Mayville, Durban 4091, South Africa
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Heredia FL, Roche-Lima A, Parés-Matos EI. A novel artificial intelligence-based approach for identification of deoxynucleotide aptamers. PLoS Comput Biol 2021; 17:e1009247. [PMID: 34343165 PMCID: PMC8362955 DOI: 10.1371/journal.pcbi.1009247] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 08/13/2021] [Accepted: 07/05/2021] [Indexed: 02/07/2023] Open
Abstract
The selection of a DNA aptamer through the Systematic Evolution of Ligands by EXponential enrichment (SELEX) method involves multiple binding steps, in which a target and a library of randomized DNA sequences are mixed for selection of a single, nucleotide-specific molecule. Usually, 10 to 20 steps are required for SELEX to be completed. Throughout this process it is necessary to discriminate between true DNA aptamers and unspecified DNA-binding sequences. Thus, a novel machine learning-based approach was developed to support and simplify the early steps of the SELEX process, to help discriminate binding between DNA aptamers from those unspecified targets of DNA-binding sequences. An Artificial Intelligence (AI) approach to identify aptamers were implemented based on Natural Language Processing (NLP) and Machine Learning (ML). NLP method (CountVectorizer) was used to extract information from the nucleotide sequences. Four ML algorithms (Logistic Regression, Decision Tree, Gaussian Naïve Bayes, Support Vector Machines) were trained using data from the NLP method along with sequence information. The best performing model was Support Vector Machines because it had the best ability to discriminate between positive and negative classes. In our model, an Accuracy (A) of 0.995, the fraction of samples that the model correctly classified, and an Area Under the Receiving Operating Curve (AUROC) of 0.998, the degree by which a model is capable of distinguishing between classes, were observed. The developed AI approach is useful to identify potential DNA aptamers to reduce the amount of rounds in a SELEX selection. This new approach could be applied in the design of DNA libraries and result in a more efficient and faster process for DNA aptamers to be chosen during SELEX. In this manuscript authors explain the development and validation of a novel artificial intelligence approach to support and simplify the early steps of the process from SELEX, to help discriminate binding between deoxynucleotide aptamers from those unspecified targets of DNA-binding sequences. The approach was implemented based on Natural Language Processing and Machine Learning. CountVectorizer, a Natural Language Processing method, was used to extract information from nucleotide sequences. Four Machine Learning algorithms (Logistic Regression, Decision Tree, Gaussian Naïve Bayes, and Support Vector Machines) were trained using data from the Natural Language Processing method along with sequence information. From these four trained machine learning algorithms, the best performance and selected model was Support Vectors Machines, because it had the best discriminatory metrics (i.e., Accuracy (A) = 0.995; AUROC (AU) = 0.998). In general, all models showed good metric results for predicting DNA aptamer sequences. The Machine Learning model complexity and difficult interpretation may hinder its application into the standard practice. For this reason, the development of a web-app is already taking place to facilitate the interpretation and application of the obtained results.
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Affiliation(s)
- Frances L. Heredia
- Department of Chemistry, University of Puerto Rico-Mayagüez Campus, Mayagüez, Puerto Rico, United States of America
| | - Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities, University of Puerto Rico-Medical Sciences Campus, San Juan, Puerto Rico, United States of America
| | - Elsie I. Parés-Matos
- Department of Chemistry, University of Puerto Rico-Mayagüez Campus, Mayagüez, Puerto Rico, United States of America
- * E-mail:
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Delcanale P, Porciani D, Pujals S, Jurkevich A, Chetrusca A, Tawiah KD, Burke DH, Albertazzi L. Aptamers with Tunable Affinity Enable Single-Molecule Tracking and Localization of Membrane Receptors on Living Cancer Cells. Angew Chem Int Ed Engl 2020; 59:18546-18555. [PMID: 32627326 PMCID: PMC7590183 DOI: 10.1002/anie.202004764] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Indexed: 12/31/2022]
Abstract
Tumor cell-surface markers are usually overexpressed or mutated protein receptors for which spatiotemporal regulation differs between and within cancers. Single-molecule fluorescence imaging can profile individual markers in different cellular contexts with molecular precision. However, standard single-molecule imaging methods based on overexpressed genetically encoded tags or cumbersome probes can significantly alter the native state of receptors. We introduce a live-cell points accumulation for imaging in nanoscale topography (PAINT) method that exploits aptamers as minimally invasive affinity probes. Localization and tracking of individual receptors are based on stochastic and transient binding between aptamers and their targets. We demonstrated single-molecule imaging of a model tumor marker (EGFR) on a panel of living cancer cells. Affinity to EGFR was finely tuned by rational engineering of aptamer sequences to define receptor motion and/or native receptor density.
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Affiliation(s)
- Pietro Delcanale
- Institute for Bioengineering of Catalonia (IBEC)The Barcelona Institute of Science and Technology (BIST)Baldiri Reixac 15–2108028BarcelonaSpain
| | - David Porciani
- Department of Molecular Microbiology & ImmunologySchool of MedicineUniversity of Missouri-Columbia1 Hospital DrColumbiaMO65212USA
- MU Bond Life Sciences CenterUniversity of Missouri-Columbia1201 Rollins StreetColumbiaMO65211-7310USA
| | - Silvia Pujals
- Institute for Bioengineering of Catalonia (IBEC)The Barcelona Institute of Science and Technology (BIST)Baldiri Reixac 15–2108028BarcelonaSpain
- Department of Electronics and Biomedical EngineeringFaculty of PhysicsUniversitat de BarcelonaMartí i Franquès 108028BarcelonaSpain
| | - Alexander Jurkevich
- Molecular Cytology Core at MU Bond Life Sciences CenterUniversity of Missouri-ColumbiaUSA
| | - Andrian Chetrusca
- Institute for Bioengineering of Catalonia (IBEC)The Barcelona Institute of Science and Technology (BIST)Baldiri Reixac 15–2108028BarcelonaSpain
| | - Kwaku D. Tawiah
- Department of BiochemistryUniversity of Missouri-Columbia117 Schweitzer HallColumbiaMO65211USA
| | - Donald H. Burke
- Department of Molecular Microbiology & ImmunologySchool of MedicineUniversity of Missouri-Columbia1 Hospital DrColumbiaMO65212USA
- MU Bond Life Sciences CenterUniversity of Missouri-Columbia1201 Rollins StreetColumbiaMO65211-7310USA
- Department of BiochemistryUniversity of Missouri-Columbia117 Schweitzer HallColumbiaMO65211USA
| | - Lorenzo Albertazzi
- Institute for Bioengineering of Catalonia (IBEC)The Barcelona Institute of Science and Technology (BIST)Baldiri Reixac 15–2108028BarcelonaSpain
- Department of Biomedical EngineeringInstitute for Complex Molecular Systems (ICMS)Eindhoven University of Technology5612AZEindhovenThe Netherlands
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Delcanale P, Porciani D, Pujals S, Jurkevich A, Chetrusca A, Tawiah KD, Burke DH, Albertazzi L. Aptamers with Tunable Affinity Enable Single‐Molecule Tracking and Localization of Membrane Receptors on Living Cancer Cells. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202004764] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Pietro Delcanale
- Institute for Bioengineering of Catalonia (IBEC) The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 15–21 08028 Barcelona Spain
| | - David Porciani
- Department of Molecular Microbiology & Immunology School of Medicine University of Missouri-Columbia 1 Hospital Dr Columbia MO 65212 USA
- MU Bond Life Sciences Center University of Missouri-Columbia 1201 Rollins Street Columbia MO 65211-7310 USA
| | - Silvia Pujals
- Institute for Bioengineering of Catalonia (IBEC) The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 15–21 08028 Barcelona Spain
- Department of Electronics and Biomedical Engineering Faculty of Physics Universitat de Barcelona Martí i Franquès 1 08028 Barcelona Spain
| | - Alexander Jurkevich
- Molecular Cytology Core at MU Bond Life Sciences Center University of Missouri-Columbia USA
| | - Andrian Chetrusca
- Institute for Bioengineering of Catalonia (IBEC) The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 15–21 08028 Barcelona Spain
| | - Kwaku D. Tawiah
- Department of Biochemistry University of Missouri-Columbia 117 Schweitzer Hall Columbia MO 65211 USA
| | - Donald H. Burke
- Department of Molecular Microbiology & Immunology School of Medicine University of Missouri-Columbia 1 Hospital Dr Columbia MO 65212 USA
- MU Bond Life Sciences Center University of Missouri-Columbia 1201 Rollins Street Columbia MO 65211-7310 USA
- Department of Biochemistry University of Missouri-Columbia 117 Schweitzer Hall Columbia MO 65211 USA
| | - Lorenzo Albertazzi
- Institute for Bioengineering of Catalonia (IBEC) The Barcelona Institute of Science and Technology (BIST) Baldiri Reixac 15–21 08028 Barcelona Spain
- Department of Biomedical Engineering Institute for Complex Molecular Systems (ICMS) Eindhoven University of Technology 5612AZ Eindhoven The Netherlands
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Fellows T, Ho L, Flanagan S, Fogel R, Ojo D, Limson J. Gold nanoparticle-streptavidin conjugates for rapid and efficient screening of aptamer function in lateral flow sensors using novel CD4-binding aptamers identified through Crossover-SELEX. Analyst 2020; 145:5180-5193. [PMID: 32567629 DOI: 10.1039/d0an00634c] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To decrease the burden of laborious and reagent-intensive screening of modified aptamers, their binding function requires assessment in assay formats compatible with the end diagnostic application. Here, we report on the use of an alternative and cost-effective approach: a rapid lateral flow assay (LFA) utilising streptavidin-conjugated gold nanoparticles (AuNP) as reporter molecules to screen novel ssDNA aptamers for their ability to detect CD4. Crossover-SELEX was employed to identify CD4-targeting aptamers from a ssDNA library enriched against a recombinant human CD4 protein (hCD4) conjugated to magnetic-beads and to endogenous CD4 expressed by U937 cells. Counter-selection with IgG-conjugated beads and CD4-negative Ramos RA-1 cells was employed. Following SELEX, four sequences (U4, U14, U20 and U26) were selected for candidate screening. Fluorescence confocal microscopy showed comparable localization of the Cy5-labeled aptamer U26, compared to antibodies binding CD4's cytoplasmic domain. Aptamer-hCD4 binding kinetics were evaluated by a qPCR-based magnetic-bead binding assay to unmodified aptamers. U26 exhibited the highest binding affinity (Kd = 2.93 ± 1.03 nM) to hCD4-conjugated beads. Citrate-stabilized gold nanoparticles (mean particle diameter, 10.59 ± 1.81 nm) were functionalized with streptavidin to allow immobilization of biotin-labeled aptamers. Except for U4, the aptamer-gold nanoparticle conjugates (Apt-AuNP) remained stable under physiological conditions with their size (approx. 15 nm) appropriate for use in the LFAs. Lateral-flow based screening was used to evaluate the suitability of the Apt-AuNPs as CD4-detecting reporter molecules by immobilizing hCD4 and flowing the nanoparticle conjugates across the LFA. Using this approach, two novel sequences were identified as being suitable for the detection of hCD4: visual detection at 9 min was obtained using U20 or U26. After 20 min, equivalent colorimetric hCD4 responses were observed between anti-CD4 monoclonal antibody (ΔI = 94.19 ± 3.71), an existing CD4 aptamer F1-62 (ΔI = 90.31 ± 19.31) and U26 (ΔI = 100.14 ± 14.61) LFA's, each demonstrating high specificity to hCD4 compared to IgG. From the above, Crossover-SELEX allowed for the successful identification of ssDNA aptamers able to detect hCD4. Streptavidin-conjugated AuNPs, when bound to candidate aptamers, show potential application here as screening tools for the rapid evaluation of aptamer performance in low-cost lateral flow diagnostics.
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Affiliation(s)
- Tamika Fellows
- Rhodes University Biotechnology Innovation Centre, Grahamstown, Eastern Cape, South Africa.
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The Growing Interest in Development of Innovative Optical Aptasensors for the Detection of Antimicrobial Residues in Food Products. BIOSENSORS-BASEL 2020; 10:bios10030021. [PMID: 32138274 PMCID: PMC7146278 DOI: 10.3390/bios10030021] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 02/20/2020] [Accepted: 02/24/2020] [Indexed: 12/26/2022]
Abstract
The presence of antimicrobial residues in food-producing animals can lead to harmful effects on the consumer (e.g., allergies, antimicrobial resistance, toxicological effects) and cause issues in food transformation (i.e., cheese, yogurts production). Therefore, to control antimicrobial residues in food products of animal origin, screening methods are of utmost importance. Microbiological and immunological methods (e.g., ELISA, dipsticks) are conventional screening methods. Biosensors are an innovative solution for the development of more performant screening methods. Among the different kinds of biosensing elements (e.g., antibodies, aptamers, molecularly imprinted polymers (MIP), enzymes), aptamers for targeting antimicrobial residues are in continuous development since 2000. Therefore, this review has highlighted recent advances in the development of aptasensors, which present multiple advantages over immunosensors. Most of the aptasensors described in the literature for the detection of antimicrobial residues in animal-derived food products are either optical or electrochemical sensors. In this review, I have focused on optical aptasensors and showed how nanotechnologies (nanomaterials, micro/nanofluidics, and signal amplification techniques) largely contribute to the improvement of their performance (sensitivity, specificity, miniaturization, portability). Finally, I have explored different techniques to develop multiplex screening methods. Multiplex screening methods are necessary for the wide spectrum detection of antimicrobials authorized for animal treatment (i.e., having maximum residue limits).
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11
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Chong C, Low C. Synthetic antibody: Prospects in aquaculture biosecurity. FISH & SHELLFISH IMMUNOLOGY 2019; 86:361-367. [PMID: 30502461 DOI: 10.1016/j.fsi.2018.11.060] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 10/12/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
The emerging technology of aptamers that is also known as synthetic antibodies is rivalling antibodies research in the recent years. The unique yet important features of aptamers are advancing antibodies in diverse applications, which include disease diagnosis, prophylactic and therapeutic. The versatility of aptamer has further extended its application to function as gene expression modulator, known as synthetic riboswitches. This report reviewed and discussed the applications of aptamers technology in the biosecurity of aquaculture, the promising developments in biosensor detection for disease diagnosis as well as prophylactic and therapeutic measurements. The application of aptamers technology in immunophenotyping study of aquatic animal is highlighted. Lastly, the future perspective of aptamers in the management of aquatic animal health is discussed, special emphasis on the potential application of aptamers as synthetic riboswitches to enhance host immunity, as well as the growth performance.
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Affiliation(s)
- ChouMin Chong
- Laboratory of Marine Biotechnology, Institute of Bioscience, Universiti Putra Malaysia, 43400, UPM Serdang, Selangor, Malaysia
| | - ChenFei Low
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, 43600, UKM Bangi, Selangor, Malaysia.
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12
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Modular cell-internalizing aptamer nanostructure enables targeted delivery of large functional RNAs in cancer cell lines. Nat Commun 2018; 9:2283. [PMID: 29891903 PMCID: PMC5995956 DOI: 10.1038/s41467-018-04691-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/09/2018] [Indexed: 02/07/2023] Open
Abstract
Large RNAs and ribonucleoprotein complexes have powerful therapeutic potential, but effective cell-targeted delivery tools are limited. Aptamers that internalize into target cells can deliver siRNAs (<15 kDa, 19–21 nt/strand). We demonstrate a modular nanostructure for cellular delivery of large, functional RNA payloads (50–80 kDa, 175–250 nt) by aptamers that recognize multiple human B cell cancer lines and transferrin receptor-expressing cells. Fluorogenic RNA reporter payloads enable accelerated testing of platform designs and rapid evaluation of assembly and internalization. Modularity is demonstrated by swapping in different targeting and payload aptamers. Both modules internalize into leukemic B cell lines and remained colocalized within endosomes. Fluorescence from internalized RNA persists for ≥2 h, suggesting a sizable window for aptamer payloads to exert influence upon targeted cells. This demonstration of aptamer-mediated, cell-internalizing delivery of large RNAs with retention of functional structure raises the possibility of manipulating endosomes and cells by delivering large aptamers and regulatory RNAs. Large RNAs and ribonucleoprotein complexes have shown potential as novel therapeutic agents, but their targeted delivery to cells is still challenging. Here the authors present a modular aptamer nanostructure for intracellular delivery of RNAs up to 250 nucleotides to cancer cells.
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Bala J, Chinnapaiyan S, Dutta RK, Unwalla H. Aptamers in HIV research diagnosis and therapy. RNA Biol 2018; 15:327-337. [PMID: 29431588 PMCID: PMC5927724 DOI: 10.1080/15476286.2017.1414131] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 11/07/2017] [Accepted: 12/03/2017] [Indexed: 12/30/2022] Open
Abstract
Aptamers are high affinity single-stranded nucleic acid or protein ligands which exhibit specificity and avidity comparable to, or exceeding that of antibodies and can be generated against most targets. The functionality of aptamers is based on their unique tertiary structure, complexity and their ability to attain unique binding pockets by folding. Aptamers are selected in vitro by a process called Systematic Evolution of Ligands by Exponential enrichment (SELEX). The Kd values for the selected aptamer are often in the picomolar to low nanomolar range. Stable and nontoxic aptamers could be selected for a wide range of ligands including small molecules to large proteins. Aptamers have shown tremendous potential and have found multipurpose application in the field of therapeutic, diagnostic, biosensor and bio-imaging. While their mechanism of action can be similar to that of monoclonal antibodies, aptamers provide additional advantages in terms of production cost, simpler regulatory approval and lower immunogenicity as they are synthesized chemically. Human immunodeficiency virus (HIV) is the primary cause of acquired immune deficiency syndrome (AIDS), which causes significant morbidity and mortality with a significant consequent decrease in the quality of patient's lives. While cART has led to good viral control, people living with HIV now suffer from non-HIV comorbidities due to viral protein expression that cannot be controlled by cART. Hence pathophysiological mechanisms that govern these comorbidities with a focus on therapies that neutralize these HIV effects gained increased attention. Recent advances in HIV/AIDS research have identified several molecular targets and for the development of therapeutic and diagnostic using aptamers against HIV/AIDS. This review presents recent advances in aptamers technology for potential application in HIV diagnostics and therapeutics towards improving the quality of life of people living with HIV.
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Affiliation(s)
- Jyoti Bala
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Srinivasan Chinnapaiyan
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Rajib Kumar Dutta
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
| | - Hoshang Unwalla
- Department of Immunology, Herbert Wertheim College of Medicine, Florida International University, Miami, FL, USA
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14
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Takahashi M. Aptamers targeting cell surface proteins. Biochimie 2017; 145:63-72. [PMID: 29198584 DOI: 10.1016/j.biochi.2017.11.019] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/28/2017] [Indexed: 02/07/2023]
Abstract
High affinity binders targeting specific cell surface proteins are vital for development of basic and applied biosciences. However, despite sustained efforts to generate such binders by chemicals and antibodies, there are still many cell surface proteins that lack high affinity binders. Nucleic acid aptamers have potential as binding molecules for cell surface proteins, because they form distinct structures that have high affinity and specificity for a wide range of targets. Aptamers are isolated from large combinatorial libraries using a unique iterative selection-amplification process known as systematic evolution of ligands by exponential enrichment (SELEX). Among advantages of this method, purified and complex heterogeneous targets, such as bacteria, viruses, and whole-living cells, can be used for selection of aptamers. Moreover, SELEX allows generation of cell-surface-specific aptamers without prior knowledge of expression profiles in target cells. Therefore, the technology has been widely used as a valid and feasible method to generate aptamers binding to cell surface proteins with intact structure. Herein, this review summarizes and updates iconic SELEX technologies that target membrane proteins.
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Affiliation(s)
- Masaki Takahashi
- Division of RNA Medical Science, The Institute of Medical Science, The University of Tokyo, 4-6-1, Shirokanedai, Minato-ku, Tokyo, Japan.
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15
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Xu C, Haque F, Jasinski DL, Binzel DW, Shu D, Guo P. Favorable biodistribution, specific targeting and conditional endosomal escape of RNA nanoparticles in cancer therapy. Cancer Lett 2017; 414:57-70. [PMID: 28987384 DOI: 10.1016/j.canlet.2017.09.043] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 09/14/2017] [Accepted: 09/25/2017] [Indexed: 01/22/2023]
Abstract
The past decades have witnessed the successful transition of several nanotechnology platforms into the clinical trials. However, specific delivery of therapeutics to tumors is hindered by several barriers including cancer recognition and tissue penetration, particle heterogeneity and aggregation, and unfavorable pharmacokinetic profiles such as fast clearance and organ accumulation. With the advent of RNA nanotechnology, a series of RNA nanoparticles have been successfully constructed to overcome many of the aforementioned challenges for in vivo cancer targeting with favorable biodistribution profiles. Compared to other nanodelivery platforms, the physiochemical properties of RNA nanoparticles can be tuned with relative ease for investigating the in vivo behavior of nanoparticles upon systemic injection. The size, shape, and surface chemistry, especially hydrophobic modifications, exert significant impacts on the in vivo fate of RNA nanoparticles. Rationally designed RNA nanoparticles with defined stoichiometry and high homogeneity have been demonstrated to specifically target tumor cells while avoiding accumulation in healthy vital organs after systemic injection. RNA nanoparticles were proven to deliver therapeutics such as siRNA and anti-miRNA to block tumor growth in several animal models. Although the release of anti-miRNA from the RNA nanoparticles has achieved high efficiency of tumor regression in multiple animal models, the efficiency of endosomal escape for siRNA delivery needs further improvement. This review focuses on the advances and perspectives of this promising RNA nanotechnology platform for cancer targeting and therapy.
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Affiliation(s)
- Congcong Xu
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
| | - Farzin Haque
- Nanobio Delivery Pharmaceutical Co. Ltd., Columbus, OH, USA
| | - Daniel L Jasinski
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
| | - Daniel W Binzel
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
| | - Dan Shu
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA
| | - Peixuan Guo
- Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, The Ohio State University, Columbus, OH, USA; College of Medicine, Dorothy M. Davis Heart and Lung Research Institute, The Ohio State University, Columbus, OH, USA; Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA; Center for RNA Nanobiotechnology and Nanomedicine, The Ohio State University, Columbus, OH, USA.
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Targeted microbicides for preventing sexual HIV transmission. J Control Release 2017; 266:119-128. [PMID: 28951320 DOI: 10.1016/j.jconrel.2017.09.030] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Revised: 09/21/2017] [Accepted: 09/22/2017] [Indexed: 12/16/2022]
Abstract
Sexual transmission remains one of the most significant hurdles in the fight against HIV infection. The use of vaginal or rectal microbicides has been proposed for topical pre-exposure prophylaxis but available results from clinical trials of candidate products have been, at best, less than optimal. While waiting for the first product to get regulatory approval, novel approaches are being explored in order to enhance efficacy, as well as to assure safety. Strategies involving specific delivery of antiviral agents to key players involved in the early steps of sexual transmission have the potential to help achieving such purposes. Engineering systems that allow targeting cells, tissues or other biological structures of interest may provide a way to modulate local pharmacokinetics of promising microbicide molecules and, thus, maximize protection. This concise review discusses the identification and use of potential targets for such purpose, while detailing on several examples of targeted systems engineered as potential microbicide candidates. Furthermore, remaining challenges and hints for future work in the field of targeted microbicides are addressed.
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Nambi Krishnan J, Park SH, Kim SK. Aptamer-Based Single-Step Assay by the Fluorescence Enhancement on Electroless Plated Nano Au Substrate. SENSORS (BASEL, SWITZERLAND) 2017; 17:E2044. [PMID: 28880198 PMCID: PMC5620733 DOI: 10.3390/s17092044] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 08/25/2017] [Accepted: 09/02/2017] [Indexed: 01/13/2023]
Abstract
A new single-step aptamer-based surface-enhanced fluorescent optical sensor is built, by combining an aptamer-target interaction for target recognition and a fluorophore interaction for signal enhancement. The developed aptasensor is simple, sensitive, specific and stable for the detection of thrombin. A new nanometallic Au structure in the range of 100 nm was constructed through effective electroless plating method on a Cu thin film. Cu⁺ ions act as sacrificial seeds for the reduction of Au2+/3+ ions to form Au nanolawns. In order to utilize the structure for a fluorescence-based sensor, aptamer conjugated with Cy3 was immobilized on the nanogold substrate through electrostatic attraction. The Au substrate was coated with chitosan (molecular weight 1000 Da). Thrombin binding aptamer (TBA) was applied as a model system demonstrating the aptamer-based fluorescence assay on nanogold substrates. Thrice-enhanced fluorescence emission was achieved with Cy3-conjugated TBA stably immobilized on the chitosan-coated Au substrate. The intensity change was proportional to the concentration of thrombin from 10 μM to 10 pM, whereas the intensity change was ignorable for other proteins such as human serum albumin (HSA). Aptamer-based assay benefited from simple immobilization of receptors and Au nanostructure contributed in building an effective surface enhancing/positively charged substrate was proved. Such an aptasensor holding high utilities for point-of-care devices by incorporating simplicity, sensitivity and selectivity in detection, low-cost for test, small sample volumes has been developed.
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Affiliation(s)
- Jegatha Nambi Krishnan
- Center for BioMicrosystems, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Sungbuk-gu, Seoul 136-791, Korea.
- School of Micro Nano System Engineering, Korea University of Science and Technology, Daejeon 305-333, Korea.
- School of Chemical Engineering, Birla Institute of Technology and Science, Pilani, K. K. Birla Goa Campus, Zuari Nagar, Goa 403-726, India.
| | - Sang-Hwi Park
- Center for BioMicrosystems, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Sungbuk-gu, Seoul 136-791, Korea.
- School of Micro Nano System Engineering, Korea University of Science and Technology, Daejeon 305-333, Korea.
| | - Sang Kyung Kim
- Center for BioMicrosystems, Korea Institute of Science and Technology, 39-1 Hawolgok-dong, Sungbuk-gu, Seoul 136-791, Korea.
- School of Micro Nano System Engineering, Korea University of Science and Technology, Daejeon 305-333, Korea.
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Aptamer-siRNA Chimeras: Discovery, Progress, and Future Prospects. Biomedicines 2017; 5:biomedicines5030045. [PMID: 28792479 PMCID: PMC5618303 DOI: 10.3390/biomedicines5030045] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 02/07/2023] Open
Abstract
Synthetic nucleic acid ligands (aptamers) have emerged as effective delivery tools for many therapeutic oligonucleotide-based drugs, including small interfering RNAs (siRNAs). In this review, we summarize recent progress in the aptamer selection technology that has made possible the identification of cell-specific, cell-internalizing aptamers for the cell-targeted delivery of therapeutic oligonucleotides. In addition, we review the original, proof-of-concept aptamer-siRNA delivery studies and discuss recent advances in aptamer-siRNA conjugate designs for applications ranging from cancer therapy to the development of targeted antivirals. Challenges and prospects of aptamer-targeted siRNA drugs for clinical development are further highlighted.
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19
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Jasinski D, Haque F, Binzel DW, Guo P. Advancement of the Emerging Field of RNA Nanotechnology. ACS NANO 2017; 11:1142-1164. [PMID: 28045501 PMCID: PMC5333189 DOI: 10.1021/acsnano.6b05737] [Citation(s) in RCA: 222] [Impact Index Per Article: 31.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 01/03/2017] [Indexed: 05/14/2023]
Abstract
The field of RNA nanotechnology has advanced rapidly during the past decade. A variety of programmable RNA nanoparticles with defined shape, size, and stoichiometry have been developed for diverse applications in nanobiotechnology. The rising popularity of RNA nanoparticles is due to a number of factors: (1) removing the concern of RNA degradation in vitro and in vivo by introducing chemical modification into nucleotides without significant alteration of the RNA property in folding and self-assembly; (2) confirming the concept that RNA displays very high thermodynamic stability and is suitable for in vivo trafficking and other applications; (3) obtaining the knowledge to tune the immunogenic properties of synthetic RNA constructs for in vivo applications; (4) increased understanding of the 4D structure and intermolecular interaction of RNA molecules; (5) developing methods to control shape, size, and stoichiometry of RNA nanoparticles; (6) increasing knowledge of regulation and processing functions of RNA in cells; (7) decreasing cost of RNA production by biological and chemical synthesis; and (8) proving the concept that RNA is a safe and specific therapeutic modality for cancer and other diseases with little or no accumulation in vital organs. Other applications of RNA nanotechnology, such as adapting them to construct 2D, 3D, and 4D structures for use in tissue engineering, biosensing, resistive biomemory, and potential computer logic gate modules, have stimulated the interest of the scientific community. This review aims to outline the current state of the art of RNA nanoparticles as programmable smart complexes and offers perspectives on the promising avenues of research in this fast-growing field.
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Affiliation(s)
| | | | - Daniel W Binzel
- College of Pharmacy, Division
of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine,
Department of Physiology & Cell Biology; and Dorothy M. Davis
Heart and Lung Research Institute, The Ohio
State University, Columbus, Ohio 43210, United States
| | - Peixuan Guo
- College of Pharmacy, Division
of Pharmaceutics and Pharmaceutical Chemistry; College of Medicine,
Department of Physiology & Cell Biology; and Dorothy M. Davis
Heart and Lung Research Institute, The Ohio
State University, Columbus, Ohio 43210, United States
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20
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Aptamers for CD Antigens: From Cell Profiling to Activity Modulation. MOLECULAR THERAPY-NUCLEIC ACIDS 2016; 6:29-44. [PMID: 28325295 PMCID: PMC5363458 DOI: 10.1016/j.omtn.2016.12.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 12/02/2016] [Accepted: 12/02/2016] [Indexed: 01/01/2023]
Abstract
Nucleic acid-based aptamers are considered to be a promising alternative to antibodies because of their strong and specific binding to diverse targets, fast and inexpensive chemical synthesis, and easy labeling with a fluorescent dye or therapeutic agent. Cluster of differentiation (CD) proteins are among the most popular antigens for aptamers on the cell surface. These anti-CD aptamers could be used in cell biology and biomedicine, from simple cell phenotyping by flow cytometry or fluorescent microscopy to diagnosis and treatment of HIV/AIDS to cancer and immune therapies. The unique feature of aptamers is that they can act simultaneously as an agonist and antagonist of CD receptors depending on a degree of aptamer oligomerization. Aptamers can also deliver small interfering RNA to silence vital genes in CD-positive cells. In this review, we summarize nucleic acid sequences of anti-CD aptamers and their use, which have been validated in multiple studies.
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Alfavian H, Mousavi Gargari SL, Rasoulinejad S, Medhat A. Development of a DNA aptamer that binds specifically to group A Streptococcus serotype M3. Can J Microbiol 2016; 63:160-168. [PMID: 28121169 DOI: 10.1139/cjm-2016-0495] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Group A streptococcus (GAS) is an important Gram-positive pathogen that causes various human diseases ranging from peripheral lesions to invasive infections. The M protein is one of the main virulence factors present on the cell surface and is associated with invasive GAS infections. Compared with other M types, serotype M3 has a predominant role in lethal infections and demonstrates epidemic behaviors, including streptococcal toxic shock syndrome, bacteremia, and necrotizing fasciitis. Traditional methods for M typing are time-consuming, tedious, contradictory, and generally restricted to reference laboratories. Therefore, development of a new M-typing technique is needed. Aptamers with the ability to detect their target with a high degree of accuracy and specificity can be ideal candidates for specific M-typing of Streptococcus pyogenes. In this study DNA aptamers with a high binding affinity towards S. pyogenes serotype M3 were selected through 12 iterative rounds of the Systematic Evolution of Ligands by EXponential (SELEX) enrichment procedure using live cells as a target. We monitored the progress of the SELEX procedure by flow cytometry analysis. Of several aptamer sequences analyzed, 12L18A showed the highest binding efficiency towards S. pyogenes type M3, with an apparent dissociation constant (Kd) of 7.47 ± 1.72 pmol/L being the lowest. Therefore the isolated aptamer can be used in any tool, such as a biosensor, for the detection of S. pyogenes and can be used in the development of a novel M-typing system.
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Affiliation(s)
- Hanif Alfavian
- a Department of Biology, Faculty of Basic Sciences, Shahed University, Tehran, Iran
| | | | - Samaneh Rasoulinejad
- a Department of Biology, Faculty of Basic Sciences, Shahed University, Tehran, Iran
| | - Arvin Medhat
- b GENEXIR Biopharma, a knowledge-based company at Pasteur Institute of Iran Health Technology Park, Tehran, Iran
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Abeydeera ND, Egli M, Cox N, Mercier K, Conde JN, Pallan PS, Mizurini DM, Sierant M, Hibti FE, Hassell T, Wang T, Liu FW, Liu HM, Martinez C, Sood AK, Lybrand TP, Frydman C, Monteiro RQ, Gomer RH, Nawrot B, Yang X. Evoking picomolar binding in RNA by a single phosphorodithioate linkage. Nucleic Acids Res 2016; 44:8052-64. [PMID: 27566147 PMCID: PMC5041495 DOI: 10.1093/nar/gkw725] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/02/2016] [Accepted: 08/06/2016] [Indexed: 11/12/2022] Open
Abstract
RNA aptamers are synthetic oligonucleotide-based affinity molecules that utilize unique three-dimensional structures for their affinity and specificity to a target such as a protein. They hold the promise of numerous advantages over biologically produced antibodies; however, the binding affinity and specificity of RNA aptamers are often insufficient for successful implementation in diagnostic assays or as therapeutic agents. Strong binding affinity is important to improve the downstream applications. We report here the use of the phosphorodithioate (PS2) substitution on a single nucleotide of RNA aptamers to dramatically improve target binding affinity by ∼1000-fold (from nanomolar to picomolar). An X-ray co-crystal structure of the α-thrombin:PS2-aptamer complex reveals a localized induced-fit rearrangement of the PS2-containing nucleotide which leads to enhanced target interaction. High-level quantum mechanical calculations for model systems that mimic the PS2 moiety and phenylalanine demonstrate that an edge-on interaction between sulfur and the aromatic ring is quite favorable, and also confirm that the sulfur analogs are much more polarizable than the corresponding phosphates. This favorable interaction involving the sulfur atom is likely even more significant in the full aptamer-protein complexes than in the model systems.
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Affiliation(s)
| | - Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Nehemiah Cox
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Karen Mercier
- Biointeractions Division, Horiba Scientific, Avenue de la Vauve - Passage JobinYvon CS 45002 Palaiseau, France
| | - Jonas Nascimento Conde
- Instituto de Biofísica Carlos Chagas Filho, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil
| | - Pradeep S Pallan
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA
| | - Daniella M Mizurini
- Instituto de Bioquimica Médica Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil
| | - Malgorzata Sierant
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Lodz, Sienkiewicza 112, Poland
| | - Fatima-Ezzahra Hibti
- Biointeractions Division, Horiba Scientific, Avenue de la Vauve - Passage JobinYvon CS 45002 Palaiseau, France
| | - Tom Hassell
- MilliporeSigma, 9186 Six Pines, The Woodlands, TX 77380, USA
| | - Tianzhi Wang
- The Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Feng-Wu Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Science Avenue 100, Zhengzhou 450001, Henan, China
| | - Hong-Min Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Science Avenue 100, Zhengzhou 450001, Henan, China
| | - Carlos Martinez
- MilliporeSigma, 9186 Six Pines, The Woodlands, TX 77380, USA
| | - Anil K Sood
- Departments of Gynecologic Oncology and Cancer Biology, and Center for RNAi and Non-coding RNA, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Terry P Lybrand
- Departments of Chemistry and Pharmacology, and Center for Structural Biology, Vanderbilt University, Nashville, TN 37232, USA
| | - Chiraz Frydman
- Biointeractions Division, Horiba Scientific, Avenue de la Vauve - Passage JobinYvon CS 45002 Palaiseau, France
| | - Robson Q Monteiro
- Instituto de Bioquimica Médica Leopoldo de Meis, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941, Brazil
| | - Richard H Gomer
- Department of Biology, Texas A&M University, College Station, TX 77843, USA
| | - Barbara Nawrot
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, 90-363 Lodz, Sienkiewicza 112, Poland
| | - Xianbin Yang
- AM Biotechnologies, LLC, 12521 Gulf Freeway, Houston, TX 77034, USA
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Abstract
This chapter focuses on the selection of RNA aptamers, which bind to specific cell surface components and thus can be internalized receptor mediated. Such aptamers discriminate between different tissues, e.g., detect malignant cells, and target them or induce apoptosis through drug internalization. However, before starting the selection process the choice of an ideal target can be challenging. To give an example for the selection of cell specific aptamers, we here used the interleukin-6 receptor (IL-6R) as a target, which is presented on hepatocytes, neutrophils, monocytes, and macrophages.
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Affiliation(s)
- Katharina Berg
- Chemistry Department, Institute for Biochemistry and Molecular Biology, MIN-Faculty, Hamburg University, Martin-Luther-King-Platz 6, 22391, Hamburg, Germany
| | - Eileen Magbanua
- Chemistry Department, Institute for Biochemistry and Molecular Biology, MIN-Faculty, Hamburg University, Martin-Luther-King-Platz 6, 22391, Hamburg, Germany
| | - Ulrich Hahn
- Chemistry Department, Institute for Biochemistry and Molecular Biology, MIN-Faculty, Hamburg University, Martin-Luther-King-Platz 6, 22391, Hamburg, Germany.
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Wheeler LA, Trifonova RT, Vrbanac V, Barteneva NS, Liu X, Bollman B, Onofrey L, Mulik S, Ranjbar S, Luster AD, Tager AM, Lieberman J. TREX1 Knockdown Induces an Interferon Response to HIV that Delays Viral Infection in Humanized Mice. Cell Rep 2016; 15:1715-27. [PMID: 27184854 DOI: 10.1016/j.celrep.2016.04.048] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 03/21/2016] [Accepted: 04/09/2016] [Indexed: 10/21/2022] Open
Abstract
Despite their antiviral effect, the in vivo effect of interferons on HIV transmission is difficult to predict, because interferons also activate and recruit HIV-susceptible cells to sites of infection. HIV does not normally induce type I interferons in infected cells, but does if TREX1 is knocked down. Here, we investigated the effect of topical TREX1 knockdown and local interferon production on HIV transmission in human cervicovaginal explants and humanized mice. In explants in which TREX1 was knocked down, HIV induced interferons, which blocked infection. In humanized mice, even though TREX1 knockdown increased infiltrating immune cells, it delayed viral replication for 3-4 weeks. Similarly intravaginal application of type I interferons the day before HIV infection induced interferon responsive genes, reduced inflammation, and decreased viral replication. However, intravenous interferon enhanced inflammation and infection. Thus, in models of human sexual transmission, a localized interferon response inhibits HIV transmission but systemic interferons do not.
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Affiliation(s)
- Lee Adam Wheeler
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA; MD-PhD Program, Harvard Medical School, Boston, MA 02115, USA
| | - Radiana T Trifonova
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Vladimir Vrbanac
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02139, USA
| | - Natasha S Barteneva
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Xing Liu
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Brooke Bollman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Lauren Onofrey
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Sachin Mulik
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Shahin Ranjbar
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew D Luster
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02139, USA
| | - Andrew M Tager
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02139, USA
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA.
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25
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Karaballi RA, Nel A, Krishnan S, Blackburn J, Brosseau CL. Development of an electrochemical surface-enhanced Raman spectroscopy (EC-SERS) aptasensor for direct detection of DNA hybridization. Phys Chem Chem Phys 2016; 17:21356-63. [PMID: 25780805 DOI: 10.1039/c4cp05077k] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Rapid detection of disease biomarkers at the patient point-of-care is essential to timely and effective treatment. The research described herein focuses on the development of an electrochemical surface-enhanced Raman spectroscopy (EC-SERS) DNA aptasensor capable of direct detection of tuberculosis (TB) DNA. Specifically, a plausible DNA biomarker present in TB patient urine was chosen as the model target for detection. Cost-effective screen printed electrodes (SPEs) modified with silver nanoparticles (AgNP) were used as the aptasensor platform, onto which the aptamer specific for the target DNA was immobilized. Direct detection of the target DNA was demonstrated through the appearance of SERS peaks characteristic for adenine, present only in the target strand. Modulation of the applied potential allowed for a sizeable increase in the observed SERS response and the use of thiol back-filling prevented non-specific adsorption of non-target DNA. To our knowledge, this work represents the first EC-SERS study of an aptasensor for the direct, label-free detection of DNA hybridization. Such a technology paves the way for rapid detection of disease biomarkers at the patient point-of-care.
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Affiliation(s)
- R A Karaballi
- Department of Chemistry, Saint Mary's University, Halifax, Nova Scotia B3H 3C3, Canada.
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Abstract
Advances and applications of synthetic genetic polymers (xeno-nucleic acids) are reviewed in this article. The types of synthetic genetic polymers are summarized. The basic properties of them are elaborated and their technical applications are presented. Challenges and prospects of synthetic genetic polymers are discussed.
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Affiliation(s)
- Qian Ma
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Danence Lee
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Yong Quan Tan
- Department of Biochemistry
- National University of Singapore
- Singapore 117597
| | - Garrett Wong
- Department of Biochemistry
- National University of Singapore
- Singapore 117597
| | - Zhiqiang Gao
- Department of Chemistry
- National University of Singapore
- Singapore 117543
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Davydova A, Vorobjeva M, Pyshnyi D, Altman S, Vlassov V, Venyaminova A. Aptamers against pathogenic microorganisms. Crit Rev Microbiol 2015; 42:847-65. [PMID: 26258445 PMCID: PMC5022137 DOI: 10.3109/1040841x.2015.1070115] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
An important current issue of modern molecular medicine and biotechnology is the search for new approaches to early diagnostic assays and adequate therapy of infectious diseases. One of the promising solutions to this problem might be a development of nucleic acid aptamers capable of interacting specifically with bacteria, protozoa, and viruses. Such aptamers can be used for the specific recognition of infectious agents as well as for blocking of their functions. The present review summarizes various modern SELEX techniques used in this field, and of several currently identified aptamers against viral particles and unicellular organisms, and their applications. The prospects of applying nucleic acid aptamers for the development of novel detection systems and antibacterial and antiviral drugs are discussed.
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Affiliation(s)
- Anna Davydova
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Maria Vorobjeva
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Dmitrii Pyshnyi
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Sidney Altman
- b Department of Molecular, Cellular and Developmental Biology , Yale University , New Haven , CT , USA
| | - Valentin Vlassov
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Alya Venyaminova
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
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28
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Shcherbinin DS, Gnedenko OV, Khmeleva SA, Usanov SA, Gilep AA, Yantsevich AV, Shkel TV, Yushkevich IV, Radko SP, Ivanov AS, Veselovsky AV, Archakov AI. Computer-aided design of aptamers for cytochrome p450. J Struct Biol 2015; 191:112-9. [PMID: 26166326 DOI: 10.1016/j.jsb.2015.07.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 06/25/2015] [Accepted: 07/09/2015] [Indexed: 10/23/2022]
Abstract
Aptamers are short single-stranded DNA or RNA oligonucleotides that can bind to their targets with high affinity and specificity. Usually, they are experimentally selected using the SELEX method. Here, we describe an approach toward the in silico selection of aptamers for proteins. This approach involves three steps: finding a potential binding site, designing the recognition and structural parts of the aptamers and evaluating the experimental affinity. Using this approach, a set of 15-mer aptamers for cytochrome P450 51A1 was designed using docking and molecular dynamics simulation. An experimental evaluation of the synthesized aptamers using SPR biosensor showed that these aptamers interact with cytochrome P450 51A1 with Kd values in the range of 10(-6)-10(-7) M.
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Affiliation(s)
- Dmitrii S Shcherbinin
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia.
| | - Oksana V Gnedenko
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | - Svetlana A Khmeleva
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | - Sergey A Usanov
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Andrei A Gilep
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Aliaksei V Yantsevich
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Tatsiana V Shkel
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Ivan V Yushkevich
- Institute of Bioorganic Chemistry of the National Academy of Sciences of Belarus, Kuprevich str., 5/2, Minsk 220141, Belarus
| | - Sergey P Radko
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | - Alexis S Ivanov
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
| | | | - Alexander I Archakov
- Institute of Biomedical Chemistry RAMS, Pogodinskaya str., 10, Moscow 119121, Russia
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29
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Manipulating the in vivo immune response by targeted gene knockdown. Curr Opin Immunol 2015; 35:63-72. [PMID: 26149459 DOI: 10.1016/j.coi.2015.06.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 06/09/2015] [Accepted: 06/19/2015] [Indexed: 02/06/2023]
Abstract
Aptamers, nucleic acids selected for high affinity binding to proteins, can be used to activate or antagonize immune mediators or receptors in a location and cell-type specific manner and to enhance antigen presentation. They can also be linked to other molecules (other aptamers, siRNAs or miRNAs, proteins, toxins) to produce multifunctional compounds for targeted immune modulation in vivo. Aptamer-siRNA chimeras (AsiCs) that induce efficient cell-specific knockdown in immune cells in vitro and in vivo can be used as an immunological research tool or potentially as an immunomodulating therapeutic.
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Wu Y, Zhan S, Wang L, Zhou P. Selection of a DNA aptamer for cadmium detection based on cationic polymer mediated aggregation of gold nanoparticles. Analyst 2015; 139:1550-61. [PMID: 24496116 DOI: 10.1039/c3an02117c] [Citation(s) in RCA: 111] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The demand for selection of aptamers against various small chemical molecules has substantially increased in recent years. To incubate and separate target-specific aptamers, the conventional SELEX procedures generally need to immobilize target molecules on a matrix, which may be impotent to screen aptamers toward small molecules without enough sites for immobilization. Herein we chose Cd(II) as a model of a small molecule with less sites, and proposed a novel SELEX strategy of immobilizing ssDNA libraries rather than target molecules on a matrix, for selection of aptamers with high affinity to Cd(II). After eleven rounds of positive and negative selection, twelve T and G-rich of nonrepeating ssDNA sequences were identified, of which the Cd-4 aptamer displayed the highest binding affinity to Cd(II). The secondary structures of these sequences revealed that a stem-loop structure folded by the domain of their 30-random sequence is critical for aptamers to bind targets. Then the interaction between the selected Cd-4 aptamer and Cd(II) was confirmed by CD analysis, and the binding specificity toward other competitive metal ions was also investigated. The dissociation constant (Kd) of Cd-4 aptamer was determined as 34.5 nM for Cd(II). Moreover, the Cd-4 aptamer was considered a recognition element for the colorimetric detection of Cd(II) based on the aggregation of AuNPs by cationic polymer. Through spectroscopic quantitative analysis, Cd(II) in aqueous solution can be detected as low as 4.6 nM. The selected Cd-4 aptamer will offer a new substitute for the detection of Cd(II) or other applications like recovery of cadmium from polluted samples.
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Affiliation(s)
- Yuangen Wu
- Key Laboratory of Urban Agriculture (South), Ministry of Agriculture, School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, P. R. China.
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31
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He X, Chen J, Yie SM, Ye SR, Dong DD, Li K. Using a sequence of estrogen response elements as a DNA aptamer for estrogen receptors in vitro. Nucleic Acid Ther 2015; 25:152-61. [PMID: 25734367 DOI: 10.1089/nat.2014.0521] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Estrogen receptors (ERs) are overexpressed in approximately 70% of breast cancer cases, and they play an important role in tumorigenesis. ERs are strong predictive factors for measuring responses to hormonal therapies. Aptamers are short and single stranded oligonucleotides that are able to recognize target molecules with high affinity. In the present study, we selected and synthesized an oligonucleotide, which has a similar sequence to estrogen response element in the Xenopus Vitellogenin A2 gene. The synthesized oligonucleotide was evaluated by using immunostaining of paraffin-embedded breast cancer tissues and treating MCF-7 human mammary carcinoma cell line in vitro. We found that the synthesized oligonucleotide had a high binding affinity to ER similar to estradiol. Using a specific anti-ER antibody as a standard control, we showed that the synthesized oligonucleotide specifically recognized and immunostained tumor cells of breast cancer without cross-reaction with normal tissues. The overall agreement of ER detection between the anti-ER antibody and the ER aptamer was 97.1% (kappa value=0.943; 95% CI=0.879-1.006; p<0.002). Similar to tamoxifen or fulvestrant, the oligonucleotide also had an inhibitory effect on cell proliferation of MCF-7 cell line in a dose- and time-dependent fashion but had no cytotoxic effect on human normal mammary epithelial cells. Therefore, the synthesized oligonucleotide may be used as an aptamer for immunostaining of paraffin-embedded tissue sections for breast cancer diagnosis, as well as a potential ER antagonist in the treatment of breast cancer.
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Affiliation(s)
- Xu He
- 1Core Laboratory, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Jie Chen
- 1Core Laboratory, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Shang-mian Yie
- 1Core Laboratory, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China.,2Research and Development Center, Sichuan HeLi Bio-pharmaceutical Co. Ltd., Sichuan HeBang Group, Chengdu, Sichuan, China
| | - Shang-rong Ye
- 2Research and Development Center, Sichuan HeLi Bio-pharmaceutical Co. Ltd., Sichuan HeBang Group, Chengdu, Sichuan, China
| | - Dan-Dan Dong
- 3Department of Pathology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
| | - Ke Li
- 3Department of Pathology, Sichuan Academy of Medical Sciences, Sichuan Provincial People's Hospital, Chengdu, Sichuan, China
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Hou Z, Meyer S, Propson NE, Nie J, Jiang P, Stewart R, Thomson JA. Characterization and target identification of a DNA aptamer that labels pluripotent stem cells. Cell Res 2015; 25:390-3. [PMID: 25591927 PMCID: PMC4349250 DOI: 10.1038/cr.2015.7] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
| | - Susanne Meyer
- Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
| | - Nicholas E Propson
- 1] Morgridge Institute for Research, Madison, WI, USA [2] Current address: Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX, USA
| | - Jeff Nie
- 1] Morgridge Institute for Research, Madison, WI, USA [2] Current address: Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN, USA
| | - Peng Jiang
- Morgridge Institute for Research, Madison, WI, USA
| | - Ron Stewart
- Morgridge Institute for Research, Madison, WI, USA
| | - James A Thomson
- 1] Morgridge Institute for Research, Madison, WI, USA [2] Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, USA [3] Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA, USA
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Ehsani M, Emamzadeh R, Zarkesh-Esfahani SH, Nazari M. CD4 D3-binding probe: a novel fluorescence tool for detection and enumeration of CD4+ cells. RSC Adv 2015. [DOI: 10.1039/c5ra05333a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A new and advanced CD4-binding reporter has been designed, produced and functionally assayed for the detection of T-helper cells.
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Affiliation(s)
- M. Ehsani
- Department of Biology
- Faculty of Science
- University of Isfahan
- Isfahan
- Iran
| | - R. Emamzadeh
- Department of Biology
- Faculty of Science
- University of Isfahan
- Isfahan
- Iran
| | | | - M. Nazari
- Nanobiotechnology Research Center
- Avicenna Research Institute, ACECR
- Tehran
- Iran
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34
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Taghdisi SM, Danesh NM, Lavaee P, Sarreshtehdar Emrani A, Ramezani M, Abnous K. Aptamer Biosensor for Selective and Rapid Determination of Insulin. ANAL LETT 2014. [DOI: 10.1080/00032719.2014.956216] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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35
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Song P, Chou YK, Zhang X, Meza-Romero R, Yomogida K, Benedek G, Chu CQ. CD4 aptamer-RORγt shRNA chimera inhibits IL-17 synthesis by human CD4(+) T cells. Biochem Biophys Res Commun 2014; 452:1040-5. [PMID: 25241192 DOI: 10.1016/j.bbrc.2014.09.037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 09/10/2014] [Indexed: 01/23/2023]
Abstract
Cell type specific delivery of RNAi to T cells has remained to be a challenge. Here we describe an aptamer mediated delivery of shRNA to CD4(+) T cells targeting RORγt to suppress Th17 cells. A cDNA encoding CD4 aptamer and RORγt shRNA was constructed and the chimeric CD4 aptamer-RORγt shRNA (CD4-AshR-RORγt) was generated using in vitro T7 RNA transcription. 2'-F-dCTP and 2'-F-dUTP were incorporated into CD4-AshR-RORγt for RNase resistance. CD4-AshR-RORγt was specifically uptaken by CD4(+) Karpas 299 cells and primary human CD4(+) T cells. The RORγt shRNA moiety of CD4-AshR-RORγt chimera was cleaved and released by Dicer. Furthermore, CD4-AshR-RORγt suppressed RORγt gene expression in Karpas 299 cells and CD4(+) T cells and consequently inhibited Th17 cell differentiation and IL-17 production. These results demonstrate that aptamer-facilitated cell specific delivery of shRNA represents a novel approach for efficient RNAi delivery and is potentially to be developed for therapeutics targeting specific T cells subtypes.
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Affiliation(s)
- Pingfang Song
- Division of Arthritis and Rheumatic Diseases, Oregon Health & Science University and Portland VA Medical Center, Portland, OR 97239, United States
| | - Yuan K Chou
- Division of Arthritis and Rheumatic Diseases, Oregon Health & Science University and Portland VA Medical Center, Portland, OR 97239, United States
| | - Xiaowei Zhang
- Division of Arthritis and Rheumatic Diseases, Oregon Health & Science University and Portland VA Medical Center, Portland, OR 97239, United States
| | - Roberto Meza-Romero
- Neuroimmunology Research, Portland VA Medical Center, Portland, OR 97239, United States
| | - Kentaro Yomogida
- Division of Arthritis and Rheumatic Diseases, Oregon Health & Science University and Portland VA Medical Center, Portland, OR 97239, United States; Department of Pediatrics, Oakland University William Beaumont Hospital, Royal Oak, MI 48073, United States
| | - Gil Benedek
- Neuroimmunology Research, Portland VA Medical Center, Portland, OR 97239, United States
| | - Cong-Qiu Chu
- Division of Arthritis and Rheumatic Diseases, Oregon Health & Science University and Portland VA Medical Center, Portland, OR 97239, United States.
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Zeng Z, Parekh P, Li Z, Shi ZZ, Tung CH, Zu Y. Specific and sensitive tumor imaging using biostable oligonucleotide aptamer probes. Am J Cancer Res 2014; 4:945-52. [PMID: 25057318 PMCID: PMC4107294 DOI: 10.7150/thno.9246] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 05/29/2014] [Indexed: 12/20/2022] Open
Abstract
Although several imaging modalities are widely used for tumor imaging, none are tumor type-specific. Different types of cancer exhibit differential therapeutic responses, thus necessitating development of an imaging modality able to detect various tumor types with high specificity. To illustrate this point, CD30-specific oligonucleotide aptamer in vivo imaging probes were conjugated to the near-infrared IRD800CW reporter. Mice bearing xenografted CD30-positive or control CD30-negative lymphoma tumors on contralateral sides of the same mouse were developed. Following a systemic administration of aptamer probes, whole body imaging of tumor-bearing mice was performed. Imaging signal from tumor sites was analyzed and imaging specificity confirmed by tissue immunostaining. The in vivo biodistribution of aptamer probes was also evaluated. Whole body scans revealed that the RNA-based aptamer probes selectively highlighted CD30-expressing lymphoma tumors immediately after systemic administration, but did not react with control tumors in the same mouse. The resultant imaging signal lasted up to 1 hr and the aptamer probes were rapidly eliminated from the body through urinary and lower intestinal tracts. For more sensitive imaging, biostable CD30-specific ssDNA-based aptamer probes were also generated. Systemic administration of these probes also selectively highlighted the CD30-positive lymphoma tumors, with imaging signal detected 4-5 folds higher than that derived from control tumors in the same animal, and lasted for up to 24hr. This study demonstrates that oligonucleotide aptamer probes can provide tumor type-specific imaging with high sensitivity and a long-lasting signal, indicating their potential for clinical applications.
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37
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Taghdisi SM, Emrani SS, Tabrizian K, Ramezani M, Abnous K, Emrani AS. Ultrasensitive detection of lead (II) based on fluorescent aptamer-functionalized carbon nanotubes. ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2014; 37:1236-1242. [PMID: 24835552 DOI: 10.1016/j.etap.2014.04.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2014] [Revised: 04/13/2014] [Accepted: 04/18/2014] [Indexed: 06/03/2023]
Abstract
Lead contamination is a serious environmental problem with toxic effects in human. Here, we developed a simple and sensitive sensing method employing ATTO 647N/aptamer-SWNT ensemble for detection of Pb(2+). This method is based on the super quenching capability of single-walled carbon nanotubes (SWNTs), high affinity of the aptamer toward Pb(2+) and different propensities of ATTO 647N-aptamer and ATTO 647N-aptamer/Pb(2+) complex for adsorption on SWNTs. In the absence of Pb(2+), the fluorescence of ATTO 647N-aptamer is efficiently quenched by SWNTs. Upon addition of Pb(2+), the aptamer binds to its target, leading to the formation of a G-quadruplex/Pb(2+) complex and does not interact with SWNTs and ATTO 647N-aptamer starts fluorescing. This sensor exhibited a high selectivity toward Pb(2+) and a limit of detection (LOD) as low as 0.42 nM was obtained. Also this sensor could be applied for detection of Pb(2+) ions in tap water and biological sample like serum with high sensitivity.
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Affiliation(s)
- Seyed Mohammad Taghdisi
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Kaveh Tabrizian
- Department of Toxicology, School of Pharmacy, Zabol University of Medical Sciences, Zabol, Iran
| | - Mohammad Ramezani
- Nanotechnology Research Center, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khalil Abnous
- Pharmaceutical Research Center, School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran.
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Zhao N, Pei SN, Parekh P, Salazar E, Zu Y. Blocking interaction of viral gp120 and CD4-expressing T cells by single-stranded DNA aptamers. Int J Biochem Cell Biol 2014; 51:10-8. [PMID: 24661998 DOI: 10.1016/j.biocel.2014.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Revised: 02/26/2014] [Accepted: 03/13/2014] [Indexed: 01/29/2023]
Abstract
To investigate the potential clinical application of aptamers to prevention of HIV infection, single-stranded DNA (ssDNA) aptamers specific for CD4 were developed using the systematic evolution of ligands by exponential enrichment approach and next generation sequencing. In contrast to RNA-based aptamers, the developed ssDNA aptamers were stable in human serum up to 12h. Cell binding assays revealed that the aptamers specifically targeted CD4-expressing cells with high binding affinity (Kd=1.59nM), a concentration within the range required for therapeutic application. Importantly, the aptamers selectively bound CD4 on human cells and disrupted the interaction of viral gp120 to CD4 receptors, which is a prerequisite step of HIV-1 infection. Functional studies showed that the aptamer polymers significantly blocked binding of viral gp120 to CD4-expressing cells by up to 70% inhibition. These findings provide a new approach to prevent HIV-1 transmission using oligonucleotide aptamers.
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Affiliation(s)
- Nianxi Zhao
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, and Cancer Pathology Laboratory, Houston Methodist Research Institute, 6565 Fannin Street, Houston, TX 77030, USA
| | - Sung-nan Pei
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, and Cancer Pathology Laboratory, Houston Methodist Research Institute, 6565 Fannin Street, Houston, TX 77030, USA
| | - Parag Parekh
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, and Cancer Pathology Laboratory, Houston Methodist Research Institute, 6565 Fannin Street, Houston, TX 77030, USA
| | - Eric Salazar
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, and Cancer Pathology Laboratory, Houston Methodist Research Institute, 6565 Fannin Street, Houston, TX 77030, USA
| | - Youli Zu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, and Cancer Pathology Laboratory, Houston Methodist Research Institute, 6565 Fannin Street, Houston, TX 77030, USA.
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Current progress on aptamer-targeted oligonucleotide therapeutics. Ther Deliv 2014; 4:1527-46. [PMID: 24304250 DOI: 10.4155/tde.13.118] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Exploiting the power of the RNAi pathway through the use of therapeutic siRNA drugs has remarkable potential for treating a vast array of human disease conditions. However, difficulties in delivery of these and similar nucleic acid-based pharmacological agents to appropriate organs or tissues, remains a major impediment to their broad clinical application. Synthetic nucleic acid ligands (aptamers) have emerged as effective delivery vehicles for therapeutic oligonucleotides, including siRNAs. In this review, we summarize recent attractive developments in creatively employing cell-internalizing aptamers to deliver therapeutic oligonucleotides (e.g., siRNAs, miRNAs, anti-miRs and antisense oligos) to target cells. We also discuss advancements in aptamer-siRNA chimera technology, as well as, aptamer-functionalized nanoparticles for siRNA delivery. In addition, the challenges and future prospects of aptamer-targeted oligonucleotide drugs for clinical translation are further highlighted.
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Pei X, Zhang J, Liu J. Clinical applications of nucleic acid aptamers in cancer. Mol Clin Oncol 2014; 2:341-348. [PMID: 24772298 DOI: 10.3892/mco.2014.255] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Accepted: 01/28/2014] [Indexed: 01/28/2023] Open
Abstract
Nucleic acid aptamers are small single-stranded DNA or RNA oligonucleotide segments, which bind to their targets with high affinity and specificity via unique three-dimensional structures. Aptamers are generated by an iterative in vitro selection process, termed as systematic evolution of ligands by exponential enrichment. Owing to their specificity, non-immunogenicity, non-toxicity, easily modified chemical structure and wide range of targets, aptamers appear to be ideal candidates for various clinical applications (diagnosis or treatment), such as cell detection, target diagnosis, molecular imaging and drug delivery. Several aptamers have entered the clinical pipeline for applications in diseases such as macular degeneration, coronary artery bypass graft surgery and various types of cancer. The aim of this review was to summarize and highlight the clinical applications of aptamers in cancer diagnosis and treatment.
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Affiliation(s)
- Xiaoyu Pei
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai 200040
| | - Jun Zhang
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai 200040
| | - Jie Liu
- Department of Digestive Diseases, Huashan Hospital, Fudan University, Shanghai 200040; ; Institute of Biomedical Sciences and Department of Immunology of Shanghai Medical School, Fudan University, Shanghai 200032, P.R. China
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41
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Meyer M, Scheper T, Walter JG. Aptamers: versatile probes for flow cytometry. Appl Microbiol Biotechnol 2013; 97:7097-109. [PMID: 23838792 DOI: 10.1007/s00253-013-5070-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/17/2013] [Accepted: 06/17/2013] [Indexed: 12/21/2022]
Abstract
Aptamers are nucleic acid oligomers with distinct conformational shapes that allow them to bind targets with high affinity and specificity. Aptamers are selected from a random oligonucleotide library by their capability to bind a certain molecular target. A variety of targets ranging from small molecules like amino acids to complex targets and whole cells have been used to select aptamers. These characteristics and the ability to create specific aptamers against virtually any cell type in a process termed "systematic evolution by exponential enrichment" make them interesting tools for flow cytometry. In this contribution, we review the application of aptamers as probes for flow cytometry, especially cell-phenotyping and detection of various cancer cell lines and virus-infected cells and pathogens. We also discuss the potential of aptamers combined with nanoparticles such as quantum dots for the generation of new multivalent detector molecules with enhanced affinity and sensitivity. With regard to recent advancements in aptamer selection and the decreasing costs for oligonucleotide synthesis, aptamers may rise as potent competitors for antibodies as molecular probes in flow cytometry.
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Affiliation(s)
- Michael Meyer
- Institut für Technische Chemie, Leibniz Universität Hannover, Callinstr. 5, 30167 Hannover, Germany
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42
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Jalalian SH, Taghdisi SM, Shahidi Hamedani N, Kalat SAM, Lavaee P, Zandkarimi M, Ghows N, Jaafari MR, Naghibi S, Danesh NM, Ramezani M, Abnous K. Epirubicin loaded super paramagnetic iron oxide nanoparticle-aptamer bioconjugate for combined colon cancer therapy and imaging in vivo. Eur J Pharm Sci 2013; 50:191-7. [PMID: 23835028 DOI: 10.1016/j.ejps.2013.06.015] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 06/26/2013] [Accepted: 06/28/2013] [Indexed: 10/26/2022]
Abstract
Every year a large number of new cases of colorectal cancer are diagnosed in the world. Application of Epirubicin (Epi) in treatment of cancer has been limited due to its cardiotoxicity. Specific delivery of chemotherapy drugs is an important factor in reducing the side effects of drugs used in chemotherapy. Enhanced permeability, retention effect and magnetic resonance (MR) traceability of super paramagnetic iron oxide nanoparticles (SPION) make them a great candidate in cancer therapy and imaging. In this study, Epirubicin-5TR1 aptamer-SPION tertiary complex was evaluated for the imaging and treatment of murine colon carcinoma cells (C26 cells, target). For cytotoxic studies (MTT assay), C26 and CHO-K1 (Chinese hamster ovary cells, nontarget) cells were treated with either Epi or Epi-Apt-SPION tertiary complex. Internalization was evaluated by flow cytometry. Finally, Apt-SPION bioconjugate was used for imaging of cancer in vivo. Flow cytometric analysis showed that the tertiary complex was internalized effectively to C26 cells, but not to CHO-K1 cells. Cytotoxicity of Epi-Apt-SPION tertiary complex also confirmed internalization data. The complex was less cytotoxic in CHO-K1 cells when compared to Epi alone. No significant change in viability between Epi- and complex-treated C26 cells was observed. Magnetic resonance imaging (MRI) indicated a high level of accumulation of the nano-magnets within the tumor site. In conclusion Epi-Apt-SPION tertiary complex is introduced as an effective system for targeted delivery of Epi to C26 cells. Moreover this complex could efficiently detect tumors when analyzed by MRI and inhibit tumor growth in vivo.
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Affiliation(s)
- Seyed Hamid Jalalian
- Academic Center For Education, Culture and Research-ACECR-Mashhad Branch, Mashhad, Iran
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43
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Taghdisi SM, Danesh NM, Sarreshtehdar Emrani A, Tabrizian K, Zandkarimi M, Ramezani M, Abnous K. Targeted delivery of Epirubicin to cancer cells by PEGylated A10 aptamer. J Drug Target 2013; 21:739-44. [PMID: 23815443 DOI: 10.3109/1061186x.2013.812095] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Clinical administrations of anthracyclines are limited by cardiotoxicity and myelosuppression. Targeted delivery of anticancer agents is especially important in reducing their side effects. In this work, A10 (Apt), an aptamer for prostate-specific membrane anytigen (PSMA), was applied for targeted delivery of Epirubicin (Epi) to LNCaP cells (PSMA(+)). Flow cytometry analysis showed that PEG-Apt-Epi complex was internalized effectively to LNCaP cells (PSMA(+)), but not to PC3 cells (PSMA(-)). This fact was confirmed by less cytotoxicity of PEG-Apt-Epi complex in PC3 cells in comparison with Epi alone. No significant change in viability between Epi- and complex-treated LNCaP cells was observed. In conclusion, PEG-Apt-Epi complex is an efficient and simple system for specific delivery of drug to PSMA-expressing cell lines.
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Affiliation(s)
- Seyed Mohammad Taghdisi
- Department of Pharmaceutical Biotechnology, Zabol University of Medical Sciences, Zabol, Iran
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44
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Imaizumi Y, Kasahara Y, Fujita H, Kitadume S, Ozaki H, Endoh T, Kuwahara M, Sugimoto N. Efficacy of base-modification on target binding of small molecule DNA aptamers. J Am Chem Soc 2013; 135:9412-9. [PMID: 23734784 DOI: 10.1021/ja4012222] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Nucleic acid aptamers are receptors of single-stranded oligonucleotides that specifically bind to their targets. Significant interest is currently focused on development of small molecule aptamers owing to their applications in biosensing, diagnostics, and therapeutics involving low molecular weight biomarkers and drugs. Despite great potential for their diverse applications, relatively few aptamers that bind to small molecules have been reported, and methodologies to enhance and broaden their functions by expanding chemical repertories have barely been examined. Here we describe construction of a modified DNA library that includes (E)-5-(2-(N-(2-(N(6)-adeninyl)ethyl))carbamylvinyl)-uracil bases and discovery of high-affinity camptothecin-binding DNA aptamers using a systematic evolution of ligands by the exponential enrichment method. Our results are the first to demonstrate the superior efficacy of base modification on affinity enhancement and the usefulness of unnatural nucleic acid libraries for development of small molecule aptamers.
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Affiliation(s)
- Yuri Imaizumi
- Graduate School of Science and Technology, Gunma University, 1-5-1 Tenjin-cho, Kiryu, Gunma 376-8515, Japan
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Kimoto M, Hikida Y, Hirao I. Site-Specific Functional Labeling of Nucleic Acids by In Vitro Replication and Transcription using Unnatural Base Pair Systems. Isr J Chem 2013. [DOI: 10.1002/ijch.201300013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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46
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Gold nanoparticle-based colorimetric detection of staphylococcal enterotoxin B using ssDNA aptamers. Eur Food Res Technol 2013. [DOI: 10.1007/s00217-013-1995-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Durable knockdown and protection from HIV transmission in humanized mice treated with gel-formulated CD4 aptamer-siRNA chimeras. Mol Ther 2013; 21:1378-89. [PMID: 23629001 DOI: 10.1038/mt.2013.77] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2013] [Accepted: 03/17/2013] [Indexed: 02/06/2023] Open
Abstract
The continued spread of HIV underscores the need to interrupt transmission. One attractive strategy, in the absence of an effective vaccine, is a topical microbicide, but the need for application around the time of sexual intercourse leads to poor patient compliance. Intravaginal (IVAG) application of CD4 aptamer-siRNA chimeras (CD4-AsiCs) targeting the HIV coreceptor CCR5, gag, and vif protected humanized mice from sexual transmission. In non-dividing cells and tissue, RNAi-mediated gene knockdown lasts for several weeks, providing an opportunity for infrequent dosing not temporally linked to sexual intercourse, when compliance is challenging. Here, we investigate the durability of gene knockdown and viral inhibition, protection afforded by CCR5 or HIV gene knockdown on their own, and effectiveness of CD4-AsiCs formulated in a gel in polarized human cervicovaginal explants and in humanized mice. CD4-AsiC-mediated gene knockdown persisted for several weeks. Cell-specific gene knockdown and protection were comparable in a hydroxyethylcellulose gel formulation. CD4-AsiCs against CCR5 or gag/vif performed as well as a cocktail in humanized mice. Transmission was completely blocked by CCR5 CD4-AsiCs applied 2 days before challenge. Significant, but incomplete, protection also occurred when exposure was delayed for 4 or 6 days. CD4-AsiCs targeting gag/vif provided some protection when administered only after exposure. These data suggest that CD4-AsiCs are a promising approach for developing an HIV microbicide.
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Identification of aptamers as specific binders and modulators of cell-surface receptor activity. Methods Mol Biol 2013; 986:17-39. [PMID: 23436403 DOI: 10.1007/978-1-62703-311-4_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In recent years, the SELEX (Systematic Evolution of Ligands by EXponential enrichment) technology has established itself as a powerful tool in basic research with promising applications in diagnostics and therapeutics. Oligonucleotides with high-affinities to their targets, denominated as aptamers, are obtained from partially random oligonucleotide pools by reiterative in vitro selection cycles and screening for binding activity. The original technique allowing the identification of aptamers binding to soluble targets, has recently been extended in order to produce aptamers binding to complex targets including receptors and ion channels embedded in the plasma membrane as well as whole cell surfaces or parasite organisms. In addition to discussing the most recent developments with focus on possible diagnostic and therapeutic application, we provide a simple protocol which has been successfully used to select for RNA aptamers as allosteric modulators of nicotinic receptor activity.
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Pratico ED, Sullenger BA, Nair SK. Identification and characterization of an agonistic aptamer against the T cell costimulatory receptor, OX40. Nucleic Acid Ther 2012; 23:35-43. [PMID: 23113766 DOI: 10.1089/nat.2012.0388] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Induction of an effective immune response that can target and eliminate malignant cells or virus-infected cells requires the stimulation of antigen-specific effector T cells. A productive and long-lasting memory response requires 2 signals: a specific signal provided by antigen recognition through engagement of the T cell receptor and a secondary signal via engagement of costimulatory molecules (such as OX40) on these newly activated T cells. The OX40-OX40-ligand interaction is critical for the generation of productive effector and memory T cell functions. Thus agonistic antibodies that stimulate OX40 on activated T cells have been used as adjuvants to augment immune responses. We previously demonstrated that an aptamer modified to stimulate murine OX40 enhanced vaccine-mediated immune responses in a murine melanoma model. In this study, we describe the development of an agonistic aptamer that targets human OX40 (hOX40). This hOX40 aptamer was isolated using systematic evolution of ligands by exponential enrichment and binds the target purified protein with high affinity [dissociation constants (K(d))<10 nM]. Moreover, the hOX40 aptamer-streptavidin complex has an apparent binding affinity of ~50 nM for hOX40 on activated T cells as determined by flow cytometry and specifically binds activated human T cells. A multivalent version of the aptamer, but not a mutant version of the aptamer, was able to stimulate OX40 on T cells and enhance cell proliferation and interferon-gamma production. Future studies will assess the therapeutic potential of hOX40 aptamers for ex vivo stimulation of antigen specific T cells in conjunction with dendritic cell-based vaccines for adoptive cellular therapy.
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Affiliation(s)
- Elizabeth D Pratico
- Department of Surgery, Duke University Medical Center, Durham, North Carolina, USA.
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50
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Zhou Q, Liu Y, Shin DS, Silangcruz J, Tuleouva N, Revzin A. Aptamer-containing surfaces for selective capture of CD4 expressing cells. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:12544-9. [PMID: 22856558 PMCID: PMC3538135 DOI: 10.1021/la2050338] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Aptamers have recently emerged as an excellent alternative to antibodies because of their inherent stability and ease of modification. In this paper, we describe the development of an aptamer-based surface for capture of cells expressing CD4 antigen. The glass or silicon surfaces were modified with amine-terminated silanes and then modified with thiolated RNA aptamer against CD4. Modification of the surface was first characterized by ellipsometry to demonstrate assembly of biointerface components and to show specific capture of recombinant CD4 protein. Subsequently, surfaces were challenged with model lymphocytes (cell lines) that were either positive or negative for CD4 antigen. Our experiments show that aptamer-functionalized surfaces have similar capture efficiency to substrates containing anti-CD4 antibody. To mimick capture of specific T-cells from a complex cell mixture, aptamer-modified surfaces were exposed to binary mixtures containing Molt-3 cells (CD4+) spiked into Daudi B cells (CD4-). 94% purity of CD4 cells was observed on aptamer-containing surfaces from an initial fraction of 15% of CD4. Given the importance of CD4 cell enumeration in HIV/AIDS diagnosis and monitoring, aptamer-based devices may offer an opportunity for novel cell detection strategies and may yield more robust and less expensive blood analysis devices in the future.
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Affiliation(s)
- Qing Zhou
- Department of Biomedical Engineering, University of California, Davis
| | - Ying Liu
- Department of Biomedical Engineering, University of California, Davis
| | - Dong-Sik Shin
- Department of Biomedical Engineering, University of California, Davis
| | - Jaime Silangcruz
- Department of Biomedical Engineering, University of California, Davis
| | - Nazgul Tuleouva
- Department of Biomedical Engineering, University of California, Davis
| | - Alexander Revzin
- Department of Biomedical Engineering, University of California, Davis
- Corresponding author: Alexander Revzin Ph.D., Department of Biomedical Engineering, University of California, Davis, 451 East Health Sciences Drive #2619, Davis, CA, 95616, , Ph: 530-752-2383, Fax: 530-754-5739
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