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Mahjoubin-Tehran M, Rezaei S, Santos RD, Jamialahmadi T, Almahmeed W, Sahebkar A. Targeting PCSK9 as a key player in lipid metabolism: exploiting the therapeutic and biosensing potential of aptamers. Lipids Health Dis 2024; 23:156. [PMID: 38796450 PMCID: PMC11128129 DOI: 10.1186/s12944-024-02151-8] [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: 12/04/2023] [Accepted: 05/17/2024] [Indexed: 05/28/2024] Open
Abstract
The degradation of low-density lipoprotein receptor (LDLR) is induced by proprotein convertase subtilisin/kexin type 9 (PCSK9), resulting in elevated plasma concentrations of LDL cholesterol. Therefore, inhibiting the interactions between PCSK9 and LDLR is a desirable therapeutic goal for managing hypercholesterolemia. Aptamers, which are RNA or single-stranded DNA sequences, can recognize their targets based on their secondary structure. Aptamers exhibit high selectivity and affinity for binding to target molecules. The systematic evolution of ligands by exponential enrichment (SELEX), a combination of biological approaches, is used to screen most aptamers in vitro. Due to their unique advantages, aptamers have garnered significant interest since their discovery and have found extensive applications in various fields. Aptamers have been increasingly utilized in the development of biosensors for sensitive detection of pathogens, analytes, toxins, drug residues, and malignant cells. Furthermore, similar to monoclonal antibodies, aptamers can serve as therapeutic tools. Unlike certain protein therapeutics, aptamers do not elicit antibody responses, and their modified sugars at the 2'-positions generally prevent toll-like receptor-mediated innate immune responses. The focus of this review is on aptamer-based targeting of PCSK9 and the application of aptamers both as biosensors and therapeutic agents.
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Affiliation(s)
- Maryam Mahjoubin-Tehran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Samaneh Rezaei
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Raul D Santos
- Lipid Clinic Heart Institute (Incor), University of São Paulo, Medical School Hospital, São Paulo, Brazil
| | - Tannaz Jamialahmadi
- Pharmaceutical Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Medical Toxicology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Wael Almahmeed
- Heart and Vascular Institute, Cleveland Clinic Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Amirhossein Sahebkar
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran.
- Applied Biomedical Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
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2
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Rahimizadeh K, Zahra QUA, Chen S, Le BT, Ullah I, Veedu RN. Nanoparticles-assisted aptamer biosensing for the detection of environmental pathogens. ENVIRONMENTAL RESEARCH 2023; 238:117123. [PMID: 37717803 DOI: 10.1016/j.envres.2023.117123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 09/08/2023] [Accepted: 09/10/2023] [Indexed: 09/19/2023]
Abstract
Given the importance of public health, it is crucial to develop quick, targeted, highly sensitive, and accurate technologies to monitor pathogenic microbes in response to the growing concerns of food and environmental safety. Although conventional approaches for microbiological detection are available, they are laborious, and often skill demanding. Therefore, such approaches are incompetent in the on-site or high-throughput assessment of pathogenic microbes. Numerous efforts have been made to develop biosensors that use nucleic acid aptamer as the biorecognition element, which would avoid the abovementioned limitations. Incorporating nanomaterials (NMs) into aptamer-based biosensors (aptasensors) improves their sensitivity and specificity, opening exciting possibilities for various applications, such as bioanalysis of food and environmental samples. Over the last decade, nanomaterial-conjugated aptasensors have seen a steadily rising demand. To this end, the main goal of this study is to demonstrate the novelty in the design of nanomaterial-conjugated aptasensors and how they can be used to detect different pathogenic microbes in water and food. The intent of this paper is to evaluate the cutting-edge techniques that have appeared in nano-aptasensors throughout the past few years, such as manufacturing procedures, analytical credibility, and sensing mechanisms. Additionally, the fundamental performance parameters of aptasensing techniques (such as detection limits, and sensing ranges response) were also used to evaluate their practical applicability. Finally, it is anticipated that this study will inspire innovative ideas and techniques for the construction and use of aptasensors for monitoring pathogenic microorganisms in food, drinks, recreational water, and wastewater.
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Affiliation(s)
- Kamal Rahimizadeh
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia; Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.
| | - Qurat Ul Ain Zahra
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia.
| | - Suxiang Chen
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia; Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.
| | - Bao T Le
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia; Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.
| | - Ismat Ullah
- State Key Laboratory of Materials Processing and Die & Mould Technology, School of Materials Science and Engineering, Huazhong University of Science and Technology, Wuhan, Hubei Province, 430074, PR China.
| | - Rakesh N Veedu
- Centre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA 6150, Australia; Perron Institute for Neurological and Translational Science, Perth, WA 6009, Australia.
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3
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Nor Nazli NA, Muthuraju S, Ahmad F, Mohamed Yusoff AA, Jaafar H, Shamsuddin S, Abdullah JM. Characterisation of Primary Human Hippocampal Astrocyte Cell Culture Following Exposure to Hypoxia. Malays J Med Sci 2023; 30:92-106. [PMID: 36875187 PMCID: PMC9984107 DOI: 10.21315/mjms2023.30.1.8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/01/2022] [Indexed: 03/05/2023] Open
Abstract
Background The present study aimed to understand the characterisation of human hippocampal astrocyte following hypoxia exposure. Based on the preliminary screening, 15 min was chosen as the time point and the cells were exposed to different oxygen percentages. Methods The Trypan blue viability assay used to examine cell death. Immunofluorescence assay, glial fibrillary acidic protein (GFAP) was used to portray the morphology of astrocytes. The hypoxia-inducible factor 1 (HIF-1) staining was performed to confirm hypoxia induced cell death and there was a dramatic expression of HIF-1α displayed in exposed astrocyte cells compared to the control. In molecular level, genes were chosen, such as glyceraldehyde 3-phosphate dehydrogenase (GAPDH), GFAP, HIF-1α and B-cell lymphoma 2 (Bcl-2) and ran the reverse transcription-polymerase chain reaction (RT-PCR). Results Microscope revealed a filamentous and clear nucleus appearance in a control whereas the rupture nuclei with no rigid structure of the cell were found in the 3% oxygen. The control and hypoxia cells were also stained with the annexin V-fluorescein isothiocyanate (annexin V-FITC). Fluorescence microscope reveals astrocyte cells after hypoxia showed higher expression of nuclei but not in control. Merging PI and FITC showed the differences of nuclei expression between the control and hypoxia. In the molecular analysis, there were significant changes of GFAP, HIF-1α and Bcl-2 in hypoxia exposed cells when compared to the control group. Conclusion Cells that were exposed to hypoxia (3% oxygen for 15 min) clearly showed damage. General view of human hippocampal astrocyte genomic response to hypoxia was obtained.
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Affiliation(s)
- Nurul Atikah Nor Nazli
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.,Brain and Behaviour Cluster, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Sangu Muthuraju
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.,Brain and Behaviour Cluster, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Farizan Ahmad
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.,Brain and Behaviour Cluster, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Abdul Aziz Mohamed Yusoff
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.,Brain and Behaviour Cluster, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Hasnan Jaafar
- Department of Pathology, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Shaharum Shamsuddin
- Department of Biomedicine, School of Health Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
| | - Jafri Malin Abdullah
- Department of Neurosciences, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia.,Brain and Behaviour Cluster, School of Medical Sciences, Universiti Sains Malaysia, Kelantan, Malaysia
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4
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Shanmugasundaram M, Senthilvelan A, Kore AR. An Efficient Gram-Scale Chemical Synthesis of Purine Locked Nucleic Acid Nucleoside-5'-O-Triphosphates. Curr Protoc 2022; 2:e436. [PMID: 35723503 DOI: 10.1002/cpz1.436] [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] [Indexed: 06/15/2023]
Abstract
This article presents a simple, reliable, straight-forward, general, and efficient chemical method for the gram-scale synthesis of purine locked nucleic acid (LNA) nucleotides, such as LNA guanosine-5'-O-triphosphate (LNA-GTP) and LNA adenosine-5'-O-triphosphate (LNA-ATP), starting from the corresponding nucleoside. The reaction pathway employs an improved protection-free "one-pot, three-step" Ludwig synthetic strategy. The first step involves monophosphorylation of nucleoside with phosphorus oxychloride followed by reaction with tributylammonium pyrophosphate and subsequent hydrolysis of the resulting cyclic intermediate to furnish the corresponding LNA nucleotide in good yields. It is noteworthy that the reaction affords high-purity (>99.5%) LNA nucleotide after diethylaminoethyl Sepharose column purification. © 2022 Wiley Periodicals LLC. Basic Protocol: Synthesis of LNA nucleoside-5'-O-triphosphates.
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Affiliation(s)
| | | | - Anilkumar R Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, Austin, Texas
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5
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Shanmugasundaram M, Senthilvelan A, Kore AR. An improved protection-free one-pot chemical synthesis of purine locked nucleic acid nucleoside-5'-triphosphates. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2021; 41:36-44. [PMID: 34696692 DOI: 10.1080/15257770.2021.1994992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A simple, reliable, straightforward, and efficient method for the gram-scale chemical synthesis of purine locked nucleic acid (LNA) nucleotides such as LNA-guanosine-5'-triphosphate (LNA-GTP) and LNA-adenosine-5'-triphosphate (LNA-ATP) starting from the corresponding nucleoside is described. The overall reaction utilizes an improved "one-pot, three-step" Ludwig synthetic strategy that involves the monophosphorylation of LNA nucleoside, followed by the reaction with tributylammonium pyrophosphate and subsequent hydrolysis of the resulting cyclic intermediate using water to furnish the corresponding purine LNA nucleotide in good yield with high purity (>99.5%).
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Affiliation(s)
| | | | - Anilkumar R Kore
- Life Sciences Solutions Group, Thermo Fisher Scientific, Austin, Texas, USA
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6
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Isomorphic building blocks for information-bearing duplexes—part 2: pyrimidine base pairs with sugar phosphate backbones. Struct Chem 2021. [DOI: 10.1007/s11224-021-01739-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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7
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Abstract
DNA polymerases play a central role in biology by transferring genetic information from one generation to the next during cell division. Harnessing the power of these enzymes in the laboratory has fueled an increase in biomedical applications that involve the synthesis, amplification, and sequencing of DNA. However, the high substrate specificity exhibited by most naturally occurring DNA polymerases often precludes their use in practical applications that require modified substrates. Moving beyond natural genetic polymers requires sophisticated enzyme-engineering technologies that can be used to direct the evolution of engineered polymerases that function with tailor-made activities. Such efforts are expected to uniquely drive emerging applications in synthetic biology by enabling the synthesis, replication, and evolution of synthetic genetic polymers with new physicochemical properties.
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8
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Martín-Alonso S, Frutos-Beltrán E, Menéndez-Arias L. Reverse Transcriptase: From Transcriptomics to Genome Editing. Trends Biotechnol 2020; 39:194-210. [PMID: 32653101 DOI: 10.1016/j.tibtech.2020.06.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/10/2020] [Accepted: 06/15/2020] [Indexed: 01/01/2023]
Abstract
Reverse transcriptases (RTs) are enzymes that can generate a complementary strand of DNA (cDNA) from RNA. Coupled with PCR, RTs have been widely used to detect RNAs and to clone expressed genes. Classical retroviral RTs have been improved by protein engineering. These enzymes and newly characterized RTs are key elements in the development of next-generation sequencing techniques that are now being applied to the study of transcriptomics. In addition, engineered RTs fused to a CRISPR/Cas9 nickase have recently shown great potential as tools to manipulate eukaryotic genomes. In this review, we discuss the properties and uses of wild type and engineered RTs in biotechnological applications, from conventional RT-PCR to recently introduced prime editing.
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Affiliation(s)
- Samara Martín-Alonso
- Centro de Biología Molecular 'Severo Ochoa' (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Estrella Frutos-Beltrán
- Centro de Biología Molecular 'Severo Ochoa' (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain
| | - Luis Menéndez-Arias
- Centro de Biología Molecular 'Severo Ochoa' (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), c/ Nicolás Cabrera 1, Campus de Cantoblanco-UAM, 28049 Madrid, Spain. @cbm.csic.es
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9
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Jackson LN, Chim N, Shi C, Chaput JC. Crystal structures of a natural DNA polymerase that functions as an XNA reverse transcriptase. Nucleic Acids Res 2020; 47:6973-6983. [PMID: 31170294 PMCID: PMC6649750 DOI: 10.1093/nar/gkz513] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/24/2019] [Accepted: 06/03/2019] [Indexed: 01/05/2023] Open
Abstract
Replicative DNA polymerases are highly efficient enzymes that maintain stringent geometric control over shape and orientation of the template and incoming nucleoside triphosphate. In a surprising twist to this paradigm, a naturally occurring bacterial DNA polymerase I member isolated from Geobacillus stearothermophilus (Bst) exhibits an innate ability to reverse transcribe RNA and other synthetic congeners (XNAs) into DNA. This observation raises the interesting question of how a replicative DNA polymerase is able to recognize templates of diverse chemical composition. Here, we present crystal structures of natural Bst DNA polymerase that capture the post-translocated product of DNA synthesis on templates composed entirely of 2′-deoxy-2′-fluoro-β-d-arabino nucleic acid (FANA) and α-l-threofuranosyl nucleic acid (TNA). Analysis of the enzyme active site reveals the importance of structural plasticity as a possible mechanism for XNA-dependent DNA synthesis and provides insights into the construction of variants with improved activity.
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Affiliation(s)
- Lynnette N Jackson
- Departments of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
| | - Nicholas Chim
- Departments of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
| | - Changhua Shi
- Departments of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA
| | - John C Chaput
- Departments of Pharmaceutical Sciences, University of California, Irvine, CA 92697-3958, USA.,Department of Chemistry, University of California, Irvine, CA 92697-3958, USA.,Department of Molecular Biology and Biochemistry, University of California, CA 92697-3958, USA
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10
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Screening substrate-binding positions by rolling circle amplification suggesting a binding model of Nt.BstNBI. Biochem J 2019; 476:1483-1496. [PMID: 31064800 DOI: 10.1042/bcj20190167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 04/29/2019] [Accepted: 05/04/2019] [Indexed: 02/05/2023]
Abstract
Nicking endonucleases (NEs) become increasingly attractive for their promising applications in isothermal amplification. Unfortunately, in comparison with their applications, their catalytic mechanism studies have relatively lagged behind due to a paucity of crystal structure information. Nt.BstNBI is one of those widely used NEs. However, many aspects of its catalytic mechanism still remained to be explored. Herein, we employed only rolling circle amplification (RCA) assay as a major analytic tool and succeeded in identifying the potential binding positions and regions of the DNA substrate based on locked nucleic acid modification, DNA duplex length of substrate, and substrate mismatch designs. Based on these data, we, for the first time, revealed that Nt.BstNBI was likely to recognize six adjacent positions of the recognition sequence (G1rt, A2rt, G3rt, A2rb, C3rb, and T4rb) in the major groove and hold three positions of the cleavage sequence (N3ct, N4ct, and N7cb) in the minor groove of DNA duplex for nicking. Moreover, this work also demonstrated the unexpected efficiency of RCA to study the macromolecular interaction for certain kind of nucleases in an easy and high-throughput way.
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11
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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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12
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Abstract
Aptamers are now used ubiquitously as binding agents for a broad range of applications. Natural (unmodified) DNA and RNA aptamers have considerably less chemical diversity than protein-based ligands such as antibodies, limiting their utility. Aptamers possessing a single chemical modification have helped bridge this diversity gap. We report the selection and identification of aptamers with two diversity-enhancing chemical modifications that bind and inhibit proprotein convertase subtilisin/kexin type 9 (PCSK9), a representative human therapeutic protein target. The addition of a second modification, especially in certain pairwise combinations, resulted in significant improvements in affinity, ligand efficiency, epitope coverage, metabolic stability, and inhibitory activity. Extensively chemically functionalized aptamers have the potential to become the next generation of nucleic-acid–based ligands. The nucleobases comprising DNA and RNA aptamers provide considerably less chemical diversity than protein-based ligands, limiting their versatility. The introduction of novel functional groups at just one of the four bases in modified aptamers has recently led to dramatic improvement in the success rate of identifying nucleic acid ligands to protein targets. Here we explore the benefits of additional enhancement in physicochemical diversity by selecting modified DNA aptamers that contain amino-acid–like modifications on both pyrimidine bases. Using proprotein convertase subtilisin/kexin type 9 as a representative protein target, we identify specific pairwise combinations of modifications that result in higher affinity, metabolic stability, and inhibitory potency compared with aptamers with single modifications. Such doubly modified aptamers are also more likely to be encoded in shorter sequences and occupy nonoverlapping epitopes more frequently than aptamers with single modifications. These highly modified DNA aptamers have broad utility in research, diagnostic, and therapeutic applications.
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13
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Maio G, Enweronye O, Zumrut HE, Batool S, Van N, Mallikaratchy P. Systematic optimization and modification of a DNA aptamer with 2'-O-methyl RNA analogues. ChemistrySelect 2017; 2:2335-2340. [PMID: 29226219 DOI: 10.1002/slct.201700359] [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] [Indexed: 01/21/2023]
Abstract
Nucleic acid aptamers (NAAs) are short synthetic DNA or RNA molecules that specifically fold into distinct three-dimensional structures able to specifically recognize a target. While NAAs show unprecedented promise in a variety of applications, including sensing, therapeutics and diagnostics, one major limitation involves the lack of stability towards omnipresent nucleases. Therefore, we herein report a systematic truncation and incorporation of 2'-O-methyl bases to a DNA aptamer, which results in increased stability without affecting affinity. One of the newly designed analogues is stable up to 24 hours, demonstrating that 2'-O-methyl RNA is an attractive modification to DNA aptamers, especially when therapeutic applications are intended.
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Affiliation(s)
- George Maio
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468
| | - Osita Enweronye
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468
| | - Hasan E Zumrut
- Ph.D. Program in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
| | - Sana Batool
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468
| | - Nabeela Van
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468
| | - Prabodhika Mallikaratchy
- Department of Chemistry, Lehman College for The City University of New York, 250 Beford Park Blvd West, Bronx, New York, NY 10468.,Ph.D. Program in Chemistry and Biochemistry, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA.,Ph.D. Program in Molecular, Cellular and Developmental Biology, CUNY Graduate Center, 365 Fifth Avenue, New York, NY 10016, USA
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14
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Lipi F, Chen S, Chakravarthy M, Rakesh S, Veedu RN. In vitro evolution of chemically-modified nucleic acid aptamers: Pros and cons, and comprehensive selection strategies. RNA Biol 2016; 13:1232-1245. [PMID: 27715478 PMCID: PMC5207382 DOI: 10.1080/15476286.2016.1236173] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Nucleic acid aptamers are single-stranded DNA or RNA oligonucleotide sequences that bind to a specific target molecule with high affinity and specificity through their ability to adopt 3-dimensional structure in solution. Aptamers have huge potential as targeted therapeutics, diagnostics, delivery agents and as biosensors. However, aptamers composed of natural nucleotide monomers are quickly degraded in vivo and show poor pharmacodynamic properties. To overcome this, chemically-modified nucleic acid aptamers are developed by incorporating modified nucleotides after or during the selection process by Systematic Evolution of Ligands by EXponential enrichment (SELEX). This review will discuss the development of chemically-modified aptamers and provide the pros and cons, and new insights on in vitro aptamer selection strategies by using chemically-modified nucleic acid libraries.
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Affiliation(s)
- Farhana Lipi
- a Western Australian Neuroscience Research Institute , Perth , Australia
| | - Suxiang Chen
- a Western Australian Neuroscience Research Institute , Perth , Australia.,b Centre for Comparative Genomics, Murdoch University , Perth , Australia
| | - Madhuri Chakravarthy
- a Western Australian Neuroscience Research Institute , Perth , Australia.,b Centre for Comparative Genomics, Murdoch University , Perth , Australia
| | - Shilpa Rakesh
- a Western Australian Neuroscience Research Institute , Perth , Australia
| | - Rakesh N Veedu
- a Western Australian Neuroscience Research Institute , Perth , Australia.,b Centre for Comparative Genomics, Murdoch University , Perth , Australia
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15
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Chumakov AM, Yuhina ES, Frolova EI, Kravchenko JE, Chumakov SP. Expanding the application potential of DNA aptamers by their functionalization. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2016. [DOI: 10.1134/s1068162016010027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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16
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Aaldering LJ, Tayeb H, Krishnan S, Fletcher S, Wilton SD, Veedu RN. Smart functional nucleic acid chimeras: enabling tissue specific RNA targeting therapy. RNA Biol 2016; 12:412-25. [PMID: 25849197 PMCID: PMC4615226 DOI: 10.1080/15476286.2015.1017234] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
A major obstacle for effective utilization of therapeutic oligonucleotides such as siRNA, antisense, antimiRs etc. is to deliver them specifically to the target tissues. Toward this goal, nucleic acid aptamers are re-emerging as a prominent class of biomolecules capable of delivering target specific therapy and therapeutic monitoring by various molecular imaging modalities. This class of short oligonucleotide ligands with high affinity and specificity are selected from a large nucleic acid pool against a molecular target of choice. Poor cellular uptake of therapeutic oligonucleotides impedes gene-targeting efficacy in vitro and in vivo. In contrast, aptamer-oligonucleotide chimeras have shown the capacity to deliver siRNA, antimiRs, small molecule drugs etc. toward various targets and showed very promising results in various studies on different diseases models. However, to further improve the bio-stability of such chimeric conjugates, it is important to introduce chemically-modified nucleic acid analogs. In this review, we highlight the applications of nucleic acid aptamers for target specific delivery of therapeutic oligonucleotides.
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Affiliation(s)
- Lukas J Aaldering
- a Nucleic Acid Center; Department of Physics, Chemistry and Pharmacy ; University of Southern Denmark ; Odense , Denmark
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Generation of Aptamers with an Expanded Chemical Repertoire. Molecules 2015; 20:16643-71. [PMID: 26389865 PMCID: PMC6332006 DOI: 10.3390/molecules200916643] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 08/28/2015] [Accepted: 09/01/2015] [Indexed: 01/03/2023] Open
Abstract
The enzymatic co-polymerization of modified nucleoside triphosphates (dN*TPs and N*TPs) is a versatile method for the expansion and exploration of expanded chemical space in SELEX and related combinatorial methods of in vitro selection. This strategy can be exploited to generate aptamers with improved or hitherto unknown properties. In this review, we discuss the nature of the functionalities appended to nucleoside triphosphates and their impact on selection experiments. The properties of the resulting modified aptamers will be described, particularly those integrated in the fields of biomolecular diagnostics, therapeutics, and in the expansion of genetic systems (XNAs).
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18
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Edwards SL, Poongavanam V, Kanwar JR, Roy K, Hillman KM, Prasad N, Leth-Larsen R, Petersen M, Marušič M, Plavec J, Wengel J, Veedu RN. Targeting VEGF with LNA-stabilized G-rich oligonucleotide for efficient breast cancer inhibition. Chem Commun (Camb) 2015; 51:9499-502. [PMID: 25968110 DOI: 10.1039/c5cc02756j] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this study, we investigated the efficacy of an LNA (locked nucleic acid)-modified DNA aptamer named RNV66 targeting VEGF against various breast cancer cell lines. Our results demonstrate that RNV66 efficiently inhibits breast cancer cell proliferation both in vitro and in vivo. Introduction of LNA nucleotides were crucial for higher efficacy. Furthermore, the binding interaction of RNV66 with VEGF was investigated using molecular dynamic simulations leading to the first computational model of the LNA aptamer-VEGF complex blocking its interaction with VEGF-receptor.
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Affiliation(s)
- Stacey L Edwards
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, 4072, Australia
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19
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Kokil GR, Veedu RN, Ramm GA, Prins JB, Parekh HS. Type 2 diabetes mellitus: limitations of conventional therapies and intervention with nucleic acid-based therapeutics. Chem Rev 2015; 115:4719-43. [PMID: 25918949 DOI: 10.1021/cr5002832] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ganesh R Kokil
- †School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Brisbane, QLD 4102, Australia
| | - Rakesh N Veedu
- §Center for Comparative Genomics, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia.,∥Western Australian Neuroscience Research Institute, Perth, WA 6150, Australia.,‡School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane QLD 4072 Australia
| | - Grant A Ramm
- ⊥The Hepatic Fibrosis Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia.,#Faculty of Medicine and Biomedical Sciences, The University of Queensland, Brisbane, QLD 4006, Australia
| | - Johannes B Prins
- ∇Mater Research Institute, The University of Queensland, Brisbane, QLD 4101, Australia
| | - Harendra S Parekh
- †School of Pharmacy, Pharmacy Australia Centre of Excellence, The University of Queensland, Brisbane, QLD 4102, Australia
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20
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Barman J. Targeting cancer cells using aptamers: cell-SELEX approach and recent advancements. RSC Adv 2015. [DOI: 10.1039/c4ra12407c] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aptamers are short single stranded nucleic acid based therapeutic and diagnostic molecules which can be isolated from a random pool of oligonucleotides by Systematic Evolution of Ligands by EXponential Enrichment (SELEX).
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Affiliation(s)
- Jharna Barman
- Agricultural and Ecological Research Unit
- Biological Science Division
- Indian Statistical Institute
- Kolkata
- India
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21
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New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization. MOLECULAR THERAPY. NUCLEIC ACIDS 2014; 3:e183. [PMID: 25093707 PMCID: PMC4221594 DOI: 10.1038/mtna.2014.34] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 06/10/2014] [Indexed: 12/24/2022]
Abstract
Single-stranded oligonucleotide aptamers have attracted great attention in the past decade because of their diagnostic and therapeutic potential. These versatile, high affinity and specificity reagents are selected by an iterative in vitro process called SELEX, Systematic Evolution of Ligands by Exponential Enrichment. Numerous SELEX methods have been developed for aptamer selections; some that are simple and straightforward, and some that are specialized and complicated. The method of SELEX is crucial for selection of an aptamer with desired properties; however, success also depends on the starting aptamer library, the target molecule, aptamer enrichment monitoring assays, and finally, the analysis and characterization of selected aptamers. Here, we summarize key recent developments in aptamer selection methods, as well as other aspects of aptamer selection that have significant impact on the outcome. We discuss potential pitfalls and limitations in the selection process with an eye to aid researchers in the choice of a proper SELEX strategy, and we highlight areas where further developments and improvements are desired. We believe carefully designed multiplexed selection methods, when complemented with high-throughput downstream analysis and characterization assays, will yield numerous high-affinity aptamers to protein and small molecule targets, and thereby generate a vast array of reagents for probing basic biological mechanisms and implementing new diagnostic and therapeutic applications in the near future.
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22
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Deng YB, Nong LG, Liang ZR, Zhang L, Qin YH, He P. Hepatitis C virus gene-specific locked nucleic acid enzyme significantly inhibits C gene expression in vitro. Shijie Huaren Xiaohua Zazhi 2014; 22:1992-1997. [DOI: 10.11569/wcjd.v22.i14.1992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the inhibitory effects of locked nucleic acid enzyme targeting the hepatitis C virus (HCV) C gene on HCV RNA replication and expression in HepG2.9706 cells.
METHODS: The sequences encoding DNAzyme, thiolmodificated DNAzyme and LNAzyme targeting the HCV C gene were designed and synthesized. The following experimental groups were set up: lipo-DNAzyme, lipo-S-DNAzyme, lipo-LNAzyme, blank control, empty liposomes, and lipo-random-LNAzyme. Transfection was performed using cationic liposomes. The level of HCV RNA and luciferase gene expression in supernatants were tested by real-time fluorescent quantitative PCR and chemiluminescence technique 24, 48 and 96 h after treatment, respectively. Cytotoxicity of LNAzyme was evaluated by MTT assay.
RESULTS: Significant down-regulation of HCV RNA replication and luciferase gene expression was noted in the lipo-LNAzyme group, lipo-DNAzyme group and lipo-S-DNAzyme group compared with the control group (P < 0.05 for all). Relative to the lipo-DNAzyme group and lipo-S-DNAzyme group, the average inhibition rates in the lipo-LNAzyme group were 47.55% and 52.44%, respectively. With the prolongation of the treatment time, the inhibition rate increased. At 96 h, HCR RNA replication and fluorescent protein expression were significantly lower than those before treatment in the lipo-LNAzyme group (P < 0.01 for both), and the average inhibition rates were 79.40% and 84.05%, respectively. No obvious toxicity was observed.
CONCLUSION: LNAzyme has a significant inhibitory effect on HCV C gene replication and expression in vitro, which is stronger than that of the thiolmodificated DNAzyme.
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23
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Kuwahara M, Obika S. In vitro selection of BNA (LNA) aptamers. ARTIFICIAL DNA, PNA & XNA 2014; 4:39-48. [PMID: 24044051 DOI: 10.4161/adna.25786] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/17/2013] [Indexed: 01/03/2023]
Abstract
Recently, we achieved the first in vitro selection of 2'-O,4'-C-methylene bridged/locked nucleic acid (2',4'-BNA/LNA) aptamers. High-affinity thrombin-binding aptamers (TBAs) were obtained from DNA-based libraries containing 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotides (B/L nucleotides) in the 5'-primer region, using the method of capillary electrophoresis systematic evolution of ligands by exponential enrichment (CE-SELEX). Furthermore, a similar selection protocol could provide TBAs that contain B/L nucleotides in both primer and random regions. We review technical challenges involved in the generation of various BNA libraries using analogs of B/L nucleoside-5'-triphosphate and polymerase variants and also discuss applications of these libraries to the selection of BNA (LNA) aptamers, as well as future prospects for their therapeutic and diagnostic uses.
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Affiliation(s)
- Masayasu Kuwahara
- Graduate School of Science and Technology; Gunma University; Gunma, Japan
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24
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Aptamer-based therapeutics of the past, present and future: from the perspective of eye-related diseases. Drug Discov Today 2014; 19:1309-21. [PMID: 24598791 DOI: 10.1016/j.drudis.2014.02.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Revised: 02/04/2014] [Accepted: 02/25/2014] [Indexed: 01/22/2023]
Abstract
Aptamers have emerged as a novel and powerful class of biomolecules with an immense untapped potential. The ability to synthesise highly specific aptamers against any molecular target make them a vital cog in the design of effective therapeutics for the future. However, only a minutia of the enormous potential of this dynamic class of molecule has been exploited. Several aptamers have been studied for the treatment of eye-related disorders, and one such strategy has been successful in therapy. This review gives an account of several eye diseases and their regulatory biomolecules where other nucleic acid therapeutics have been attempted with limited success and how aptamers, with their exceptional flexibility to chemical modifications, can overcome those inherent shortcomings.
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Shigdar S, Macdonald J, O'Connor M, Wang T, Xiang D, Al.Shamaileh H, Qiao L, Wei M, Zhou SF, Zhu Y, Kong L, Bhattacharya S, Li C, Duan W. Aptamers as theranostic agents: modifications, serum stability and functionalisation. SENSORS 2013; 13:13624-37. [PMID: 24152925 PMCID: PMC3859083 DOI: 10.3390/s131013624] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Revised: 09/24/2013] [Accepted: 09/27/2013] [Indexed: 02/07/2023]
Abstract
Aptamers, and the selection process known as Systematic Evolution of Ligands by Exponential Enrichment (SELEX) used to generate them, were first described more than twenty years ago. Since then, there have been numerous modifications to the selection procedures. This review discusses the use of modified bases as a means of enhancing serum stability and producing effective therapeutic tools, as well as functionalising these nucleic acids to be used as potential diagnostic agents.
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Affiliation(s)
- Sarah Shigdar
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
- Authors to whom correspondence should be addressed; E-Mails: (S.S.); (W.D.)
| | - Joanna Macdonald
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
| | - Michael O'Connor
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
| | - Tao Wang
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
| | - Dongxi Xiang
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
| | - Hadi Al.Shamaileh
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
| | - Liang Qiao
- Storr Liver Unit, at the Westmead Millennium Institute, The University of Sydney at the Westmead Hospital, Westmead NSW 2145, Australia; E-Mail:
| | - Ming Wei
- School of Medical Science and Griffith Health Institute, Griffith University, Gold Coast Campus, Southport 4222, Australia; E-Mail:
| | - Shu-Feng Zhou
- Department of Pharmaceutical Sciences, College of Pharmacy, University of South Florida, Tampa, FL 33612, USA; E-Mail:
| | - Yimin Zhu
- Suzhou Key Laboratory of Nanobiomedicine, Division of Nanobiomedicine, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, Jiangsu 215123, China; E-Mail:
| | - Lingxue Kong
- Institute for Frontier Materials, Deakin University, Waurn Ponds, Victoria 3217, Australia; E-Mail:
| | - Santanu Bhattacharya
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560 012, India; E-Mail:
| | - ChunGuang Li
- Centre for Complimentary Medicine Research, National Institute of Complementary Medicine, University of Western Sydney, Campbelltown Campus, Penrith, NSW 2751, Australia; E-Mail:
| | - Wei Duan
- School of Medicine, Deakin University, Pigdons Road, Waurn Ponds, Victoria 3217, Australia; E-Mails: (J.M.); (M.O.); (T.W.); (D.X.); (H.A.)
- Authors to whom correspondence should be addressed; E-Mails: (S.S.); (W.D.)
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26
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Affiliation(s)
- Kasper K Karlsen
- Nucleic Acid Center, Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark, Odense M, Denmark
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27
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Kasahara Y, Irisawa Y, Fujita H, Yahara A, Ozaki H, Obika S, Kuwahara M. Capillary electrophoresis-systematic evolution of ligands by exponential enrichment selection of base- and sugar-modified DNA aptamers: target binding dominated by 2'-O,4'-C-methylene-bridged/locked nucleic acid primer. Anal Chem 2013; 85:4961-7. [PMID: 23662585 DOI: 10.1021/ac400058z] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chemically modified DNA aptamers specific to human α-thrombin were obtained from oligodeoxyribonucleotide (ODN) libraries by using a capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX) method. These libraries contained 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotides (B/L nucleotides) in the primer region and/or C5-modified thymidine bearing N(6)-ethyladenine (t) in the nonprimer region. Modified DNA aptamers showed high binding affinities to the target, with dissociation constants (Kd) values in the range of subnanomolar to several ten nanomolar levels. The introduction of base modification significantly suppressed the frequency of G-quadruplex motifs, which are often seen in thrombin-binding DNA aptamers. The resulting alternatives contained the 10-mer consensus sequence t5Gt2G2, which is frequently found in modified DNA aptamers with subnanomolar protein binding affinities. Furthermore, some base- and sugar-modified DNA aptamers with the 12-mer consensus sequence t2G2tC(A/G)A2G2t displayed binding activities that were dependent on the presence of B/L nucleotides in the primer region. Such aptamers were interestingly not recovered from a natural DNA library or from DNA libraries modified with either B/L nucleotides or t's. This emerging characteristic binding property will enable the creation of a direct selection methodology for DNA-based molecular switches that are triggered by chemical conversion of B/L nucleotides introduced to constant sequence regions in ODN libraries.
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Affiliation(s)
- Yuuya Kasahara
- Graduate School of Science and Technology, Gunma University, Kiryu, Gunma, Japan
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28
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Lundin KE, Højland T, Hansen BR, Persson R, Bramsen JB, Kjems J, Koch T, Wengel J, Smith CIE. Biological activity and biotechnological aspects of locked nucleic acids. ADVANCES IN GENETICS 2013; 82:47-107. [PMID: 23721720 DOI: 10.1016/b978-0-12-407676-1.00002-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Locked nucleic acid (LNA) is one of the most promising new nucleic acid analogues that has been produced under the past two decades. In this chapter, we have tried to cover many of the different areas, where this molecule has been used to improve the function of synthetic oligonucleotides (ONs). The use of LNA in antisense ONs, including gapmers, splice-switching ONs, and siLNA, as well as antigene ONs, is reviewed. Pharmacokinetics as well as pharmacodynamics of LNA ONs and a description of selected compounds in, or close to, clinical testing are described. In addition, new LNA modifications and the adaptation of enzymes for LNA incorporation are reviewed. Such enzymes may become important for the development of stabilized LNA-containing aptamers.
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Affiliation(s)
- Karin E Lundin
- Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Novum, Huddinge, Stockholm, Sweden.
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Deng YB, Wen WR. Antiviral effects of locked nucleic acid antisense oligonucleotides targeting the HBV preS1 gene in HepG2 2.2.15 cells. Shijie Huaren Xiaohua Zazhi 2012; 20:2024-2029. [DOI: 10.11569/wcjd.v20.i22.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To investigate the inhibitory effects of locked nucleic acid (LNA) antisense oligonucleotides targeting the purine region of the hepatitis B virus (HBV) preS1 gene in HepG2 2.2.15 cells, and to screen effective LNA anti-gene oligonucleotides.
METHODS: LNA anti-gene oligonucleotides of different lengths that were complementary to the purine-abundant regions (2 941-2 962 nt, 3 015-3 036 nt and 3 089-3 110 nt) of the HBV preS1 gene were designed, synthesized, and introduced into HepG2 2.2.15 cells by cationic liposome-mediated transfection. Hepatitis B surface antigen (HBsAg) and HBV DNA levels in cell supernatants were tested by time-resolved fluorescence immune assay (TRFIA) and fluorescent quantitative polymerase chain reaction (FQ-PCR) 1, 3, 5 and 7 d after transfection. The cell toxicity of LNA anti-gene oligonucleotides was detected by methyl thiazolyl tetrazolium (MTT) assay.
RESULTS: LNA anti-gene oligonucleotides targeting the HBV preS1 gene showed strong inhibitory effects on HBV DNA replication and HBsAg expression in vitro, and the effects were time-dependent. Seven days after transfection, the reduced rates of HBV DNA and HBsAg levels were 64.32% and 67.51%, respectively. The inhibitory effects were significantly different between each experimental group and control group (all P < 0.05). The inhibitory effect of the LNA anti-gene oligonucleotide targeting the region 2 941-2 962 nt was most strong. The optimal length of LNA anti-gene oligonucleotides ranges from 20 to 30 bases. No obvious cell toxicity was observed with LNA anti-gene oligonucleotides.
CONCLUSION: LNA anti-gene oligonucleotides targeting the HBV preS1 gene showed strong inhibitory effects on HBV replication in vitro. The inhibitory effect of the LNA anti-gene oligonucleotide targeting the region 2 941-2 962 nt was most strong, and the optimal length of LNA anti-gene oligonucleotides ranges from 20 to 30 bases.
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