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Ai L, Jiang X, Zhang K, Cui C, Liu B, Tan W. Tools and techniques for the discovery of therapeutic aptamers: recent advances. Expert Opin Drug Discov 2023; 18:1393-1411. [PMID: 37840268 DOI: 10.1080/17460441.2023.2264187] [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: 03/15/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023]
Abstract
INTRODUCTION The pursuit of novel therapeutic agents for serious diseases such as cancer has been a global endeavor. Aptamers characteristic of high affinity, programmability, low immunogenicity, and rapid permeability hold great promise for the treatment of diseases. Yet obtaining the approval for therapeutic aptamers remains challenging. Consequently, researchers are increasingly devoted to exploring innovative strategies and technologies to advance the development of these therapeutic aptamers. AREAS COVERED The authors provide a comprehensive summary of the recent progress of the SELEX (Systematic Evolution of Ligands by EXponential enrichment) technique, and how the integration of modern tools has facilitated the identification of therapeutic aptamers. Additionally, the engineering of aptamers to enhance their functional attributes, such as inhibiting and targeting, is discussed, demonstrating the potential to broaden their scope of utility. EXPERT OPINION The grand potential of aptamers and the insufficient development of relevant drugs have spurred countless efforts for stimulating their discovery and application in the therapeutic field. While SELEX techniques have undergone significant developments with the aid of advanced analysis instruments and ingeniously updated aptameric engineering strategies, several challenges still impede their clinical translation. A key challenge lies in the insufficient understanding of binding conformation and susceptibility to degradation under physiological conditions. Despite the hurdles, our opinion is optimistic. With continued progress in overcoming these obstacles, the widespread utilization of aptamers for clinical therapy is envisioned to become a reality soon.
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Affiliation(s)
- Lili Ai
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, The People's Republic of China
| | - Xinyi Jiang
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, The People's Republic of China
| | - Kejing Zhang
- Department of Geriatrics and Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, The People's Republic of China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, The People's Republic of China
| | - Cheng Cui
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, The People's Republic of China
| | - Bo Liu
- Department of Geriatrics and Department of General Surgery, Xiangya Hospital, Central South University, Changsha, Hunan, The People's Republic of China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, The People's Republic of China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, The People's Republic of China
- Institute of Molecular Medicine (IMM), Renji Hospital, School of Medicine and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, The People's Republic of China
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Aptamers targeting SARS-COV-2: a promising tool to fight against COVID-19. Trends Biotechnol 2023; 41:528-544. [PMID: 35995601 PMCID: PMC9340053 DOI: 10.1016/j.tibtech.2022.07.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 12/02/2022]
Abstract
SARS-CoV-2, the causative agent of COVID-19, remains among the main causes of global mortality. Although antigen/antibody-based immunoassays and neutralizing antibodies targeting SARS-CoV-2 have been successfully developed over the past 2 years, they are often inefficient and unreliable for emerging SARS-CoV-2 variants. Novel approaches against SARS-CoV-2 and its variants are therefore urgently needed. Aptamers have been developed for the detection and inhibition of several different viruses such as HIV, influenza viruses, Middle East respiratory syndrome coronavirus (MERS-CoV), and SARS-CoV. Aptamers targeting SARS-CoV-2 represent a promising tool in the fight against COVID-19, which is of paramount importance for the current and any future pandemics. This review presents recent advances and future trends in the development of aptamer-based approaches for SARS-CoV-2 diagnosis and treatment.
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Abreu RDS, Antunes D, Moreira ADS, Passetti F, Mendonça JB, de Araújo NS, Sassaro TF, Alberto AVP, Carrossini N, Fernandes PV, Costa MA, Guimarães ACR, Degrave WMS, Waghabi MC. Next Generation of Ovarian Cancer Detection Using Aptamers. Int J Mol Sci 2023; 24:ijms24076315. [PMID: 37047289 PMCID: PMC10094455 DOI: 10.3390/ijms24076315] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 03/30/2023] Open
Abstract
Ovarian cancer is among the seven most common types of cancer in women, being the most fatal gynecological tumor, due to the difficulty of detection in early stages. Aptamers are important tools to improve tumor diagnosis through the recognition of specific molecules produced by tumors. Here, aptamers and their potential targets in ovarian cancer cells were analyzed by in silico approaches. Specific aptamers were selected by the Cell-SELEX method using Caov-3 and OvCar-3 cells. The five most frequent aptamers obtained from the last round of selection were computationally modeled. The potential targets for those aptamers in cells were proposed by analyzing proteomic data available for the Caov-3 and OvCar-3 cell lines. Overexpressed proteins for each cell were characterized as to their three-dimensional model, cell location, and electrostatic potential. As a result, four specific aptamers for ovarian tumors were selected: AptaC2, AptaC4, AptaO1, and AptaO2. Potential targets were identified for each aptamer through Molecular Docking, and the best complexes were AptaC2-FXYD3, AptaC4-ALPP, AptaO1-TSPAN15, and AptaO2-TSPAN15. In addition, AptaC2 and AptaO1 could detect different stages and subtypes of ovarian cancer tissue samples. The application of this technology makes it possible to propose new molecular biomarkers for the differential diagnosis of epithelial ovarian cancer.
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Affiliation(s)
- Rayane da Silva Abreu
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Deborah Antunes
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Aline dos Santos Moreira
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Fabio Passetti
- Instituto Carlos Chagas, Fundação Oswaldo Cruz (FIOCRUZ), Curitiba 81350-010, Brazil
| | - Julia Badaró Mendonça
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Natássia Silva de Araújo
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Tayanne Felippe Sassaro
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Anael Viana Pinto Alberto
- Laboratório de Tecnologia de Pós, Instituto Nacional de Tecnologia, Rio de Janeiro 20081-312, Brazil
| | - Nina Carrossini
- Divisão de Patologia (DIPAT), Instituto Nacional do Câncer (INCA), Rio de Janeiro 20220-400, Brazil
| | | | - Mayla Abrahim Costa
- Laboratório de Tecnologia Imunológica, Instituto de Tecnologia em Imunobiológicos, Bio-Manguinhos, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Ana Carolina Ramos Guimarães
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
- Correspondence: (A.C.R.G.); (M.C.W.); Tel.: +55-21-3865-8159 (M.C.W.); Fax: +55-21-2590-3495 (M.C.W.)
| | - Wim Maurits Sylvain Degrave
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
| | - Mariana Caldas Waghabi
- Laboratório de Genômica Funcional e Bioinformática, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro 21040-900, Brazil
- Correspondence: (A.C.R.G.); (M.C.W.); Tel.: +55-21-3865-8159 (M.C.W.); Fax: +55-21-2590-3495 (M.C.W.)
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Gruenke PR, Aneja R, Welbourn S, Ukah OB, Sarafianos SG, Burke DH, Lange MJ. Selection and identification of an RNA aptamer that specifically binds the HIV-1 capsid lattice and inhibits viral replication. Nucleic Acids Res 2022; 50:1701-1717. [PMID: 35018437 PMCID: PMC8860611 DOI: 10.1093/nar/gkab1293] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/23/2021] [Accepted: 12/16/2021] [Indexed: 01/25/2023] Open
Abstract
The HIV-1 capsid core participates in several replication processes. The mature capsid core is a lattice composed of capsid (CA) monomers thought to assemble first into CA dimers, then into ∼250 CA hexamers and 12 CA pentamers. CA assembly requires conformational flexibility of each unit, resulting in the presence of unique, solvent-accessible surfaces. Significant advances have improved our understanding of the roles of the capsid core in replication; however, the contributions of individual CA assembly forms remain unclear and there are limited tools available to evaluate these forms in vivo. Here, we have selected aptamers that bind CA lattice tubes. We describe aptamer CA15-2, which selectively binds CA lattice, but not CA monomer or CA hexamer, suggesting that it targets an interface present and accessible only on CA lattice. CA15-2 does not compete with PF74 for binding, indicating that it likely binds a non-overlapping site. Furthermore, CA15-2 inhibits HIV-1 replication when expressed in virus producer cells, but not target cells, suggesting that it binds a biologically-relevant site during virus production that is either not accessible during post-entry replication steps or is accessible but unaltered by aptamer binding. Importantly, CA15-2 represents the first aptamer that specifically recognizes the HIV-1 CA lattice.
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Affiliation(s)
- Paige R Gruenke
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
| | - Rachna Aneja
- Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Sarah Welbourn
- Emory Vaccine Center and Yerkes National Primate Research Center, Emory University, Atlanta, GA 30329, USA
| | - Obiaara B Ukah
- Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Donald H Burke
- Department of Biochemistry, University of Missouri, Columbia, MO 65211, USA.,Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA.,Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
| | - Margaret J Lange
- Department of Molecular Microbiology & Immunology, School of Medicine, University of Missouri, Columbia, MO 65211, USA
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Xeno-Nucleic Acid (XNA) 2'-Fluoro-Arabino Nucleic Acid (FANA) Aptamers to the Receptor-Binding Domain of SARS-CoV-2 S Protein Block ACE2 Binding. Viruses 2021; 13:v13101983. [PMID: 34696413 PMCID: PMC8539646 DOI: 10.3390/v13101983] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 01/03/2023] Open
Abstract
The causative agent of COVID-19, SARS-CoV-2, gains access to cells through interactions of the receptor-binding domain (RBD) on the viral S protein with angiotensin-converting enzyme 2 (ACE2) on the surface of human host cells. Systematic evolution of ligands by exponential enrichment (SELEX) was used to generate aptamers (nucleic acids selected for high binding affinity to a target) to the RBD made from 2ʹ-fluoro-arabinonucleic acid (FANA). The best selected ~79 nucleotide aptamers bound the RBD (Arg319-Phe541) and the larger S1 domain (Val16-Arg685) of the 1272 amino acid S protein with equilibrium dissociation constants (KD,app) of ~10–20 nM, and binding half-life for the RBD, S1 domain, and full trimeric S protein of 53 ± 18, 76 ± 5, and 127 ± 7 min, respectively. Aptamers inhibited the binding of the RBD to ACE2 in an ELISA assay. Inhibition, on a per weight basis, was similar to neutralizing antibodies that were specific for RBD. Aptamers demonstrated high specificity, binding with about 10-fold lower affinity to the related S1 domain from the original SARS virus, which also binds to ACE2. Overall, FANA aptamers show affinities comparable to previous DNA aptamers to RBD and S1 protein and directly block receptor interactions while using an alternative Xeno-nucleic acid (XNA) platform.
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Schilling-Loeffler K, Rodriguez R, Williams-Woods J. Target Affinity and Structural Analysis for a Selection of Norovirus Aptamers. Int J Mol Sci 2021; 22:ijms22168868. [PMID: 34445583 PMCID: PMC8396345 DOI: 10.3390/ijms22168868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 11/30/2022] Open
Abstract
Aptamers, single-stranded oligonucleotides that specifically bind a molecule with high affinity, are used as ligands in analytical and therapeutic applications. For the foodborne pathogen norovirus, multiple aptamers exist but have not been thoroughly characterized. Consequently, there is little research on aptamer-mediated assay development. This study characterized seven previously described norovirus aptamers for target affinity, structure, and potential use in extraction and detection assays. Norovirus-aptamer affinities were determined by filter retention assays using norovirus genotype (G) I.1, GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney virus-like particles. Of the seven aptamers characterized, equilibrium dissociation constants for GI.7, GII.3, GII.4 New Orleans and GII.4 Sydney ranged from 71 ± 38 to 1777 ± 1021 nM. Four aptamers exhibited affinity to norovirus GII.4 strains; three aptamers additionally exhibited affinity toward GII.3 and GI.7. Aptamer affinity towards GI.1 was not observed. Aptamer structure analysis by circular dichroism (CD) spectroscopy showed that six aptamers exhibit B-DNA structure, and one aptamer displays parallel/antiparallel G-quadruplex hybrid structure. CD studies also showed that biotinylated aptamer structures were unchanged from non-biotinylated aptamers. Finally, norovirus aptamer assay feasibility was demonstrated in dot-blot and pull-down assays. This characterization of existing aptamers provides a knowledge base for future aptamer-based norovirus detection and extraction assay development and aptamer modification.
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Ferreira-Bravo IA, DeStefano JJ. Xeno-nucleic Acid (XNA) 2'-Fluoro-Arabino Nucleic Acid (FANA) Aptamers to the Receptor Binding Domain of SARS-CoV-2 S Protein Block ACE2 Binding. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34282416 DOI: 10.1101/2021.07.13.452259] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The causative agent of COVID-19, SARS-CoV-2, gains access to cells through interactions of the receptor binding domain (RBD) on the viral S protein with angiotensin converting enzyme 2 (ACE2) on the surface of human host cells. Systematic Evolution of Ligands by Exponential Enrichment (SELEX) was used to generate aptamers (nucleic acids selected for high binding affinity to a target) to the RBD made from 2'-fluoroarabinonucleic acid (FANA). The best selected ~ 79 nucleotide aptamers bound the RBD (Arg319-Phe541) and the larger S1 domain (Val16-Arg685) of the 1272 amino acid S protein with equilibrium dissociation constants ( K D,app ) of ~ 10-20 nM and a binding half-life for the RBD of 53 ± 18 minutes. Aptamers inhibited the binding of the RBD to ACE2 in an ELISA assay. Inhibition, on a per weight basis, was similar to neutralizing antibodies that were specific for RBD. Aptamers demonstrated high specificity, binding with about 10-fold lower affinity to the related S1 domain from the original SARS virus, which also binds to ACE2. Overall, FANA aptamers show affinities comparable to previous DNA aptamers to RBD and S protein and directly block receptor interactions while using an alternative Xeno-nucleic acid (XNA) platform.
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Selection and applications of functional nucleic acids for infectious disease detection and prevention. Anal Bioanal Chem 2021; 413:4563-4579. [PMID: 33506341 PMCID: PMC7840224 DOI: 10.1007/s00216-020-03124-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 11/30/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023]
Abstract
Infectious diseases caused by pathogenic microorganisms such as viruses and bacteria pose a great threat to human health. Although a significant progress has been obtained in the diagnosis and prevention of infectious diseases, it still remains challenging to develop rapid and cost-effective detection approaches and overcome the side effects of therapeutic agents and pathogen resistance. Functional nucleic acids (FNAs), especially the most widely used aptamers and DNAzymes, hold the advantages of high stability and flexible design, which make them ideal molecular recognition tools for bacteria and viruses, as well as potential therapeutic drugs for infectious diseases. This review summarizes important advances in the selection and detection of bacterial- and virus-associated FNAs, along with their potential prevention ability of infectious disease in recent years. Finally, the challenges and future development directions are concluded.
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Dunn MR, McCloskey CM, Buckley P, Rhea K, Chaput JC. Generating Biologically Stable TNA Aptamers that Function with High Affinity and Thermal Stability. J Am Chem Soc 2020; 142:7721-7724. [PMID: 32298104 DOI: 10.1021/jacs.0c00641] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Aptamers are often prone to nuclease digestion, which limits their utility in many biomedical applications. Here we describe a xeno-nucleic acid system based on α-l-threofuranosyl nucleic acid (TNA) that is completely refractory to nuclease digestion. The use of an engineered TNA polymerase permitted the isolation of functional TNA aptamers that bind to HIV reverse transcriptase (HIV RT) with KD's of ∼0.4-4.0 nM. The aptamers were identified using a display strategy that provides a powerful genotype-phenotype linkage. The TNA aptamers remain active in the presence of nuclease and exhibit markedly higher thermal stability than monoclonal antibodies. The combined properties of biological stability, high binding affinity, and thermal stability make TNA aptamers a powerful system for the development of diagnostic and therapeutic agents.
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Affiliation(s)
| | | | - Patricia Buckley
- U.S. Army CCDC Chemical Biological Center, APG, Maryland 21010, United States
| | - Katherine Rhea
- Excet, Inc., 8001 Braddock Road, Ste. 303, Springfield, Virginia 22151, United States
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Bhardwaj J, Chaudhary N, Kim H, Jang J. Subtyping of influenza A H1N1 virus using a label-free electrochemical biosensor based on the DNA aptamer targeting the stem region of HA protein. Anal Chim Acta 2019; 1064:94-103. [PMID: 30982523 DOI: 10.1016/j.aca.2019.03.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 10/27/2022]
Abstract
Rapid subtyping of influenza viruses in clinical laboratories has been increasingly important because three subtypes (seasonal H1N1, H3N2, and 2009 H1N1) of influenza A virus currently disseminated in humans have variable susceptibilities to antiviral drug. Herein, we present DNA aptamers for selective detection of influenza A H1N1 (seasonal and 2009 pandemic H1N1) viruses by targeting recombinant influenza A mini-hemagglutinin (mini-HA) protein (the stable stem region of HA) and whole H1N1 viruses. The dissociation constants (KD) of aptamer candidates V46 and V57 were 19.2 nM and 29.6 nM, respectively, according to electrochemical characterization (differential pulse voltammetry), demonstrating strong binding to mini-HA. In comparison, the KD of the influenza virus antibodies is in the range of 1 μM-10 nM. Aptamer V46 showed higher specificity and binding affinity to the mini-HA protein and H1N1 subtypes, and it was also incorporated into an indium tin oxide-based electrochemical sensor, showing sensitive and specific detection of H1N1 viruses, with a limit of detection (LOD) of 3.7 plaque-forming units per mL. The binding affinity, specificity, and LOD achieved with the electrochemical sensor suggest that it can be used for rapid subtyping of H1N1. We also propose that this aptamer can be used for the neutralization of H1N1 subtypes, suggesting potential therapeutic and diagnostic applications.
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Affiliation(s)
- Jyoti Bhardwaj
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Narendra Chaudhary
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea; Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea
| | - Hajin Kim
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea; Center for Genomic Integrity, Institute for Basic Science, Ulsan, 44919, Republic of Korea
| | - Jaesung Jang
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea; School of Mechanical, Aerospace and Nuclear Engineering, UNIST, Ulsan, 44919, Republic of Korea.
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Pan Q, Luo F, Liu M, Zhang XL. Oligonucleotide aptamers: promising and powerful diagnostic and therapeutic tools for infectious diseases. J Infect 2018; 77:83-98. [PMID: 29746951 PMCID: PMC7112547 DOI: 10.1016/j.jinf.2018.04.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 01/02/2018] [Accepted: 04/08/2018] [Indexed: 12/21/2022]
Abstract
The entire human population is at risk of infectious diseases worldwide. Thus far, the diagnosis and treatment of human infectious diseases at the molecular and nanoscale levels have been extremely challenging tasks because of the lack of effective probes to identify and recognize biomarkers of pathogens. Oligonucleotide aptamers are a class of small nucleic acid ligands that are composed of single-stranded DNA (ssDNA) or RNA and act as affinity probes or molecular recognition elements for a variety of targets. These aptamers have an exciting potential for diagnose and/or treatment of specific diseases. In this review, we highlight areas where aptamers have been developed as diagnostic and therapeutic agents for both bacterial and viral infectious diseases as well as aptamer-based detection.
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Affiliation(s)
- Qin Pan
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Fengling Luo
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Min Liu
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Department of Immunology School of Basic Medical Sciences, Medical Research Institute and Hubei Province Key Laboratory of Allergy Wuhan University School of Medicine, Donghu Road 185#, Wuhan 430071, PR China.
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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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Vorobyeva MA, Davydova AS, Vorobjev PE, Pyshnyi DV, Venyaminova AG. Key Aspects of Nucleic Acid Library Design for in Vitro Selection. Int J Mol Sci 2018; 19:E470. [PMID: 29401748 PMCID: PMC5855692 DOI: 10.3390/ijms19020470] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Revised: 01/31/2018] [Accepted: 02/02/2018] [Indexed: 02/07/2023] Open
Abstract
Nucleic acid aptamers capable of selectively recognizing their target molecules have nowadays been established as powerful and tunable tools for biospecific applications, be it therapeutics, drug delivery systems or biosensors. It is now generally acknowledged that in vitro selection enables one to generate aptamers to almost any target of interest. However, the success of selection and the affinity of the resulting aptamers depend to a large extent on the nature and design of an initial random nucleic acid library. In this review, we summarize and discuss the most important features of the design of nucleic acid libraries for in vitro selection such as the nature of the library (DNA, RNA or modified nucleotides), the length of a randomized region and the presence of fixed sequences. We also compare and contrast different randomization strategies and consider computer methods of library design and some other aspects.
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Affiliation(s)
- Maria A. Vorobyeva
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
| | - Anna S. Davydova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
| | - Pavel E. Vorobjev
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova St., 2, 630090 Novosibirsk, Russia
| | - Dmitrii V. Pyshnyi
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova St., 2, 630090 Novosibirsk, Russia
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentiev Ave., 8, 630090 Novosibirsk, Russia; (A.S.D.); (P.E.V.); (D.V.P.); (A.G.V.)
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Aeksiri N, Warakulwit C, Hannongbua S, Unajak S, Choowongkomon K. Use of Capillary Electrophoresis to Study the Binding Interaction of Aptamers with Wild-Type, K103N, and Double Mutant (K103N/Y181C) HIV-1 RT : Studying the Binding Interaction of Wild-Type, K103N, and Double Mutant (K103N/Y181C) HIV-1 RT with Aptamers by Performing the Capillary Electrophoresis. Appl Biochem Biotechnol 2016; 182:546-558. [PMID: 27900665 DOI: 10.1007/s12010-016-2343-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 11/24/2016] [Indexed: 12/22/2022]
Abstract
A number of nucleic acid aptamers with high affinities to human immunodeficiency virus reverse transcriptase (HIV-1 RT) are currently known. They can potentially be developed as broad-spectrum antiviral drugs, but there is little known about their binding interaction with mutant HIV-1 RT. Therefore, we utilized non-equilibrium capillary electrophoresis of equilibrium mixture (NECEEM) to study the interaction of three HIV-1 RTs (wild type, K103N, and double mutant (K103N/Y181C)) with RT1t49 and RT12 aptamers. This approach was used to study and evaluate the K d values of these molecules. The results showed that the K d values of the tested aptamers were lower than that of the DNA substrate. The results also pointed out that RT1t49 could bind with all HIV-1 RTs and compete with the DNA substrate at the active site. Moreover, we studied the binding stoichiometry of HIV-1 RT using aptamers as probes. The findings showed evidence of two binding stoichiometries with HIV-1 RT and the RT12 aptamer but only one binding stoichiometry for RT1t49. In addition, RT1t49 could bind specifically with the wild-type, K103N, and double mutants in Escherichia coli lysate. This result also indicated that the aptamer could detect HIV-1 RT in the presence of E. coli lysate.
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Affiliation(s)
- Niran Aeksiri
- Interdisciplinary Program in Genetic Engineering, Graduate School, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
- Department of Agricultural Science, Faculty of Agriculture, Natural Resources and Environment, Naresuan University, Phitsanulok, 65000, Thailand
| | - Chompunuch Warakulwit
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Supa Hannongbua
- Department of Chemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Sasimanas Unajak
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Kiattawee Choowongkomon
- Interdisciplinary Program in Genetic Engineering, Graduate School, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
- Department of Biochemistry, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
- Center for Advanced Studies in Tropical Natural Resources, NRU-KU, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
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16
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Alves Ferreira-Bravo I, Cozens C, Holliger P, DeStefano JJ. Selection of 2'-deoxy-2'-fluoroarabinonucleotide (FANA) aptamers that bind HIV-1 reverse transcriptase with picomolar affinity. Nucleic Acids Res 2015; 43:9587-99. [PMID: 26476448 PMCID: PMC4751925 DOI: 10.1093/nar/gkv1057] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2015] [Accepted: 10/02/2015] [Indexed: 11/17/2022] Open
Abstract
Using a Systematic Evolution of Ligands by Exponential Enrichment (SELEX) protocol capable of selecting xeno-nucleic acid (XNA) aptamers, a 2′-deoxy-2′-fluoroarabinonucleotide (FANA) aptamer (referred to as FA1) to HIV-1 reverse transcriptase (HIV-1 RT) was selected. FA1 bound HIV-1 RT with KD,app values in the low pM range under different ionic conditions. Comparisons to published HIV-1 RT RNA and DNA aptamers indicated that FA1 bound at least as well as these aptamers. FA1 contained a 20 nucleotide 5′ DNA sequence followed by a 57 nucleotide region of FANA nucleotides. Removal of the fourteen 5′ DNA nucleotides did not affect binding. FA1's predicted structure was composed of four stems and four loops. All stem nucleotides could be modified to G-C base pairs (14 total changes) with a small effect on binding. Eliminating or altering most loop sequences reduced or abolished tight binding. Overall, results suggested that the structure and the sequence of FA1 were important for binding. FA1 showed strong inhibition of HIV-1 RT in extension assays while no specific binding to avian myeloblastosis or Moloney murine leukemia RTs was detected. A complete DNA version of FA1 showed low binding to HIV-1 RT, emphasizing the unique properties of FANA in HIV-1 RT binding.
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Affiliation(s)
- Irani Alves Ferreira-Bravo
- Cell Biology and Molecular Genetics, Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Maryland Pathogen Research Institute, College Park, MD 20742, USA
| | - Christopher Cozens
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Jeffrey J DeStefano
- Cell Biology and Molecular Genetics, Bioscience Research Building, University of Maryland, College Park, MD 20742, USA Maryland Pathogen Research Institute, College Park, MD 20742, USA
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17
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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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18
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Single-Stranded DNA Aptamers against Pathogens and Toxins: Identification and Biosensing Applications. BIOMED RESEARCH INTERNATIONAL 2015. [PMID: 26199940 PMCID: PMC4493287 DOI: 10.1155/2015/419318] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Molecular recognition elements (MREs) can be short sequences of single-stranded DNA, RNA, small peptides, or antibody fragments. They can bind to user-defined targets with high affinity and specificity. There has been an increasing interest in the identification and application of nucleic acid molecular recognition elements, commonly known as aptamers, since they were first described in 1990 by the Gold and Szostak laboratories. A large number of target specific nucleic acids MREs and their applications are currently in the literature. This review first describes the general methodologies used in identifying single-stranded DNA (ssDNA) aptamers. It then summarizes advancements in the identification and biosensing application of ssDNA aptamers specific for bacteria, viruses, their associated molecules, and selected chemical toxins. Lastly, an overview of the basic principles of ssDNA aptamer-based biosensors is discussed.
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Aptamer-based therapeutics: new approaches to combat human viral diseases. Pharmaceuticals (Basel) 2013; 6:1507-42. [PMID: 24287493 PMCID: PMC3873675 DOI: 10.3390/ph6121507] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2013] [Revised: 11/12/2013] [Accepted: 11/15/2013] [Indexed: 12/18/2022] Open
Abstract
Viruses replicate inside the cells of an organism and continuously evolve to contend with an ever-changing environment. Many life-threatening diseases, such as AIDS, SARS, hepatitis and some cancers, are caused by viruses. Because viruses have small genome sizes and high mutability, there is currently a lack of and an urgent need for effective treatment for many viral pathogens. One approach that has recently received much attention is aptamer-based therapeutics. Aptamer technology has high target specificity and versatility, i.e., any viral proteins could potentially be targeted. Consequently, new aptamer-based therapeutics have the potential to lead a revolution in the development of anti-infective drugs. Additionally, aptamers can potentially bind any targets and any pathogen that is theoretically amenable to rapid targeting, making aptamers invaluable tools for treating a wide range of diseases. This review will provide a broad, comprehensive overview of viral therapies that use aptamers. The aptamer selection process will be described, followed by an explanation of the potential for treating virus infection by aptamers. Recent progress and prospective use of aptamers against a large variety of human viruses, such as HIV-1, HCV, HBV, SCoV, Rabies virus, HPV, HSV and influenza virus, with particular focus on clinical development of aptamers will also be described. Finally, we will discuss the challenges of advancing antiviral aptamer therapeutics and prospects for future success.
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20
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Grozio A, Gonzalez VM, Millo E, Sturla L, Vigliarolo T, Bagnasco L, Guida L, D'Arrigo C, De Flora A, Salis A, Martin EM, Bellotti M, Zocchi E. Selection and characterization of single stranded DNA aptamers for the hormone abscisic Acid. Nucleic Acid Ther 2013; 23:322-31. [PMID: 23971905 PMCID: PMC3760064 DOI: 10.1089/nat.2013.0418] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The hormone abscisic acid (ABA) is a small molecule involved in pivotal physiological functions in higher plants. Recently, ABA has been also identified as an endogenous hormone in mammals, regulating different cell functions including inflammatory processes, stem cell expansion, insulin release, and glucose uptake. Aptamers are short, single-stranded (ss) oligonucleotidesable to recognize target molecules with high affinity. The small size of the ABA molecule represented a challenge for aptamer development and the aim of this study was to develop specific anti-ABA DNA aptamers. Biotinylated abscisic acid (bio-ABA) was immobilized on streptavidin-coated magnetic beads. DNA aptamers against bio-ABA were selected with 7 iterative rounds of the systematic evolution of ligands by exponential enrichment method (SELEX), each round comprising incubation of the ABA-binding beads with the ssDNA sequences, DNA elution, electrophoresis, and polymerase chain reaction (PCR) amplification. The PCR product was cloned and sequenced. The binding affinity of several clones was determined using bio-ABA immobilized on streptavidin-coated plates. Aptamer 2 and aptamer 9 showed the highest binding affinity, with dissociation constants values of 0.98 ± 0.14 μM and 0.80 ± 0.07 μM, respectively. Aptamers 2 and 9 were also able to bind free, unmodified ABA and to discriminate between different ABA enantiomers and isomers. Our findings indicate that ssDNA aptamers can selectively bind ABA and could be used for the development of ABA quantitation assays.
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Affiliation(s)
- Alessia Grozio
- Department of Experimental Medicine, Section of Biochemistry, University of Genova, Genova, Italy
| | - Victor M. Gonzalez
- Departamento de Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - Enrico Millo
- Center of Excellence for Biomedical Research (CEBR), University of Genova, Genova, Italy
| | - Laura Sturla
- Center of Excellence for Biomedical Research (CEBR), University of Genova, Genova, Italy
| | - Tiziana Vigliarolo
- Department of Experimental Medicine, Section of Biochemistry, University of Genova, Genova, Italy
| | - Luca Bagnasco
- Department of Internal Medicine, University of Genova, Genova, Italy
| | - Lucrezia Guida
- Center of Excellence for Biomedical Research (CEBR), University of Genova, Genova, Italy
| | - Cristina D'Arrigo
- Institute for Macromolecular Studies, National Research Council, Genova, Italy
| | - Antonio De Flora
- Center of Excellence for Biomedical Research (CEBR), University of Genova, Genova, Italy
| | - Annalisa Salis
- Center of Excellence for Biomedical Research (CEBR), University of Genova, Genova, Italy
| | - Elena M. Martin
- Departamento de Bioquímica-Investigación, IRYCIS-Hospital Ramón y Cajal, Madrid, Spain
| | - Marta Bellotti
- Center of Excellence for Biomedical Research (CEBR), University of Genova, Genova, Italy
| | - Elena Zocchi
- Center of Excellence for Biomedical Research (CEBR), University of Genova, Genova, Italy
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Radom F, Jurek PM, Mazurek MP, Otlewski J, Jeleń F. Aptamers: molecules of great potential. Biotechnol Adv 2013; 31:1260-74. [PMID: 23632375 DOI: 10.1016/j.biotechadv.2013.04.007] [Citation(s) in RCA: 136] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2012] [Revised: 03/27/2013] [Accepted: 04/19/2013] [Indexed: 01/08/2023]
Abstract
Aptamers emerged over 20 years ago as a class of nucleic acids able to recognize specific targets. Today, aptamer-related studies constitute a large and important field of biotechnology. Functional oligonucleotides have proved to be a versatile tool in biomedical research due to the ease of synthesis, a wide range of potentially recognized molecular targets and the simplicity of selection. Similarly to antibodies, aptamers can be used to detect or isolate specific molecules, as well as to act as targeting and therapeutic agents. In this review we present different approaches to aptamer application in nanobiotechnology, diagnostics and medicine.
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Affiliation(s)
- Filip Radom
- Department of Protein Engineering, Faculty of Biotechnology, University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland
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22
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Ray P, Viles KD, Soule EE, Woodruff RS. Application of aptamers for targeted therapeutics. Arch Immunol Ther Exp (Warsz) 2013; 61:255-71. [PMID: 23563807 DOI: 10.1007/s00005-013-0227-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 03/25/2013] [Indexed: 12/30/2022]
Abstract
Aptamers are short, single-stranded oligonucleotides that are isolated through a process termed systematic evolution of ligands by exponential enrichment. With the advent of cell-based selection technology, aptamers can be selected to bind protein targets that are expressed on the cell surface. These aptamers demonstrate excellent specificity and high affinity toward their target proteins and are often internalized upon binding to their targets. This has opened up the possibility of using aptamers for cell-specific targeted drug delivery. In this review, we will discuss cell-surface protein targets, the aptamers that bind them, and their applications for targeted therapeutics.
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Affiliation(s)
- Partha Ray
- Department of Surgery, Duke University Medical Center, DUMC Box 103035, Durham, NC 27710, USA.
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Lieberman OJ, DeStefano JJ, Lee VT. Detection of cyclic diguanylate G-octaplex assembly and interaction with proteins. PLoS One 2013; 8:e53689. [PMID: 23308275 PMCID: PMC3538687 DOI: 10.1371/journal.pone.0053689] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 12/04/2012] [Indexed: 01/23/2023] Open
Abstract
Bacterial signaling networks control a wide variety of cellular processes including growth, metabolism, and pathogenesis. Bis-(3'-5')-cyclic dimeric guanosine monophosphate (cdiGMP) is a secondary signaling nucleotide that controls cellulose synthesis, biofilm formation, motility and virulence in a wide range of gram-negative bacterial species. CdiGMP is a dynamic molecule that forms different tertiary structures in vitro, including a trans-monomer, cis-monomer, cis-dimer and G-octaplex (G8). Although the monomer and dimer have been shown to be physiologically relevant in modulating protein activity and transcription, the biological effects of the cdiGMP G8 has not yet been described. Here, we have developed a TLC-based assay to detect radiolabeled cdiGMP G8 formation. Utilizing the radiolabeled cdiGMP G8, we have also shown a novel inhibitory interaction between the cdiGMP G8 and HIV-1 reverse transcriptase and that the cdiGMP G8 does not interact with proteins from Pseudomonas aeruginosa known to bind monomeric and dimeric cdiGMP. These results suggest that the radiolabeled cdiGMP G8 can be used to measure interactions between the cdiGMP G8 and cellular proteins, providing an avenue through which the biological significance of this molecule could be investigated.
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Affiliation(s)
- Ori J. Lieberman
- Department of Cell Biology and Molecular Genetics, University of Maryland at College Park, College Park, Maryland, United States of America
- Maryland Pathogen Research Institute, College Park, Maryland, United States of America
| | - Jeffery J. DeStefano
- Department of Cell Biology and Molecular Genetics, University of Maryland at College Park, College Park, Maryland, United States of America
- Maryland Pathogen Research Institute, College Park, Maryland, United States of America
| | - Vincent T. Lee
- Department of Cell Biology and Molecular Genetics, University of Maryland at College Park, College Park, Maryland, United States of America
- Maryland Pathogen Research Institute, College Park, Maryland, United States of America
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Singh K, Marchand B, Rai DK, Sharma B, Michailidis E, Ryan EM, Matzek KB, Leslie MD, Hagedorn AN, Li Z, Norden PR, Hachiya A, Parniak MA, Xu HT, Wainberg MA, Sarafianos SG. Biochemical mechanism of HIV-1 resistance to rilpivirine. J Biol Chem 2012; 287:38110-23. [PMID: 22955279 DOI: 10.1074/jbc.m112.398180] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Rilpivirine (RPV) is a second generation nonnucleoside reverse transcriptase (RT) inhibitor (NNRTI) that efficiently inhibits HIV-1 resistant to first generation NNRTIs. Virological failure during therapy with RPV and emtricitabine is associated with the appearance of E138K and M184I mutations in RT. Here we investigate the biochemical mechanism of RT inhibition and resistance to RPV. We used two transient kinetics approaches (quench-flow and stopped-flow) to determine how subunit-specific mutations in RT p66 or p51 affect association and dissociation of RPV to RT as well as their impact on binding of dNTP and DNA and the catalytic incorporation of nucleotide. We compared WT with four subunit-specific RT mutants, p66(M184I)/p51(WT), p66(E138K)/p51(E138K), p66(E138K/M184I)/p51(E138K), and p66(M184I)/p51(E138K). Ile-184 in p66 (p66(184I)) decreased the catalytic efficiency of RT (k(pol)/K(d)(.dNTP)), primarily through a decrease in dNTP binding (K(d)(.dNTP)). Lys-138 either in both subunits or in p51 alone abrogated the negative effect of p66(184I) by restoring dNTP binding. Furthermore, p51(138K) reduced RPV susceptibility by altering the ratio of RPV dissociation to RPV association, resulting in a net reduction in RPV equilibrium binding affinity (K(d)(.RPV) = k(off.RPV)/k(on.RPV)). Quantum mechanics/molecular mechanics hybrid molecular modeling revealed that p51(E138K) affects access to the RPV binding site by disrupting the salt bridge between p51(E138) and p66(K101). p66(184I) caused repositioning of the Tyr-183 active site residue and decreased the efficiency of RT, whereas the addition of p51(138K) restored Tyr-183 to a WT-like conformation, thus abrogating the Ile-184-induced functional defects.
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Affiliation(s)
- Kamalendra Singh
- Christopher Bond Life Sciences Center, University of Missouri School of Medicine, Columbia, Missouri 65211, USA
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