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Kumar S, Mohan A, Sharma NR, Kumar A, Girdhar M, Malik T, Verma AK. Computational Frontiers in Aptamer-Based Nanomedicine for Precision Therapeutics: A Comprehensive Review. ACS OMEGA 2024; 9:26838-26862. [PMID: 38947800 PMCID: PMC11209897 DOI: 10.1021/acsomega.4c02466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/09/2024] [Accepted: 05/28/2024] [Indexed: 07/02/2024]
Abstract
In the rapidly evolving landscape of nanomedicine, aptamers have emerged as powerful molecular tools, demonstrating immense potential in targeted therapeutics, diagnostics, and drug delivery systems. This paper explores the computational features of aptamers in nanomedicine, highlighting their advantages over antibodies, including selectivity, low immunogenicity, and a simple production process. A comprehensive overview of the aptamer development process, specifically the Systematic Evolution of Ligands by Exponential Enrichment (SELEX) process, sheds light on the intricate methodologies behind aptamer selection. The historical evolution of aptamers and their diverse applications in nanomedicine are discussed, emphasizing their pivotal role in targeted drug delivery, precision medicine and therapeutics. Furthermore, we explore the integration of artificial intelligence (AI), machine learning (ML), Internet of Things (IoT), Internet of Medical Things (IoMT), and nanotechnology in aptameric development, illustrating how these cutting-edge technologies are revolutionizing the selection and optimization of aptamers for tailored biomedical applications. This paper also discusses challenges in computational methods for advancing aptamers, including reliable prediction models, extensive data analysis, and multiomics data incorporation. It also addresses ethical concerns and restrictions related to AI and IoT use in aptamer research. The paper examines progress in computer simulations for nanomedicine. By elucidating the importance of aptamers, understanding their superiority over antibodies, and exploring the historical context and challenges, this review serves as a valuable resource for researchers and practitioners aiming to harness the full potential of aptamers in the rapidly evolving field of nanomedicine.
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Affiliation(s)
- Shubham Kumar
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
| | - Anand Mohan
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
| | - Neeta Raj Sharma
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
| | - Anil Kumar
- Gene
Regulation Laboratory, National Institute
of Immunology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Madhuri Girdhar
- Division
of Research and Development, Lovely Professional
University, Phagwara 144401, Punjab, India
| | - Tabarak Malik
- Department
of Biomedical Sciences, Institute of Health, Jimma University, MVJ4+R95 Jimma, Ethiopia
| | - Awadhesh Kumar Verma
- School
of Bioengineering and Biosciences, Lovely
Professional University, Phagwara, Punjab 144001, India
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2
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Wang B, Pan X, Teng IT, Li X, Kobeissy F, Wu ZY, Zhu J, Cai G, Yan H, Yan X, Liang M, Yu F, Lu J, Yang Z, Biondi E, Haskins W, Cao YC, Benner SA, Tan W, Wang KK. Functional Selection of Tau Oligomerization-Inhibiting Aptamers. Angew Chem Int Ed Engl 2024; 63:e202402007. [PMID: 38407551 DOI: 10.1002/anie.202402007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/19/2024] [Accepted: 02/21/2024] [Indexed: 02/27/2024]
Abstract
Pathological hyperphosphorylation and aggregation of microtubule-associated Tau protein contribute to Alzheimer's Disease (AD) and other related tauopathies. Currently, no cure exists for Alzheimer's Disease. Aptamers offer significant potential as next-generation therapeutics in biotechnology and the treatment of neurological disorders. Traditional aptamer selection methods for Tau protein focus on binding affinity rather than interference with pathological Tau. In this study, we developed a new selection strategy to enrich DNA aptamers that bind to surviving monomeric Tau protein under conditions that would typically promote Tau aggregation. Employing this approach, we identified a set of aptamer candidates. Notably, BW1c demonstrates a high binding affinity (Kd=6.6 nM) to Tau protein and effectively inhibits arachidonic acid (AA)-induced Tau protein oligomerization and aggregation. Additionally, it inhibits GSK3β-mediated Tau hyperphosphorylation in cell-free systems and okadaic acid-mediated Tau hyperphosphorylation in cellular milieu. Lastly, retro-orbital injection of BW1c tau aptamer shows the ability to cross the blood brain barrier and gain access to neuronal cell body. Through further refinement and development, these Tau aptamers may pave the way for a first-in-class neurotherapeutic to mitigate tauopathy-associated neurodegenerative disorders.
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Affiliation(s)
- Bang Wang
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 7, Alachua, FL 32615, USA
| | - Xiaoshu Pan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - I-Ting Teng
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - Xiaowei Li
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - Firas Kobeissy
- Center for Neurotrauma, Multiomics & Biomarkers, Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, 720 Westview Dr. SW, Atlanta, GA 30310-1458, (USA). Department of Emergency Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Zo-Yu Wu
- Center for Neurotrauma, Multiomics & Biomarkers, Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, 720 Westview Dr. SW, Atlanta, GA 30310-1458, (USA). Department of Emergency Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Jiepei Zhu
- Center for Neurotrauma, Multiomics & Biomarkers, Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, 720 Westview Dr. SW, Atlanta, GA 30310-1458, (USA). Department of Emergency Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - Guangzheng Cai
- Center for Neurotrauma, Multiomics & Biomarkers, Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, 720 Westview Dr. SW, Atlanta, GA 30310-1458, (USA). Department of Emergency Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
| | - He Yan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - Xin Yan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - Mingwei Liang
- Department of Biochemistry and Molecular Biology, UF Health Cancer Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Fahong Yu
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - Jianrong Lu
- Department of Biochemistry and Molecular Biology, UF Health Cancer Center, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Zunyi Yang
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 7, Alachua, FL 32615, USA
| | - Elisa Biondi
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 7, Alachua, FL 32615, USA
| | - William Haskins
- Gryphon Bio, Inc., 611 Gateway Blvd. Suite 120 #253, South San Francisco, CA 94080-7066, USA
| | - Y Charles Cao
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
| | - Steven A Benner
- Foundation for Applied Molecular Evolution, Firebird Biomolecular Sciences LLC, 13709 Progress Boulevard, No. 7, Alachua, FL 32615, USA
| | - Weihong Tan
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at Bio/Nano Interface, Health Cancer Center, UF Genetics Institute and McKnight Brain Institute, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL 32611, USA
- Molecular Science and Biomedicine Laboratory (MBL), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Aptamer Engineering Center of Hunan Province, Hunan University, Changsha, Hunan, 410082, China
- Zhejiang Cancer Hospital, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Kevin K Wang
- Center for Neurotrauma, Multiomics & Biomarkers, Department of Neurobiology, Neuroscience Institute, Morehouse School of Medicine, 720 Westview Dr. SW, Atlanta, GA 30310-1458, (USA). Department of Emergency Medicine, McKnight Brain Institute, University of Florida, Gainesville, FL 32611, USA
- Gryphon Bio, Inc., 611 Gateway Blvd. Suite 120 #253, South San Francisco, CA 94080-7066, USA
- Brain Rehabilitation Research Center, Malcom Randall VA Medical Center, North Florida/South Georgia Veterans Health System, Gainesville, FL 32608, USA
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Yu Y, Gu Z, Li M, Pu Y, Geballa Koukoula A, Peters J, Yang Y, Hong X. Cytosine-rich mismatched DNA aptamer combined with superparamagnetic photonic crystal sensing material for the specific visual detection of silver ions. Talanta 2024; 270:125551. [PMID: 38103284 DOI: 10.1016/j.talanta.2023.125551] [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: 07/27/2023] [Revised: 12/07/2023] [Accepted: 12/11/2023] [Indexed: 12/19/2023]
Abstract
DNA aptamer superparamagnetic photonic crystals (DSPCs), enriched with a highly selective cytosine-rich mismatched single-stranded DNA aptamer (CRDA), were successfully employed in a novel visual detection strategy for the detection of silver ions (Ag+). The technologies of superparamagnetic colloidal nanospheres (SCNs), DNA aptamer, and photonic crystals were combined to fabricate DPSCs. The aptamer was immobilized via electrostatic adsorption with amino groups that were chemically introduced on the surface of the SCNs, forming D-NH-SCNs. The detection is achieved by forming an Ag+ complex (C-Ag+-C) between Ag+ and D-NH-SCN. The DSPCs assembled under a magnetic field by D-NH-SCNs effectively detected Ag+ in the range of 1 μg/L to 5 mg/L, corresponding to the critical concentration range for heavy metals in drinking water. During the detection, the DSPC exhibited a wavelength blueshift from 652.8 nm to 626.4 nm (26.4 nm), as well as changes in reflection intensity. Notably, when detecting Ag+, a change in DSPC color from orange to yellow was observed. In summary, the developed visual detection material facilitates direct Ag + sensing. In the future, different DNA aptamers will be modified further to detect various targets in the fields of medicine, environmental monitoring, and food safety.
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Affiliation(s)
- Ying Yu
- College of Vocational Education, Yunnan Normal University, Kunming, 650092, China
| | - Zhijia Gu
- Key Laboratory for Plant Biodiversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Maokang Li
- College of Vocational Education, Yunnan Normal University, Kunming, 650092, China
| | - Yongfu Pu
- College of Vocational Education, Yunnan Normal University, Kunming, 650092, China
| | - Ariadni Geballa Koukoula
- Wageningen Food Safety Research (WFSR), Wageningen University & Research, Wageningen, 6708WB, Netherlands
| | - Jeroen Peters
- Wageningen Food Safety Research (WFSR), Wageningen University & Research, Wageningen, 6708WB, Netherlands
| | - Ying Yang
- College of Vocational Education, Yunnan Normal University, Kunming, 650092, China
| | - Xiaodi Hong
- Department of Cellular Biophysics, Max Planck Institute for Medical Research, Heidelberg, 69120, Germany; College of Vocational Education, Yunnan Normal University, Kunming, 650092, China.
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Park KS, Park TI, Lee JE, Hwang SY, Choi A, Pack SP. Aptamers and Nanobodies as New Bioprobes for SARS-CoV-2 Diagnostic and Therapeutic System Applications. BIOSENSORS 2024; 14:146. [PMID: 38534253 DOI: 10.3390/bios14030146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 03/10/2024] [Accepted: 03/12/2024] [Indexed: 03/28/2024]
Abstract
The global challenges posed by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic have underscored the critical importance of innovative and efficient control systems for addressing future pandemics. The most effective way to control the pandemic is to rapidly suppress the spread of the virus through early detection using a rapid, accurate, and easy-to-use diagnostic platform. In biosensors that use bioprobes, the binding affinity of molecular recognition elements (MREs) is the primary factor determining the dynamic range of the sensing platform. Furthermore, the sensitivity relies mainly on bioprobe quality with sufficient functionality. This comprehensive review investigates aptamers and nanobodies recently developed as advanced MREs for SARS-CoV-2 diagnostic and therapeutic applications. These bioprobes might be integrated into organic bioelectronic materials and devices, with promising enhanced sensitivity and specificity. This review offers valuable insights into advancing biosensing technologies for infectious disease diagnosis and treatment using aptamers and nanobodies as new bioprobes.
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Affiliation(s)
- Ki Sung Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Tae-In Park
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Jae Eon Lee
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seo-Yeong Hwang
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Anna Choi
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
| | - Seung Pil Pack
- Department of Biotechnology and Bioinformatics, Korea University, Sejong 30019, Republic of Korea
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5
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Du Y, Deng T, Cheng Y, Zhao Q, Xia H, Ji Y, Zhang Y, He Q. Enhancing Bone Regeneration through CDC20-Loaded ZIF-8 Nanoparticles Wrapped in Erythrocyte Membranes with Targeting Aptamer. Adv Healthc Mater 2024; 13:e2302725. [PMID: 38030141 DOI: 10.1002/adhm.202302725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 11/15/2023] [Indexed: 12/01/2023]
Abstract
In the context of bone regeneration, nanoparticles harboring osteogenic factors have emerged as pivotal agents for modulating the differentiation fate of stem cells. However, persistent challenges surrounding biocompatibility, loading efficiency, and precise targeting ability warrant innovative solution. In this study, a novel nanoparticle platform founded upon the zeolitic imidazolate framework-8 (ZIF-8) is introduced. This new design, CDC20@ZIF-8@eM-Apt, involves the envelopment of ZIF-8 within an erythrocyte membrane (eM) cloak, and is coupled with a targeting aptamer. ZIF-8, distinguished by its porosity, biocompatibility, and robust cargo transport capabilities, constitutes the core framework. Cell division cycle protein 20 homolog (CDC20) is illuminated as a new target in bone regeneration. The eM plays a dual role in maintaining nanoparticle stability and facilitating fusion with target cell membranes, while the aptamer orchestrates the specific recruitment of bone marrow mesenchymal stem cells (BMSCs) within bone defect sites. Significantly, CDC20@ZIF-8@eM-Apt amplifies osteogenic differentiation of BMSCs via the inhibition of NF-κB p65, and concurrently catalyzes bone regeneration in two bone defect models. Consequently, CDC20@ZIF-8@eM-Apt introduces a pioneering strategy for tackling bone defects and associated maladies, opening novel avenues in therapeutic intervention.
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Affiliation(s)
- Yangge Du
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Tian Deng
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Yihong Cheng
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Qin Zhao
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Haibin Xia
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Yaoting Ji
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Yufeng Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
| | - Qing He
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Taikang Center for Life and Medical Sciences, Wuhan University, Wuhan, 430079, China
- Medical Research Institute, School of Medicine, Wuhan University, Wuhan, 430071, China
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Chen C, Song X, Yu Y, Wang X, Xu H, Ji W, Ma J, Zhao C, Feng S, Wang Y, Su XD, Wang W. Aptamer-based nanointerferometer enables amplification-free ultrasensitive detection and differentiation of SARS-CoV-2 variants. Anal Chim Acta 2023; 1260:341207. [PMID: 37121656 PMCID: PMC10085716 DOI: 10.1016/j.aca.2023.341207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 03/07/2023] [Accepted: 04/10/2023] [Indexed: 05/02/2023]
Abstract
The state-of-the-art SARS-CoV-2 detection methods include qRT-PCR and antibody-based lateral flow assay (LFA) point-of-care tests. Despite the high sensitivity and selectivity, qRT-PCR is slow, expensive and needs well-trained operators. On the other extreme, LFA suffers from low sensitivity albeit its fast detection speed, low detection cost and ease of use. Therefore, the continuing COVID-19 pandemic calls for a SARS-CoV-2 detection method that is rapid, convenient and cost-effective without compromise in sensitivity. Here we provide a proof-of-principle demonstration of an optimized aptamer-based nanointerferometer that enables rapid and amplification-free detection of SARS-CoV-2 spike protein-coated pseudovirus directly from human saliva with the limit of detection (LOD) of about 400 copies per mL. This LOD is on par with that of qRT-PCR, making it 1000 to 100,000-fold more sensitive than commercial LFA tests. Using various combinations of negative selections during the screens for the aptamer targeting the receptor binding domain of the spike protein of SARS-CoV-2, we isolated two aptamers that can distinguish the Omicron and Delta variants. Integrating these two aptamers with LFA strips or the nanointerferometer sensors allows both detection and differentiation of the Omicron and Delta variants which has the potential to realize rapid triage of patients infected different SARS-CoV-2 variants.
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Affiliation(s)
- Changtian Chen
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China; Center for Life Sciences, Beijing, 100871, China
| | - Xiaohui Song
- State Key Laboratory of Protein and Plant Gene Research, And Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Yuanling Yu
- Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing, China
| | - Xingwei Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Hua Xu
- State Key Laboratory of Protein and Plant Gene Research, And Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China
| | - Weiwei Ji
- College of Physics and Electronic Science, Hubei Normal University, Hubei, 435002, China
| | - Jingchen Ma
- School of Materials and Energy, Guangdong University of Technology, Guangzhou, 510006, China
| | - Chenyan Zhao
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, 102629, China
| | - Silu Feng
- School of Integrated Circuits, Guangdong University of Technology, Guangzhou, 510006, China.
| | - Youchun Wang
- Division of HIV/AIDS and Sex-transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing, 102629, China; Changping Laboratory, Yard 28, Science Park Road, Changping District, Beijing, China.
| | - Xiao-Dong Su
- State Key Laboratory of Protein and Plant Gene Research, And Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing, 100871, China.
| | - Wei Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China; Center for Life Sciences, Beijing, 100871, China.
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Zhu L, Yuhan J, Yu H, Zhang B, Zhu L, He X, Huang K, Xu W. Aptamer functionalized nucleic acid nano drug for targeted synergistic therapy for colon cancer. J Nanobiotechnology 2023; 21:182. [PMID: 37280622 DOI: 10.1186/s12951-023-01941-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Accepted: 05/29/2023] [Indexed: 06/08/2023] Open
Abstract
Due to its complicated pathophysiology, propensity for metastasis, and poor prognosis, colon cancer is challenging to treat and must be managed with a combination of therapy. Using rolling circle transcription (RCT), this work created a nanosponge therapeutic medication system (AS1411@antimiR-21@Dox). Using the AS1411 aptamer, this approach accomplished targeted delivery to cancer cells. Furthermore, analysis of cell viability, cell apoptosis, cell cycle arrest, reactive oxygen species (ROS) content, and mitochondrial membrane potential (MMP) levels revealed that functional nucleic acid nanosponge drug (FND) can kill cancer cells. Moreover, transcriptomics uncovered a putative mechanism for the FND anti-tumor effect. These pathways, which included mitotic metaphase and anaphase as well as the SMAC-mediated dissociation of the IAP: caspase complexes, were principally linked to the cell cycle and cell death. In conclusion, by triggering cell cycle arrest and apoptosis, the nano-synergistic therapeutic system allowed for the intelligent and effective targeted administration of RNA and chemotherapeutic medicines for colon cancer treatment. The system allowed for payload efficiency while being customizable, targeted, reliable, stable, and affordable.
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Affiliation(s)
- Liye Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, No. 17 Qinghua Donglu, Beijing, 100083, China
- College of Veterinary Medicine, China Agricultural University, Beijing, 100094, China
| | - Jieyu Yuhan
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, No. 17 Qinghua Donglu, Beijing, 100083, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Hao Yu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, No. 17 Qinghua Donglu, Beijing, 100083, China
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Boyang Zhang
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, No. 17 Qinghua Donglu, Beijing, 100083, China
| | - Longjiao Zhu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, No. 17 Qinghua Donglu, Beijing, 100083, China
| | - Xiaoyun He
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Kunlun Huang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Wentao Xu
- Food Laboratory of Zhongyuan, Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, No. 17 Qinghua Donglu, Beijing, 100083, China.
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China.
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8
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Chen Z, Deng XH, Jiang C, Wang JS, Li WP, Zhu KL, Li YH, Song B, Zhang ZZ. Repairing Avascular Meniscal Lesions by Recruiting Endogenous Targeted Cells Through Bispecific Synovial-Meniscal Aptamers. Am J Sports Med 2023; 51:1177-1193. [PMID: 36917829 DOI: 10.1177/03635465231159668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
BACKGROUND Tissue engineering is a promising treatment option for meniscal lesions in the avascular area, but a favorable cell source and its utilization in tissue-engineered menisci remain uncertain. Therefore, a more controllable and convenient method for cell recruitment is required. HYPOTHESIS Circular bispecific synovial-meniscal (S-M) aptamers with a gelatin methacryloyl (GelMA) hydrogel can recruit endogenous synovial and meniscal cells to the site of the defect, thereby promoting in situ meniscal regeneration and chondroprotection. STUDY DESIGN Controlled laboratory study. METHODS Synovial and meniscal aptamers were filtered through systematic evolution of ligands by exponential enrichment (SELEX) and cross-linked to synthesize the S-M aptamer. A GelMA-aptamer system was constructed. An in vitro analysis of the bi-recruitment of synovial and meniscal cells was performed, and the migration and proliferation of the GelMA-aptamer hydrogel were also tested. For the in vivo assay, rabbits (n = 90) with meniscal defects in the avascular zone were divided into 3 groups: repair with the GelMA-aptamer hydrogel (GelMA-aptamer group), repair with the GelMA hydrogel (GelMA group), and no repair (blank group). Regeneration of the repaired meniscus and degeneration of the cartilage were assessed by gross and histological evaluations at 4, 8, and 12 weeks postoperatively. The mechanical properties of repaired menisci were also evaluated. RESULTS In vitro synovial and meniscal cells were recruited simultaneously by the S-M aptamer with high affiliation and specificity. The GelMA-aptamer hydrogel promoted the migration of targeted cells. Compared with the other groups, the GelMA-aptamer group showed enhanced fibrocartilaginous regeneration, lower cartilage degeneration, and better mechanical strength at 12 weeks after meniscal repair. CONCLUSION/CLINICAL RELEVANCE Bispecific S-M aptamers could be used for avascular meniscal repair by recruiting endogenous synovial and meniscal cells and promoting fibrocartilaginous regeneration.
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Affiliation(s)
- Zhong Chen
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xing-Hao Deng
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Chuan Jiang
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jing-Song Wang
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Wei-Ping Li
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ke-Long Zhu
- School of Chemistry, Sun Yat-sen University, Guangzhou, China
| | - Yu-Heng Li
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Bin Song
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zheng-Zheng Zhang
- Department of Orthopedics, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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9
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Islam S, Mukherjee C. Molecular regulation of hypoxia through the lenses of noncoding RNAs and epitranscriptome. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1750. [PMID: 35785444 DOI: 10.1002/wrna.1750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 05/27/2022] [Accepted: 06/06/2022] [Indexed: 11/09/2022]
Abstract
Cells maintain homeostasis in response to environmental stress through specific cell stress responses. Hypoxic stress, well known to be associated with diverse solid tumors, is one of the main reasons for cancer-related mortality. Although cells can balance themselves well during hypoxic stress, the underlying molecular mechanisms are not well understood. The enhanced appreciation of diverse roles played by noncoding transcriptome and epigenome in recent years has brought to light the involvement of noncoding RNAs and epigenetic modifiers in hypoxic regulation. The emergence of techniques like deep sequencing has facilitated the identification of large numbers of long noncoding RNAs (lncRNAs) that are differentially regulated in various cancers. Similarly, proteomic studies have identified diverse epigenetic modifiers such as HATs, HDACs, DNMTs, polycomb groups of proteins, and their possible roles in the regulation of hypoxia. The crosstalk between lncRNAs and epigenetic modifiers play a pivotal role in hypoxia-induced cancer initiation and progression. Besides the lncRNAs, several other noncoding RNAs like circular RNAs, miRNAs, and so forth are also expressed during hypoxic conditions. Hypoxia has a profound effect on the expression of noncoding RNAs and epigenetic modifiers. Conversely, noncoding RNAs/epigenetic modifies can regulate the hypoxia signaling axis by modulating the stability of the hypoxia-inducible factors (HIFs). The focus of this review is to illustrate the molecular orchestration underlying hypoxia biology, especially in cancers, which can help in identifying promising therapeutic targets in hypoxia-induced cancers. This article is categorized under: RNA Turnover and Surveillance > Regulation of RNA Stability RNA in Disease and Development > RNA in Disease RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry.
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Affiliation(s)
- Safirul Islam
- Institute of Health Sciences (erstwhile School of Biotechnology), Presidency University, Kolkata, India
| | - Chandrama Mukherjee
- Institute of Health Sciences (erstwhile School of Biotechnology), Presidency University, Kolkata, India
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10
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Yildirim-Tirgil N. Development of aptamer-based ELISA method for d-dimer detection. Biotechnol Appl Biochem 2023; 70:249-256. [PMID: 35426180 DOI: 10.1002/bab.2347] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 03/23/2022] [Indexed: 11/10/2022]
Abstract
This study developed an aptamer-based enzyme-linked immunosorbent assay (ELISA) system for sensitive detection of the d -dimer molecule, which is significantly elevated in several severe diseases. Aptamers are known to have advantages, such as longer stability and usability at different temperatures and in different complex samples, over antibodies, which are generally used in traditional ELISA methods. In the present work, the aptamer-based ELISA system was capable of quantitatively determining in a wide range (100 ng/ml─10 μg/ml) and remain stable for a couple of months even under ordinary room conditions. Validation of the developed system was evaluated by spiked human serum samples with high accuracy. With more comprehensive project steps, the developed aptamer-based ELISA system could be transformed into a platform that offers a sensitive, portable, and easy-to-use tool for analyzing d -dimer molecules.
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Affiliation(s)
- Nimet Yildirim-Tirgil
- Biomedical Engineering Department, Ankara Yildirim Beyazit University, Ankara, Turkey
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11
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Biomimetic functional material-based sensors for food safety analysis: a review. Food Chem 2022; 405:134974. [DOI: 10.1016/j.foodchem.2022.134974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 11/04/2022] [Accepted: 11/13/2022] [Indexed: 11/18/2022]
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12
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Chung S, Singh NK, Gribkoff VK, Hall DA. Electrochemical Carbamazepine Aptasensor for Therapeutic Drug Monitoring at the Point of Care. ACS OMEGA 2022; 7:39097-39106. [PMID: 36340178 PMCID: PMC9631757 DOI: 10.1021/acsomega.2c04865] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/22/2022] [Indexed: 06/02/2023]
Abstract
Monitoring the anti-epileptic drug carbamazepine (CBZ) is crucial for proper dosing, optimizing a patient's clinical outcome, and managing their medication regimen. Due to its narrow therapeutic window and concentration-related toxicity, CBZ is prescribed and monitored in a highly personalized manner. We report an electrochemical conformation-changing aptasensor with two assay formats: a 30 min assay for routine monitoring and a 5 min assay for rapid emergency testing. To enable "sample-to-answer" testing, a de novo CBZ aptamer (K d < 12 nM) with conformational switching due to a G-quadruplex motif was labeled with methylene blue and immobilized on a gold electrode. The electrode fabrication and detection conditions were optimized using electrochemical techniques and visualized by atomic force microscopy (AFM). The aptasensor performance, including reproducibility, stability, and interference, was characterized using electrochemical impedance spectroscopy and voltammetry techniques. The aptasensor exhibited a wide dynamic range in buffer (10 nM to 100 μM) with limits of detection of 1.25 and 1.82 nM for the 5 and 30 min assays, respectively. The clinical applicability is demonstrated by detecting CBZ in finger prick blood samples (<50 μL). The proposed assays provide a promising method to enable point-of-care monitoring for timely personalized CBZ dosing.
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Affiliation(s)
- Saeromi Chung
- Department
of Electrical and Computer Engineering, University of California San Diego, La Jolla, California 92093, United States
| | - Naveen K. Singh
- Department
of Electrical and Computer Engineering, University of California San Diego, La Jolla, California 92093, United States
| | | | - Drew A. Hall
- Department
of Electrical and Computer Engineering, University of California San Diego, La Jolla, California 92093, United States
- Department
of Bioengineering, University of California
San Diego, La Jolla, California 92093, United States
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13
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Takao J, Nagai R, Endo T, Hisamoto H, Sueyoshi K. Aptamer Selection Based on Microscale Electrophoretic Filtration Using a Hydrogel-Plugged Capillary Device. Molecules 2022; 27:molecules27185818. [PMID: 36144553 PMCID: PMC9505737 DOI: 10.3390/molecules27185818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/20/2022] [Accepted: 09/02/2022] [Indexed: 11/16/2022] Open
Abstract
This study reports a novel aptamer selection method based on microscale electrophoretic filtration. Aptamers are versatile materials that recognize specific targets and are attractive for their applications in biosensors, diagnosis, and therapy. However, their practical applications remain scarce due to issues with conventional selection methods, such as complicated operations, low-efficiency separation, and expensive apparatus. To overcome these drawbacks, a selection method based on microscale electrophoretic filtration using a capillary partially filled with hydrogel was developed. The electrophoretic filtration of model target proteins (immunoglobulin E (IgE)) using hydrogel, the electrokinetic injection of DNAs to interact with the trapped proteins, the elimination of DNAs with weak interactions, and the selective acquisition of aptamer candidates with strong interactions were successfully demonstrated, revealing the validity of the proposed concept. Two aptamer candidates for IgE were obtained after three selection cycles, and their affinity for the target was confirmed to be less than 1 nM based on their dissociation constant (KD) values. Therefore, the proposed method allows for the selection of aptamers with simple operations, highly effective separation based on electrophoresis and filtration, and a relatively cheap apparatus with disposable devices.
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Affiliation(s)
- Junku Takao
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, Osaka 545-0051, Japan
| | - Reina Nagai
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, Osaka 545-0051, Japan
| | - Tatsuro Endo
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, Osaka 545-0051, Japan
| | - Hideaki Hisamoto
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, Osaka 545-0051, Japan
| | - Kenji Sueyoshi
- Department of Applied Chemistry, Graduate School of Engineering, Osaka Metropolitan University, Osaka 545-0051, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Japan Science and Technology Agency (JST), Saitama 332-0012, Japan
- Correspondence:
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14
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González-González RB, Flores-Contreras EA, González-González E, Torres Castillo NE, Parra-Saldívar R, Iqbal HMN. Biosensor Constructs for the Monitoring of Persistent Emerging Pollutants in Environmental Matrices. Ind Eng Chem Res 2022. [DOI: 10.1021/acs.iecr.2c00421] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
| | | | | | | | | | - Hafiz M. N. Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Monterrey 64849, Mexico
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15
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Chen S, Zhang L, Yuan Q, Tan J. Current Advances in Aptamer-based Biomolecular Recognition and Biological Process Regulation. Chem Res Chin Univ 2022; 38:847-855. [PMID: 35573821 PMCID: PMC9077342 DOI: 10.1007/s40242-022-2087-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 04/08/2022] [Indexed: 12/01/2022]
Abstract
The interaction between biomolecules with their target ligands plays a great role in regulating biological functions. Aptamers are short oligonucleotide sequences that can specifically recognize target biomolecules via structural complementarity and thus regulate related biological functions. In the past ten years, aptamers have made great progress in target biomolecule recognition, becoming a powerful tool to regulate biological functions. At present, there are many reviews on aptamers applied in biomolecular recognition, but few reviews pay attention to aptamer-based regulation of biological functions. Here, we summarize the approaches to enhancing aptamer affinity and the advancements of aptamers in regulating enzymatic activity, cellular immunity and cellular behaviors. Furthermore, this review discusses the challenges and future perspectives of aptamers in target recognition and biological functions regulation, aiming to provide some promising ideas for future regulation of biomolecular functions in a complex biological environment.
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Affiliation(s)
- Sisi Chen
- Molecular Science and Biomedicine Laboratory(MBL), Institute of Chemical Biology and Nanomedicine(ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Lei Zhang
- Molecular Science and Biomedicine Laboratory(MBL), Institute of Chemical Biology and Nanomedicine(ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Quan Yuan
- Molecular Science and Biomedicine Laboratory(MBL), Institute of Chemical Biology and Nanomedicine(ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
| | - Jie Tan
- Molecular Science and Biomedicine Laboratory(MBL), Institute of Chemical Biology and Nanomedicine(ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082 P. R. China
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16
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Yuhan J, Zhu L, Zhu L, Huang K, He X, Xu W. Cell-specific aptamers as potential drugs in therapeutic applications: A review of current progress. J Control Release 2022; 346:405-420. [PMID: 35489545 DOI: 10.1016/j.jconrel.2022.04.039] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 04/23/2022] [Accepted: 04/24/2022] [Indexed: 12/23/2022]
Abstract
Cell-specific aptamers are a promising emerging player in the field of disease therapy. This paper reviews the multidimensional research progress made in terms of their classification, modification, and application. Based on the target location of cell-specific aptamers, it is defined and classified cell-specific aptamers into three groups including aptamers for cell surface markers, aptamers for intracellular components, and aptamers for extracellular components. Moreover, the modification methods of aptamers to achieve improved stability and affinity are concluded. In addition, recent advances in the application of cell-specific aptamers are discussed, mainly focusing on the increasing research attraction of cell state improving helpers and cell recruitment mediators in the improvement of cellular microenvironments to achieve successful disease therapy. This review also highlights 11 types of clinical aptamer drugs. Finally, the challenges and future directions of potential clinical applications are presented. In summary, we believe that cell-specific aptamers are promising drugs in disease therapy.
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Affiliation(s)
- Jieyu Yuhan
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Liye Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China; College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Longjiao Zhu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China
| | - Kunlun Huang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiaoyun He
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Wentao Xu
- Key Laboratory of Precision Nutrition and Food Quality, Department of Nutrition and Health, China Agricultural University, Beijing 100083, China.
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17
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Kim HK, Nguyen PT, Kim MI, Chan Kim B. Aptamer-functionalized and silver-coated polydopamine-copper hybrid nanoflower adsorbent embedded with magnetic nanoparticles for efficient mercury removal. CHEMOSPHERE 2022; 288:132584. [PMID: 34656629 DOI: 10.1016/j.chemosphere.2021.132584] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 10/12/2021] [Accepted: 10/14/2021] [Indexed: 06/13/2023]
Abstract
Mercury (Hg) emissions are increasing annually owing to rapid global industrialization. Hg poisoning can severely affect the human body owing to its persistence and bioaccumulation. In this study, hybrid nanoflowers (NFs) were synthesized by promoting the formation of primary copper-phosphate crystals coordinated with polydopamine (PDA) and Fe3O4 magnetic nanoparticles (MNPs), followed by coating with silver nanoparticles on the surface of the NFs (Ag-MNP-PDA-Cu NFs). The results suggest that the hierarchical structure of the NFs enabled a large surface area with nanosized pores, which were exploited for Hg adsorption. The adsorbed Hg ions could be further eliminated from the solution based on the magnetic characteristics of the NFs. Additionally, hybrid NFs functionalized with Hg2+-binding aptamers (Apt-Ag-MNP-PDA-Cu NFs) were prepared based on the silver-sulfur interactions between the Ag-MNP-PDA-Cu NFs and thiol-modified aptamers. The performance of both adsorbents demonstrated that the immobilization of Hg2+-binding aptamers significantly improved the elimination of Hg from solution. The Hg2+ adsorption isotherm of the Apt-Ag-MNP-PDA-Cu NFs followed the Dubinin-Radushkevich model, with a maximum adsorption capacity of 1073.19 mg/g. The Apt-Ag-MNP-PDA-Cu NFs adsorbed greater amounts of Hg2+ than the non-functionalized NFs at the same concentrations, which confirmed that the functionalization of Hg2+-binding aptamers on the NFs improved the Hg2+ removal performance. The results suggest that Apt-Ag-MNP-PDA-Cu NFs could serve as an efficient Hg-removing adsorbent, possibly by providing binding sites for the formation of T-Hg2+-T complexes.
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Affiliation(s)
- Ho Kyeong Kim
- Center for Environment, Health and Welfare Research, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea; Department of Chemical and Biological Engineering, Korea University, Seoul, 02841, Republic of Korea
| | - Phuong Thy Nguyen
- Department of BioNano Technology, Gachon University, Seongnam, Gyeonggi, 13120, Republic of Korea
| | - Moon Il Kim
- Department of BioNano Technology, Gachon University, Seongnam, Gyeonggi, 13120, Republic of Korea.
| | - Byoung Chan Kim
- Center for Environment, Health and Welfare Research, Korea Institute of Science and Technology (KIST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea; Division of Energy and Environment Technology, KIST School, University of Science and Technology (UST), Hwarangno 14-gil 5, Seongbuk-gu, Seoul, 02792, Republic of Korea.
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18
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Ozturk M, Nilsen-Hamilton M, Ilgu M. Aptamer Applications in Neuroscience. Pharmaceuticals (Basel) 2021; 14:1260. [PMID: 34959661 PMCID: PMC8709198 DOI: 10.3390/ph14121260] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/29/2021] [Accepted: 12/01/2021] [Indexed: 02/07/2023] Open
Abstract
Being the predominant cause of disability, neurological diseases have received much attention from the global health community. Over a billion people suffer from one of the following neurological disorders: dementia, epilepsy, stroke, migraine, meningitis, Alzheimer's disease, Parkinson's disease, multiple sclerosis, amyotrophic lateral sclerosis, Huntington's disease, prion disease, or brain tumors. The diagnosis and treatment options are limited for many of these diseases. Aptamers, being small and non-immunogenic nucleic acid molecules that are easy to chemically modify, offer potential diagnostic and theragnostic applications to meet these needs. This review covers pioneering studies in applying aptamers, which shows promise for future diagnostics and treatments of neurological disorders that pose increasingly dire worldwide health challenges.
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Affiliation(s)
- Meric Ozturk
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (M.O.); (M.N.-H.)
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
| | - Marit Nilsen-Hamilton
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (M.O.); (M.N.-H.)
- Ames Laboratory, US DOE (United States Department of Energy), Ames, IA 50011, USA
- Aptalogic Inc., Ames, IA 50014, USA
| | - Muslum Ilgu
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA; (M.O.); (M.N.-H.)
- Department of Biological Sciences, Middle East Technical University, Ankara 06800, Turkey
- Ames Laboratory, US DOE (United States Department of Energy), Ames, IA 50011, USA
- Aptalogic Inc., Ames, IA 50014, USA
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19
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Alijanianzadeh M, Qadami F, Molaeirad A. Detection of methamphetamine using aptamer-based biosensor chip and cyclic voltammetry technique. J INDIAN CHEM SOC 2021. [DOI: 10.1016/j.jics.2021.100189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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20
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Feng R, Patil S, Zhao X, Miao Z, Qian A. RNA Therapeutics - Research and Clinical Advancements. Front Mol Biosci 2021; 8:710738. [PMID: 34631795 PMCID: PMC8492966 DOI: 10.3389/fmolb.2021.710738] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 09/07/2021] [Indexed: 12/16/2022] Open
Abstract
RNA therapeutics involve the use of coding RNA such as mRNA as well as non-coding RNAs such as small interfering RNAs (siRNA), antisense oligonucleotides (ASO) to target mRNA, aptamers, ribozymes, and clustered regularly interspaced short palindromic repeats-CRISPR-associated (CRISPR/Cas) endonuclease to target proteins and DNA. Due to their diverse targeting ability and research in RNA modification and delivery systems, RNA-based formulations have emerged as suitable treatment options for many diseases. Therefore, in this article, we have summarized different RNA therapeutics, their targeting strategies, and clinical progress for various diseases as well as limitations; so that it might help researchers formulate new and advanced RNA therapeutics for various diseases. Additionally, U.S. Food and Drug Administration (USFDA)-approved RNA-based therapeutics have also been discussed.
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Affiliation(s)
- Rundong Feng
- Shaanxi Institute for Food and Drug Control, Xi'an, China
| | - Suryaji Patil
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Xin Zhao
- School of Pharmacy, Shaanxi Institute of International Trade & Commerce, Xi'an, China
| | - Zhiping Miao
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
| | - Airong Qian
- Lab for Bone Metabolism, Xi'an Key Laboratory of Special Medicine and Health Engineering, Key Lab for Space Biosciences and Biotechnology, Research Center for Special Medicine and Health Systems Engineering, NPU-UAB Joint Laboratory for Bone Metabolism, School of Life Sciences, Northwestern Polytechnical University, Xi'an, China
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21
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Beyond G-Quadruplexes-The Effect of Junction with Additional Structural Motifs on Aptamers Properties. Int J Mol Sci 2021; 22:ijms22189948. [PMID: 34576112 PMCID: PMC8466185 DOI: 10.3390/ijms22189948] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 09/08/2021] [Accepted: 09/09/2021] [Indexed: 12/02/2022] Open
Abstract
G-quadruplexes constitute an important type of nucleic acid structure, which can be found in living cells and applied by cell machinery as pivotal regulatory elements. Importantly, robust development of SELEX technology and modern, nucleic acid-based therapeutic strategies targeted towards various molecules have also revealed a large group of potent aptamers whose structures are grounded in G-quadruplexes. In this review, we analyze further extension of tetraplexes by additional structural elements and investigate whether G-quadruplex junctions with duplex, hairpin, triplex, or second G-quadruplex motifs are favorable for aptamers stability and biological activity. Furthermore, we indicate the specific and pivotal role of the G-quadruplex domain and the additional structural elements in interactions with target molecules. Finally, we consider the potency of G-quadruplex junctions in future applications and indicate the emerging research area that is still waiting for development to obtain highly specific and effective nucleic acid-based molecular tools.
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22
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Tapp M, Dennis P, Naik RR, Milam VT. Competition-Enhanced Ligand Selection to Screen for DNA Aptamers for Spherical Gold Nanoparticles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:9043-9052. [PMID: 34279112 DOI: 10.1021/acs.langmuir.1c01053] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The Competition-Enhanced Ligand Selection (CompELS) approach was used to identify aptamer candidates for spherical gold nanoparticles (AuNPs). This approach differs from conventional Systematic Evolution of Ligands by EXponential enrichment (SELEX)-based aptamer screening by eliminating repeated elution and polymerase chain reaction (PCR) amplification steps of bound candidate sequences between each selection round to continually enrich the candidate aptamer pool with oligonucleotides remaining from an earlier SELEX selection round. Instead, a new pool of unenriched oligonucleotides is added during each CompELS selection round to compete with existing target-bound oligonucleotides species for target binding sites. In this study, 24 aptamer candidates for AuNPs were identified using the CompELS approach and then compared to reveal similarities in their primary structures and their predicted secondary structures. No strong patterns in individual base identities (position-dependent) nor in segments of consecutive bases (independent of position) prevailed among the identified sequences. Motifs in predicted secondary structures, on the other hand, were shared among otherwise unrelated aptamer sequences. These motifs were revealed using a systematic classification and enumeration of distinct secondary structure elements, namely, hairpins, duplexes, single-stranded segments, interior loops, bulges, and multibranched loops.
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Affiliation(s)
| | - Patrick Dennis
- Materials & Manufacturing Directorate, Soft Matter Materials Branch, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
| | - Rajesh R Naik
- 711th Human Performance Wing, Air Force Research Laboratory, Wright-Patterson AFB, Ohio 45433, United States
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23
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He J, Wang J, Zhang M, Shi G. Selection of a Structure-Switching Aptamer for the Specific Methotrexate Detection. ACS Sens 2021; 6:2436-2441. [PMID: 34132539 DOI: 10.1021/acssensors.1c00749] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Methotrexate (MTX), a folate antagonist drug, has been widely used for treating various cancers. Since high-dose MTX treatment can cause unwanted serious side effects, tracking the blood concentration of MTX is essential for safe medication. However, available methods are often complex, time-consuming, and expensive. In this study, a highly selective DNA aptamer was selected for recognizing MTX based on a capture-systematic evolution of ligands by an exponential enrichment (C-SELEX) approach. Taking advantage of our selected MTX aptamer, we further unveil a novel structure-switching fluorescent sensor for the specific and rapid monitoring of MTX with good analytical performances (i.e., a linear detection range of 0.1-2 μM with a low detection limit (LOD) of 0.03 μM in buffer and a linear detection range of 0.5-10 μM with an LOD of 0.18 μM in 50% serum). Compared with conventional methods, this assay has great potential for detecting the blood concentration of MTX in clinical use. By coupling with other sensory techniques, our presented aptamer will potentially inspire the development of various sensors toward the monitoring of MTX.
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Affiliation(s)
- Junqing He
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Junyan Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Min Zhang
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
| | - Guoyue Shi
- School of Chemistry and Molecular Engineering, Shanghai Key Laboratory for Urban Ecological Processes and Eco-Restoration, East China Normal University, Dongchuan Road 500, Shanghai 200241, China
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24
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Development of a fluorescence aptasensor for rapid and sensitive detection of Listeria monocytogenes in food. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107808] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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25
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Connelly RP, Madalozzo PF, Mordeson JE, Pratt AD, Gerasimova YV. Promiscuous dye binding by a light-up aptamer: application for label-free multi-wavelength biosensing. Chem Commun (Camb) 2021; 57:3672-3675. [PMID: 33725073 DOI: 10.1039/d1cc00594d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Light-up DNA aptamers are promising label-free signal-transducers for biosensing applications due to their high chemical stability and low synthetic cost. Herein, we demonstrate that a dapoxyl DNA aptamer DAP-10-42 can be converted into a sensor generating a fluorescence signal at different wavelengths in the range of 500-660 nm depending on the dye that is present. This results from the discovered promiscuity of DAP-10-42 in binding fluorogenic dyes including arylmethane dyes. We have designed a split DAP-10-42 aptasensor for the detection of a katG gene fragment from Mycobacterium tuberculosis with a point mutation causing isoniazid resistance. Efficient interrogation of the gene fragment after nucleic acid sequence-based amplification (NASBA) is achieved directly in a protein-containing NASBA sample. This report lays a foundation for the application of the DAP-10-42 aptamer as a versatile sensing platform.
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Affiliation(s)
- Ryan P Connelly
- Department of Chemistry, University of Central Florida, 4111 Libra Dr, PSB 255, Orlando, Fl 32816, USA.
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26
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Ahmad E, Ali A, Fatima MT, Nimisha, Apurva, Kumar A, Sumi MP, Sattar RSA, Mahajan B, Saluja SS. Ligand decorated biodegradable nanomedicine in the treatment of cancer. Pharmacol Res 2021; 167:105544. [PMID: 33722711 DOI: 10.1016/j.phrs.2021.105544] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/09/2021] [Accepted: 03/09/2021] [Indexed: 12/14/2022]
Abstract
Cancer is one of the major global health problems, responsible for the second-highest number of deaths. The genetic and epigenetic changes in the oncogenes or tumor suppressor genes alter the regulatory pathways leading to its onset and progression. Conventional methods are used in appropriate combinations for the treatment. Surgery effectively treats localized tumors; however, it fails to treat metastatic tumors, leading to a spread in other organs, causing a high recurrence rate and death. Among the different strategies, the nanocarriers-based approach is highly sought for, but its nonspecific delivery can cause a profound side effect on healthy cells. Targeted nanomedicine has the advantage of targeting cancer cells specifically by interacting with the receptors overexpressed on their surface, overcoming its non-specificity to target healthy cells. Nanocarriers prepared from biodegradable and biocompatible materials are decorated with different ligands by encapsulating therapeutic or diagnostic agents or both to target cancer cells overexpressing the receptors. Scientists are now utilizing a theranostic approach to simultaneously evaluate nanocarrier bio-distribution and its effect on the treatment regime. Herein, we have summarized the recent 5-year efforts in the development of the ligands decorated biodegradable nanocarriers, as a targeted nanomedicine approach, which has been highly promising in the treatment of cancer.
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Affiliation(s)
- Ejaj Ahmad
- Central Molecular Laboratory, Govind Ballabh Pant, Postgraduate Institute of Medica, Education and Research (GIPMER), New Delhi 110002, India
| | - Asgar Ali
- Department of Biochemistry, All India Institute of Medical Science, Patna 810507, India
| | - Munazza Tamkeen Fatima
- Department of Pharmaceutical Science, College of Pharmacy, QU health, Qatar University, P.O. Box 2713, Doha, Qatar
| | - Nimisha
- Central Molecular Laboratory, Govind Ballabh Pant, Postgraduate Institute of Medica, Education and Research (GIPMER), New Delhi 110002, India
| | - Apurva
- Central Molecular Laboratory, Govind Ballabh Pant, Postgraduate Institute of Medica, Education and Research (GIPMER), New Delhi 110002, India
| | - Arun Kumar
- Central Molecular Laboratory, Govind Ballabh Pant, Postgraduate Institute of Medica, Education and Research (GIPMER), New Delhi 110002, India
| | - Mamta P Sumi
- Central Molecular Laboratory, Govind Ballabh Pant, Postgraduate Institute of Medica, Education and Research (GIPMER), New Delhi 110002, India
| | - Real Sumayya Abdul Sattar
- Central Molecular Laboratory, Govind Ballabh Pant, Postgraduate Institute of Medica, Education and Research (GIPMER), New Delhi 110002, India
| | - Bhawna Mahajan
- Department of Biochemistry, Govind Ballabh Pant, Postgraduate Institute of Medical, Education and Research (GIPMER), New Delhi 110002, India
| | - Sundeep Singh Saluja
- Central Molecular Laboratory, Govind Ballabh Pant, Postgraduate Institute of Medica, Education and Research (GIPMER), New Delhi 110002, India; Department of GI Surgery, Govind Ballabh Pant, Postgraduate Institute of Medica, Education and Research (GIPMER), New Delhi 110002, India.
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27
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Chyży P, Kulik M, Re S, Sugita Y, Trylska J. Mutations of N1 Riboswitch Affect its Dynamics and Recognition by Neomycin Through Conformational Selection. Front Mol Biosci 2021; 8:633130. [PMID: 33708793 PMCID: PMC7942488 DOI: 10.3389/fmolb.2021.633130] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/07/2021] [Indexed: 11/13/2022] Open
Abstract
Short, structured fragments of non-coding mRNA may act as molecular switches upon binding specific ligands, regulating the translation of proteins encoded downstream this mRNA sequence. One switch, called riboswitch N1, is regulated by aminoglycosides such as neomycin. Nucleobase mutations in the apical loop, although distant from the binding pocket, significantly affect neomycin affinity and riboswitch regulatory efficiency. To explain this influence, we conducted molecular dynamics simulations using generalized replica exchange with solute tempering (gREST). Translation assay of a reporter protein in a yeast system shows that mutating A17 to G in the riboswitch apical loop reduces 6-fold the translation regulation efficiency of the mutant. Indeed, simulations of the unbound riboswitch show that G17 frequently stacks with base 7, while base 8 is stabilized towards the binding site in a way that it may interfere with the conformational selection mechanism and decrease riboswitch regulatory activity. In the riboswitch complexes, this single-point A to G mutation disrupts a strong hydrogen bond between nucleotides 5 and 17 and, instead, a new hydrogen bond between residue 17 and neomycin is created. This change forces neomycin to occupy a slightly shifted position in the binding pocket, which increases neomycin flexibility. Our simulations of the U14C mutation suggest that the riboswitch complex with neomycin is more stable if cytosine 14 is protonated. A hydrogen bond between the RNA phosphate and protonated cytosine appears as the stabilizing factor. Also, based on the cell-free translation assay and isothermal titration calorimetry experiments, mutations of nucleotides 14 and 15 affect only slightly the riboswitch ability to bind the ligand and its activity. Indeed, the simulation of the unbound U15A mutant suggests conformations preformed for ligand binding, which may explain slightly higher regulatory activity of this mutant. Overall, our results corroborate the in vivo and in vitro experiments on the N1 riboswitch-neomycin system, detail the relationship between nucleobase mutations and RNA dynamics, and reveal the conformations playing the major role in the conformational selection mechanism.
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Affiliation(s)
- Piotr Chyży
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.,Faculty of Physics, University of Warsaw, Warsaw, Poland
| | - Marta Kulik
- Centre of New Technologies, University of Warsaw, Warsaw, Poland.,Department of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Suyong Re
- RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.,National Institutes of Biomedical Innovation, Health and Nutrition, Ibaraki, Japan
| | - Yuji Sugita
- RIKEN Center for Biosystems Dynamics Research (BDR), Kobe, Japan.,RIKEN Cluster for Pioneering Research (CPR), Wako, Japan.,RIKEN Center for Computational Science, Kobe, Japan
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Warsaw, Poland
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28
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Mirian M, Kouhpayeh S, Shariati L, Boshtam M, Rahimmanesh I, Darzi L, Taghizadeh R, Jahanian-Najafabadi A, Khanahmad H. Generation of HBsAg DNA aptamer using modified cell-based SELEX strategy. Mol Biol Rep 2021; 48:139-146. [PMID: 33400073 DOI: 10.1007/s11033-020-05995-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 11/10/2020] [Indexed: 11/30/2022]
Abstract
Aptamers as potential alternatives for antibodies could be employed against hepatitis B surface antigen (HBsAg), the great hallmark and first serological marker in HBV, for further theragnostic applications. Therefore, isolation HBsAg specific aptamer was performed in this study with a modified Cell-SELEX method. HEK293T overexpressing HBsAg and HEK293T as target and control cells respectively, were incubated with single-stranded rounds of DNA library during six SELEX and Counter SELEX rounds. Here, we introduced the new modified Cell-SELEX using deoxyribonuclease I digestion to separate single stranded DNA aptamers against the HBsAg. Characterization and evaluation of selected sequences were performed using flow cytometry analysis. The results led to isolation of 15 different ssDNA clones in six rounds of selection which were categorized to four clusters based on common structural motifs. The evaluation of SELEX progress showed growth in aptamer affinity with increasing in the cycle number. Taken together, the application of modified cell-SELEX demonstrated the isolation of HBsAg-specific ssDNA aptamers with proper affinity. Modified cell-SELEX as an efficient method can shorten the selection procedure and increase the success rate while the benefits of cell-based SELEX will be retained. Selected aptamers could be applied in purification columns, diagnostic kits, and drug delivery system against HBV-related liver cancer.
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Affiliation(s)
- Mina Mirian
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran
| | - Shirin Kouhpayeh
- Isfahan Neurosciences Research Center, Alzahra Research Institute, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran
| | - Laleh Shariati
- Applied Physiology Research Center, Cardiovascular Research Institute, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran.,Department of Biomaterials, Nanotechnology and Tissue Engineering, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran
| | - Maryam Boshtam
- Department of Biomaterials, Nanotechnology and Tissue Engineering, School of Advanced Technologies in Medicine, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran
| | - Ilnaz Rahimmanesh
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran
| | - Leila Darzi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran
| | - Razieh Taghizadeh
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran
| | - Ali Jahanian-Najafabadi
- Department of Pharmaceutical Biotechnology, School of Pharmacy and Pharmaceutical Science, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran
| | - Hossein Khanahmad
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Islamic Republic of Iran.
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29
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Tickner ZJ, Zhong G, Sheptack KR, Farzan M. Selection of High-Affinity RNA Aptamers That Distinguish between Doxycycline and Tetracycline. Biochemistry 2020; 59:3473-3486. [PMID: 32857495 DOI: 10.1021/acs.biochem.0c00586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligonucleotide aptamers are found in prokaryotes and eukaryotes, and they can be selected from large synthetic libraries to bind protein or small-molecule ligands with high affinities and specificities. Aptamers can function as biosensors, as protein recognition elements, and as components of riboswitches allowing ligand-dependent control of gene expression. One of the best studied laboratory-selected aptamers binds the antibiotic tetracycline, but it binds with a much lower affinity to the closely related but more bioavailable antibiotic doxycycline. Here we report enrichment of doxycycline binding aptamers from a selectively randomized library of tetracycline aptamer variants over four selection rounds. Selected aptamers distinguish between doxycycline, which they bind with dissociation constants of approximately 7 nM, and tetracycline, which they bind undetectably. They thus function as orthogonal complements to the original tetracycline aptamer. Unexpectedly, doxycycline aptamers adopt a conformation distinct from that of the tetracycline aptamer and depend on constant regions originally installed as primer binding sites. We show that the fluorescence emission intensity of doxycycline increases upon aptamer binding, permitting their use as biosensors. This new class of aptamers can be used in multiple contexts where doxycycline detection, or doxycycline-mediated regulation, is necessary.
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Affiliation(s)
- Zachary J Tickner
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Guocai Zhong
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Kelly R Sheptack
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, United States
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30
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Marshall ML, Wagstaff KM. Internalized Functional DNA Aptamers as Alternative Cancer Therapies. Front Pharmacol 2020; 11:1115. [PMID: 32848740 PMCID: PMC7396948 DOI: 10.3389/fphar.2020.01115] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 07/08/2020] [Indexed: 01/22/2023] Open
Abstract
Despite major advances, cancer remains one of the largest burdens of disease worldwide. One reason behind this is that killing tumor cells without affecting healthy surrounding tissue remains a largely elusive prospect, despite the widespread availability of cytotoxic chemotherapeutic agents. To meet these modern healthcare requirements, it is essential to develop precision therapeutics that minimise off-target side-effects for various cancer types. To this end, highly specific molecular targeting agents against cancer are of great interest. These agents may work by targeting intracellular signalling pathways following receptor binding, or via internalization and targeting to specific subcellular compartments. DNA aptamers represent a promising molecular tool in this arena that can be used for both specific cell surface targeting and subsequent internalization and can also elicit a functional effect upon internalization. This review examines various cancer targeting cell-internalizing aptamers, with a particular focus towards functional aptamers that do not require additional conjugation to nanoparticles or small molecules to elicit a biological response. With a deeper understanding and precise exploitation of cancer specific molecular pathways, functional intracellular DNA aptamers may be a powerful step towards more widespread development of precision therapeutics.
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Affiliation(s)
- Morgan L Marshall
- Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
| | - Kylie M Wagstaff
- Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia
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31
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Nieto C, Vega MA, Martín del Valle EM. Trastuzumab: More than a Guide in HER2-Positive Cancer Nanomedicine. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E1674. [PMID: 32859026 PMCID: PMC7557948 DOI: 10.3390/nano10091674] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/24/2020] [Accepted: 08/24/2020] [Indexed: 02/07/2023]
Abstract
HER2 overexpression, which occurs in a fifth of diagnosed breast cancers as well as in other types of solid tumors, has been traditionally linked to greater aggressiveness. Nevertheless, the clinical introduction of trastuzumab has helped to improve HER2-positive patients' outcomes. As a consequence, nanotechnology has taken advantage of the beneficial effects of the administration of this antibody and has employed it to develop HER2-targeting nanomedicines with promising therapeutic activity and limited toxicity. In this review, the molecular pathways that could be responsible for trastuzumab antitumor activity will be briefly summarized. In addition, since the conjugation strategies that are followed to develop targeting nanomedicines are essential to maintaining their efficacy and tolerability, the ones most employed to decorate drug-loaded nanoparticles and liposomes with trastuzumab will be discussed here. Thus, the advantages and disadvantages of performing this trastuzumab conjugation through adsorption or covalent bindings (through carbodiimide, maleimide, and click-chemistry) will be described, and several examples of targeting nanovehicles developed following these strategies will be commented on. Moreover, conjugation methods employed to synthesized trastuzumab-based antibody drug conjugates (ADCs), among which T-DM1 is well known, will be also examined. Finally, although trastuzumab-decorated nanoparticles and liposomes and trastuzumab-based ADCs have proven to have better selectivity and efficacy than loaded drugs, trastuzumab administration is sometimes related to side toxicities and the apparition of resistances. For this reason also, this review focuses at last on the important role that newer antibodies and peptides are acquiring these days in the development of HER2-targeting nanomedicines.
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Affiliation(s)
- Celia Nieto
- Departamento de Ingeniería Química, Facultad de Ciencias Químicas, Universidad de Salamanca, 37008 Salamanca, Spain;
| | | | - Eva M. Martín del Valle
- Departamento de Ingeniería Química, Facultad de Ciencias Químicas, Universidad de Salamanca, 37008 Salamanca, Spain;
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32
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Li L, Xu S, Yan H, Li X, Yazd HS, Li X, Huang T, Cui C, Jiang J, Tan W. Nucleic Acid Aptamers for Molecular Diagnostics and Therapeutics: Advances and Perspectives. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Long Li
- Department of Chemistry and Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute McKnight Brain Institute University of Florida Gainesville Florida 32611 USA
| | - Shujuan Xu
- Department of Chemistry and Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute McKnight Brain Institute University of Florida Gainesville Florida 32611 USA
- 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 410082 China
| | - He Yan
- Department of Chemistry and Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute McKnight Brain Institute University of Florida Gainesville Florida 32611 USA
- 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 410082 China
| | - Xiaowei Li
- Department of Chemistry and Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute McKnight Brain Institute University of Florida Gainesville Florida 32611 USA
| | - Hoda Safari Yazd
- Department of Chemistry and Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute McKnight Brain Institute University of Florida Gainesville Florida 32611 USA
| | - Xiang Li
- Department of Chemistry and Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute McKnight Brain Institute University of Florida Gainesville Florida 32611 USA
| | - Tong Huang
- Department of Chemistry and Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute McKnight Brain Institute University of Florida Gainesville Florida 32611 USA
| | - 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 410082 China
- Institute of Cancer and Basic Medicine (IBMC) Chinese Academy of Sciences The Cancer Hospital of the University of Chinese Academy of Sciences Hangzhou Zhejiang 310022 China
| | - Jianhui 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 410082 China
| | - Weihong Tan
- Department of Chemistry and Physiology and Functional Genomics Center for Research at the Bio/Nano Interface Health Cancer Center UF Genetics Institute McKnight Brain Institute University of Florida Gainesville Florida 32611 USA
- 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 410082 China
- Institute of Molecular Medicine (IMM) Renji Hospital State Key Laboratory of Oncogenes and Related Genes Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering Shanghai Jiao Tong University Shanghai 200240 China
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33
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Li L, Xu S, Yan H, Li X, Yazd HS, Li X, Huang T, Cui C, Jiang J, Tan W. Nucleic Acid Aptamers for Molecular Diagnostics and Therapeutics: Advances and Perspectives. Angew Chem Int Ed Engl 2020; 60:2221-2231. [PMID: 32282107 DOI: 10.1002/anie.202003563] [Citation(s) in RCA: 174] [Impact Index Per Article: 43.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Indexed: 12/11/2022]
Abstract
The advent of SELEX (systematic evolution of ligands by exponential enrichment) technology has shown the ability to evolve artificial ligands with affinity and specificity able to meet growing clinical demand for probes that can, for example, distinguish between the target leukemia cells and other cancer cells within the matrix of heterogeneity, which characterizes cancer cells. Though antibodies are the conventional and ideal choice as a molecular recognition tool for many applications, aptamers complement the use of antibodies due to many unique advantages, such as small size, low cost, and facile chemical modification. This Minireview will focus on the novel applications of aptamers and SELEX, as well as opportunities to develop molecular tools able to meet future clinical needs in biomedicine.
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Affiliation(s)
- Long Li
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Shujuan Xu
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611, USA.,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, 410082, China
| | - He Yan
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611, USA.,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, 410082, China
| | - Xiaowei Li
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Hoda Safari Yazd
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Xiang Li
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - Tong Huang
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611, USA
| | - 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, 410082, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, China
| | - Jianhui 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, 410082, China
| | - Weihong Tan
- Department of Chemistry and Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Health Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida, Gainesville, Florida, 32611, USA.,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, 410082, China.,Institute of Molecular Medicine (IMM), Renji Hospital, State Key Laboratory of Oncogenes and Related Genes, Shanghai Jiao Tong University School of Medicine, and College of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai, 200240, China
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34
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Wan Q, Liu X, Zeng Z, Chen Z, Liu Y, Zu Y. Aptamer Cocktail to Detect Multiple Species of Mycoplasma in Cell Culture. Int J Mol Sci 2020; 21:E3784. [PMID: 32471128 PMCID: PMC7312096 DOI: 10.3390/ijms21113784] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 05/21/2020] [Accepted: 05/25/2020] [Indexed: 02/07/2023] Open
Abstract
Mycoplasma contamination of cell line cultures is a common, yet often undetected problem in research laboratories. Many of the existing techniques to detect mycoplasma contamination of cultured cells are time-consuming, expensive, and have significant drawbacks. Here, we describe a mycoplasma detection system that is useful for detecting multiple species of mycoplasma in infected cell lines. The system contains three dye-labeled detection aptamers that can specifically bind to mycoplasma-infected cells and a dye-labeled control aptamer that minimally binds to cells. With this system, mycoplasma-contaminated cells can be detected within 30 min by using a flow cytometer, fluorescence microscope, or microplate reader. Further, this system may be used to detect mycoplasma-contaminated culture medium. This study presents an novel mycoplasma detection model that is simple, rapid, inexpensive, and sensitive.
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Affiliation(s)
| | | | | | | | | | - Youli Zu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, TX 77030, USA; (Q.W.); (X.L.); (Z.Z.); (Z.C.); (Y.L.)
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35
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Shen R, Tan J, Yuan Q. Chemically Modified Aptamers in Biological Analysis. ACS APPLIED BIO MATERIALS 2020; 3:2816-2826. [DOI: 10.1021/acsabm.0c00062] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Ruichen Shen
- Institute of Chemical Biology and Nanomedicine (ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Jie Tan
- Institute of Chemical Biology and Nanomedicine (ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
| | - Quan Yuan
- Institute of Chemical Biology and Nanomedicine (ICBN), State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China
- Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
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36
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Predicting Future Prospects of Aptamers in Field-Effect Transistor Biosensors. Molecules 2020; 25:molecules25030680. [PMID: 32033448 PMCID: PMC7036789 DOI: 10.3390/molecules25030680] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 01/26/2020] [Accepted: 01/29/2020] [Indexed: 02/07/2023] Open
Abstract
Aptamers, in sensing technology, are famous for their role as receptors in versatile applications due to their high specificity and selectivity to a wide range of targets including proteins, small molecules, oligonucleotides, metal ions, viruses, and cells. The outburst of field-effect transistors provides a label-free detection and ultra-sensitive technique with significantly improved results in terms of detection of substances. However, their combination in this field is challenged by several factors. Recent advances in the discovery of aptamers and studies of Field-Effect Transistor (FET) aptasensors overcome these limitations and potentially expand the dominance of aptamers in the biosensor market.
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Liu Q, Zhang W, Chen S, Zhuang Z, Zhang Y, Jiang L, LIN JS. SELEX tool: a novel and convenient gel-based diffusion method for monitoring of aptamer-target binding. J Biol Eng 2020; 14:1. [PMID: 31956340 PMCID: PMC6956507 DOI: 10.1186/s13036-019-0223-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/29/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Aptamers, single-stranded DNAs or RNAs, can be selected from a library containing random sequences using a method called Systematic Evolution of Ligands by EXponential Enrichment (SELEX). In SELEX, monitoring the enriching statuses of aptamer candidates during the process is a key step until today. Conformational change of an aptamer caused by target-binding in gel can be used to indicate its statuses of binding. RESULTS In this study, an easy-to-implement gel-based diffusion method (GBDM) was developed to monitor the interaction between enriched aptamer candidates and their targets. In order to prove the concept, characterization of aptamers targeting their targets including protein (thrombin) and non-protein molecules (acetamiprid, ATP, atrazine, profenofos and roxithromycin), respectively, were performed using mini gels. Our method has advantages over the common methods including easy performed with labor- and time- saving in experimental operation. The concept has been proven by monitoring enrichment of dynamic aptamer candidate libraries targeting a small molecule 2,2-bis(4-chlorophenyl) acetic acid (DDA) during SELEX process. A mini gel cassette was designed and fabricated by our laboratory to make mini agarose gels for diffusion with different directions. CONCLUSIONS These results indicate that GBDM, in particular, chasing diffusion is suitable for monitoring the interaction between enriched aptamer candidates and their targets. These pioneering efforts are helpful for novel aptamer selection by breaking through the technical bottleneck of aptamer development and helpful for development of novel aptasensors.
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Affiliation(s)
- Qingxiu Liu
- School of Medicine, Huaqiao University, 269 Chenghua Rd, Fengze, Quanzhou, 362021 Fujian China
| | - Wei Zhang
- School of Medicine, Huaqiao University, 269 Chenghua Rd, Fengze, Quanzhou, 362021 Fujian China
| | - Siying Chen
- School of Medicine, Huaqiao University, 269 Chenghua Rd, Fengze, Quanzhou, 362021 Fujian China
| | - Zhenjing Zhuang
- School of Medicine, Huaqiao University, 269 Chenghua Rd, Fengze, Quanzhou, 362021 Fujian China
| | - Yi Zhang
- School of Medicine, Huaqiao University, 269 Chenghua Rd, Fengze, Quanzhou, 362021 Fujian China
| | - Lingli Jiang
- School of Medicine, Huaqiao University, 269 Chenghua Rd, Fengze, Quanzhou, 362021 Fujian China
| | - Jun Sheng LIN
- School of Medicine, Huaqiao University, 269 Chenghua Rd, Fengze, Quanzhou, 362021 Fujian China
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38
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Osorio CE, Mejías JH, Rustgi S. Gluten Detection Methods and Their Critical Role in Assuring Safe Diets for Celiac Patients. Nutrients 2019; 11:E2920. [PMID: 31810336 PMCID: PMC6949940 DOI: 10.3390/nu11122920] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 11/20/2019] [Accepted: 11/26/2019] [Indexed: 12/16/2022] Open
Abstract
Celiac disease, wheat sensitivity, and allergy represent three different reactions, which may occur in genetically predisposed individuals on the ingestion of wheat and derived products with various manifestations. Improvements in the disease diagnostics and understanding of disease etiology unveiled that these disorders are widespread around the globe affecting about 7% of the population. The only known treatment so far is a life-long gluten-free diet, which is almost impossible to follow because of the contamination of allegedly "gluten-free" products. Accidental contamination of inherently gluten-free products could take place at any level from field to shelf because of the ubiquity of these proteins/grains. Gluten contamination of allegedly "gluten-free" products is a constant threat to celiac patients and a major health concern. Several detection procedures have been proposed to determine the level of contamination in products for celiac patients. The present article aims to review the advantages and disadvantages of different gluten detection methods, with emphasis on the recent technology that allows identification of the immunogenic-gluten peptides without the use of antibodies. The possibility to detect gluten contamination by different approaches with similar or better detection efficiency in different raw and processed foods will guarantee the safety of the foods for celiac patients.
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Affiliation(s)
- Claudia E. Osorio
- Agriaquaculture Nutritional Genomic Center, CGNA, Las Heras 350, Temuco 4781158, Chile
| | - Jaime H. Mejías
- Centro Regional de Investigación Carillanca, Instituto de Investigaciones Agropecuarias INIA, Temuco 4880000, Chile
| | - Sachin Rustgi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
- Department of Plant and Environmental Sciences, School of Health Research, Clemson University Pee Dee Research and Education Center, Florence, SC 29506, USA
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39
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Wakui K, Abe A, Yoshitomi T, Furusho H, Yoshimoto K. High Enrichment of Nucleobase-modified Aptamers in Early Selection Rounds by Microbeads-assisted Capillary Electrophoresis SELEX. ANAL SCI 2019; 35:585-588. [PMID: 31080213 DOI: 10.2116/analsci.18sdn04] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Nucleobase-modified aptamers are attractive candidates for diagnostic and therapeutic agents due to the high affinity, stability and functionality. However, since even conventional SELEX requires many selection rounds, acquisition of modified aptamers is much more laborious. Herein, microbeads-assisted capillary electrophoresis (MACE)-SELEX was applied against thrombin using the indole-modified DNA library. After only three selection rounds, we successfully enriched the modified aptamers and they showed slower off-rate than reported aptamers, suggesting MACE-SELEX is a promising approach for rapid identification of modified aptamers.
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Affiliation(s)
- Koji Wakui
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo
| | - Akihito Abe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo
| | - Toru Yoshitomi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo
| | - Hitoshi Furusho
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo.,Chemical General Division, Nissan Chemical Industries, Ltd
| | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo.,JST, PRESTO, The University of Tokyo
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40
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Liu Y, Jiang W, Yang S, Hu J, Lu H, Han W, Wen J, Zeng Z, Qi J, Xu L, Zhou H, Sun H, Zu Y. Rapid Detection of Mycoplasma-Infected Cells by an ssDNA Aptamer Probe. ACS Sens 2019; 4:2028-2038. [PMID: 31403764 DOI: 10.1021/acssensors.9b00582] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Mycoplasmas are unique cell wall-free bacteria. Because they lack a cell wall and have resistance to β-lactam antibiotics, mycoplasma is the major pathogen that infects cultured cells in research laboratories. For rapid detection of mycoplasma-infected cells, we developed an ssDNA aptamer sequence composed of 40 nucleotides. Flow cytometry analysis showed that the synthetic aptamer probe selectively targeted mycoplasma-infected culture cells with high specificity identical to commercially available PCR-based assays. Additionally, fluorescent microscopy studies revealed that the aptamer probe rapidly stained mycoplasma-infected cells with higher sensitivity compared to Hoechst dye-mediated cellular DNA content stains. Moreover, confocal microscopy studies of trypsin-treated cells validated that the aptamer probes selectively targeted mycoplasma components on the surface of infected cells. Finally, preclinical studies of peripheral blood cells demonstrated that the aptamer probe was able to detect in vitro mycoplasma infection of primary lymphocytes. Taken together, these findings indicate that the aptamer probe will not only allow rapid detection of mycoplasma-infected culture cells for research purposes but also provide a simple method to monitor mycoplasma infection in primary cell products for clinical use.
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Affiliation(s)
- Yanting Liu
- Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Wenqi Jiang
- Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Shuanghui Yang
- Xiangya Hospital, Central South University, Changsha 410008, China
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Jianzhong Hu
- Xiangya Hospital, Central South University, Changsha 410008, China
| | - Hongbin Lu
- Xiangya Hospital, Central South University, Changsha 410008, China
| | - Wei Han
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Jianguo Wen
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Zihua Zeng
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Jianjun Qi
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Ling Xu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Haijun Zhou
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
| | - Hongguang Sun
- The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Youli Zu
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital, 6565 Fannin Street, Houston, Texas 77030, United States
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41
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A DNA-Based Biosensor Assay for the Kinetic Characterization of Ion-Dependent Aptamer Folding and Protein Binding. Molecules 2019; 24:molecules24162877. [PMID: 31398834 PMCID: PMC6718989 DOI: 10.3390/molecules24162877] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 08/02/2019] [Accepted: 08/05/2019] [Indexed: 11/16/2022] Open
Abstract
Therapeutic and diagnostic nucleic acid aptamers are designed to bind tightly and specifically to their target. The combination of structural and kinetic analyses of aptamer interactions has gained increasing importance. Here, we present a fluorescence-based switchSENSE aptasensor for the detailed kinetic characterization of aptamer-analyte interaction and aptamer folding, employing the thrombin-binding aptamer (TBA) as a model system. Thrombin-binding aptamer folding into a G-quadruplex and its binding to thrombin strongly depend on the type and concentration of ions present in solution. We observed conformational changes induced by cations in real-time and determined the folding and unfolding kinetics of the aptamer. The aptamer's affinity for K+ was found to be more than one order of magnitude higher than for other cations (K+ > NH4+ >> Na+ > Li+). The aptamer's affinity to its protein target thrombin in the presence of different cations followed the same trend but differed by more than three orders of magnitude (KD = 0.15 nM to 250 nM). While the stability (kOFF) of the thrombin-TBA complex was similar in all conditions, the cation type strongly influenced the association rate (kON). These results demonstrated that protein-aptamer binding is intrinsically related to the correct aptamer fold and, hence, to the presence of stabilizing ions. Because fast binding kinetics with on-rates exceeding 108 M-1s-1 can be quantified, and folding-related phenomena can be directly resolved, switchSENSE is a useful analytical tool for in-depth characterization of aptamer-ion and aptamer-protein interactions.
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42
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Kulik M, Mori T, Sugita Y, Trylska J. Molecular mechanisms for dynamic regulation of N1 riboswitch by aminoglycosides. Nucleic Acids Res 2019; 46:9960-9970. [PMID: 30239867 PMCID: PMC6212780 DOI: 10.1093/nar/gky833] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 09/07/2018] [Indexed: 01/14/2023] Open
Abstract
A synthetic riboswitch N1, inserted into the 5'-untranslated mRNA region of yeast, regulates gene expression upon binding ribostamycin and neomycin. Interestingly, a similar aminoglycoside, paromomycin, differing from neomycin by only one substituent (amino versus hydroxyl), also binds to the N1 riboswitch, but without affecting gene expression, despite NMR evidence that the N1 riboswitch binds all aminoglycosides in a similar way. Here, to explore the details of structural dynamics of the aminoglycoside-N1 riboswitch complexes, we applied all-atom molecular dynamics (MD) and temperature replica-exchange MD simulations in explicit solvent. Indeed, we found that ribostamycin and neomycin affect riboswitch dynamics similarly but paromomycin allows for more flexibility because its complex lacks the contact between the distinctive 6' hydroxyl group and the G9 phosphate. Instead, a transient hydrogen bond of 6'-OH with A17 is formed, which partially diminishes interactions between the bulge and apical loop of the riboswitch, likely contributing to riboswitch inactivity. In many ways, the paromomycin complex mimics the conformations, interactions, and Na+ distribution of the free riboswitch. The MD-derived interaction network helps understand why riboswitch activity depends on aminoglycoside type, whereas for another aminoglycoside-binding site, aminoacyl-tRNA site in 16S rRNA, activity is not discriminatory.
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Affiliation(s)
- Marta Kulik
- RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan.,Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
| | | | - Yuji Sugita
- RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2c, 02-097 Warsaw, Poland
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43
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Ali MH, Elsherbiny ME, Emara M. Updates on Aptamer Research. Int J Mol Sci 2019; 20:E2511. [PMID: 31117311 PMCID: PMC6566374 DOI: 10.3390/ijms20102511] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/26/2019] [Accepted: 04/30/2019] [Indexed: 02/07/2023] Open
Abstract
For many years, different probing techniques have mainly relied on antibodies for molecular recognition. However, with the discovery of aptamers, this has changed. The science community is currently considering using aptamers in molecular targeting studies because of the many potential advantages they have over traditional antibodies. Some of these possible advantages are their specificity, higher binding affinity, better target discrimination, minimized batch-to-batch variation, and reduced side effects. Overall, these characteristics of aptamers have attracted scholars to use them as molecular probes in place of antibodies, with some aptamer-based targeting products being now available in the market. The present review is aimed at discussing the potential of aptamers as probes in molecular biology and in super-resolution microscopy.
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Affiliation(s)
- Mohamed H Ali
- Center for Aging and Associated Diseases, Zewail City of Science and Technology, Giza 12578, Egypt.
- current address: Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA.
| | - Marwa E Elsherbiny
- Department of Pharmacology and Toxicology, Ahram Canadian University, 6th of October City, Giza 12566, Egypt.
| | - Marwan Emara
- Center for Aging and Associated Diseases, Zewail City of Science and Technology, Giza 12578, Egypt.
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44
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Wakui K, Yoshitomi T, Yamaguchi A, Tsuchida M, Saito S, Shibukawa M, Furusho H, Yoshimoto K. Rapidly Neutralizable and Highly Anticoagulant Thrombin-Binding DNA Aptamer Discovered by MACE SELEX. MOLECULAR THERAPY-NUCLEIC ACIDS 2019; 16:348-359. [PMID: 30986696 PMCID: PMC6462803 DOI: 10.1016/j.omtn.2019.03.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 03/08/2019] [Accepted: 03/08/2019] [Indexed: 02/07/2023]
Abstract
We present a rapidly neutralizable and highly anticoagulant thrombin-binding aptamer with a short toehold sequence, originally discovered by systematic evolution of ligands by exponential enrichment (SELEX) with microbead-assisted capillary electrophoresis (MACE). MACE is a novel CE-partitioning method for SELEX and able to separate aptamers from a library of unbound nucleic acids, where the aptamer and target complexes can be detected reliably and partitioned with high purity even in the first selection cycle. Three selection rounds of MACE-SELEX discovered several TBAs with a nanomolar affinity (Kd = 4.5-8.2 nM) that surpasses previously reported TBAs such as HD1, HD22, and NU172 (Kd = 118, 13, and 12 nM, respectively). One of the obtained aptamers, M08, showed a 10- to 20-fold longer prolonged clotting time than other anticoagulant TBAs, such as HD1, NU172, RE31, and RA36. Analyses of the aptamer and thrombin complexes using both bare and coated capillaries suggested that a large number of efficient aptamers are missed in conventional CE-SELEX because of increased interaction between the complex and the capillary. In addition, the toehold-mediated rapid antidote was designed for safe administration. The efficient aptamer and antidote system developed in the present study could serve as a new candidate for anticoagulant therapy.
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Affiliation(s)
- Koji Wakui
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Toru Yoshitomi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Akane Yamaguchi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan
| | - Maho Tsuchida
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Shingo Saito
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Masami Shibukawa
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Hitoshi Furusho
- Chemical General Division, Nissan Chemical Industries, Ltd., 2-10-2 Tsuboi-nishi, Funabashi, Chiba 274-8507, Japan
| | - Keitaro Yoshimoto
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan; JST, PRESTO, The University of Tokyo, 3-8-1 Komaba, Meguro, Tokyo 153-8902, Japan.
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45
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Belal ASF, Ismail A, Elnaggar MM, Belal TS. Click chemistry inspired copper sulphide nanoparticle-based fluorescence assay of kanamycin using DNA aptamer. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 205:48-54. [PMID: 30007899 DOI: 10.1016/j.saa.2018.07.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 06/30/2018] [Accepted: 07/05/2018] [Indexed: 06/08/2023]
Abstract
A highly selective and sensitive fluorescence assay for kanamycin has been developed that depends on complementation of two splits of DNA aptamer. One DNA split was labeled with CuS nanoparticle and the other was decorated with biotin, which enabled coupling with streptavidin magnesphere paramagnetic particles (PMPs). Complementation of the two-aptamer splits happened only in the presence of kanamycin and the subsequent sandwich was separated via a magnet. The released Cu(II) was reduced to Cu(I) by sodium ascorbate and finally catalyzed the click reaction between fluorogenic 3-azido-7-hydroxycoumarin and propargyl alcohol to afford the corresponding fluorescent 1,4-disubstituted-1,2,3-triazole. The fluorescence signal produced (λex. = 365 nm, λem. = 470 nm) was dependent on kanamycin concentration. Fluorescence signal amplification was found to be in good linear relationship with the logarithm of kanamycin concentration in the range of 0.04-20 nM. Furthermore, the proposed assay showed a good reproducibility, high selectivity and low detection limits for kanamycin determination. In addition, the capability of the proposed method to detect kanamycin in biological samples with satisfactory results was demonstrated.
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Affiliation(s)
- Ahmed S F Belal
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt.
| | - Azza Ismail
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Mai M Elnaggar
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
| | - Tarek S Belal
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria 21521, Egypt
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Russo V, Paciocco A, Affinito A, Roscigno G, Fiore D, Palma F, Galasso M, Volinia S, Fiorelli A, Esposito CL, Nuzzo S, Inghirami G, de Franciscis V, Condorelli G. Aptamer-miR-34c Conjugate Affects Cell Proliferation of Non-Small-Cell Lung Cancer Cells. MOLECULAR THERAPY. NUCLEIC ACIDS 2018; 13:334-346. [PMID: 30340138 PMCID: PMC6197774 DOI: 10.1016/j.omtn.2018.09.016] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Revised: 09/20/2018] [Accepted: 09/23/2018] [Indexed: 11/07/2022]
Abstract
MicroRNAs (miRNAs) are key regulators of different human processes that represent a new promising class of cancer therapeutics or therapeutic targets. Indeed, in several tumor types, including non-small-cell lung carcinoma (NSCLC), the deregulated expression of specific miRNAs has been implicated in cell malignancy. As expression levels of the oncosuppressor miR-34c-3p are decreased in NSCLC compared to normal lung, we show that reintroduction of miR-34c-3p reduces NSCLC cell survival in vitro. Further, in order to deliver the miR-34c-based therapeutic selectively to tumor cells, we took advantage of a reported nucleic acid aptamer (GL21.T) that binds and inhibits the AXL transmembrane receptor and is rapidly internalized in the target cells. By applying methods successfully used in our laboratory, we conjugated miR-34c to the GL21.T aptamer as targeting moiety for the selective delivery to AXL-expressing NSCLC cells. We demonstrate that miR-34c-3p and the GL21.T/miR-34c chimera affect NSCLC cell proliferation and are able to overcome acquired RTK-inhibitor resistance by targeting AXL receptor. Thus, the GL21.T/miR-34c chimera exerts dual inhibition of AXL at functional and transcriptional levels and represents a novel therapeutic tool for the treatment of NSCLC.
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Affiliation(s)
- Valentina Russo
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Naples, Italy
| | - Alessia Paciocco
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Naples, Italy
| | - Alessandra Affinito
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Naples, Italy
| | - Giuseppina Roscigno
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Naples, Italy
| | - Danilo Fiore
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Naples, Italy; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Francesco Palma
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Naples, Italy
| | - Marco Galasso
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Stefano Volinia
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Alfonso Fiorelli
- Thoracic Surgery Unit, Università degli Studi della Campania "Luigi Vanvitelli," Naples, Italy
| | - Carla Lucia Esposito
- Istituto di Endocrinologia ed Oncologia Sperimentale, Consiglio Nazionale delle Ricerche (CNR), Naples, Italy
| | | | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Vittorio de Franciscis
- Istituto di Endocrinologia ed Oncologia Sperimentale, Consiglio Nazionale delle Ricerche (CNR), Naples, Italy
| | - Gerolama Condorelli
- Department of Molecular Medicine and Medical Biotechnology, "Federico II" University of Naples, Naples, Italy; Istituto di Endocrinologia ed Oncologia Sperimentale, Consiglio Nazionale delle Ricerche (CNR), Naples, Italy.
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47
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Wang Y, Hoinka J, Liang Y, Adamus T, Swiderski P, Przytycka TM. AptaBlocks: Designing RNA complexes and accelerating RNA-based drug delivery systems. Nucleic Acids Res 2018; 46:8133-8142. [PMID: 29986050 PMCID: PMC6144873 DOI: 10.1093/nar/gky577] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/12/2018] [Accepted: 07/04/2018] [Indexed: 12/15/2022] Open
Abstract
RNA-based therapeutics, i.e. the utilization of synthetic RNA molecules to alter cellular functions, have the potential to address targets which are currently out of scope for traditional drug design pipelines. This potential however hinges on the ability to selectively deliver and internalize therapeutic RNAs into cells of interest. Cell internalizing RNA aptamers selected against surface receptors and discriminatively expressed on target cells hold particular promise as suitable candidates for such delivery agents. Specifically, these aptamers can be combined with a therapeutic cargo and facilitate internalization of the cargo into the cell of interest. A recently proposed method to obtain such aptamer-cargo constructs employs a double-stranded "sticky bridge" where the complementary strands constituting the bridge are conjugated with the aptamer and the cargo respectively. The design of appropriate sticky bridge sequences however has proven highly challenging given the structural and functional constraints imposed on them during synthesis and administration. These include, but are not limited to, guaranteed formation and stability of the complex, non-interference with the aptamer or the cargo, as well as the prevention of spurious aggregation of the molecules during incubation. In order to address these issues, we have developed AptaBlocks - a computational method to design RNA complexes that hybridize via sticky bridges. The effectiveness of our approach has been verified computationally, and experimentally in the context of drug delivery to pancreatic cancer cells. Importantly, AptaBlocks is a general method for the assembly of nucleic acid systems that, in addition to designing of RNA-based drug delivery systems, can be used in other applications of RNA nanotechnology. AptaBlocks is available at https://github.com/wyjhxq/AptaBlocks.
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Affiliation(s)
- Yijie Wang
- National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda MD 20894, USA
| | - Jan Hoinka
- National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda MD 20894, USA
| | - Yong Liang
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Tomasz Adamus
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Piotr Swiderski
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Teresa M Przytycka
- National Center of Biotechnology Information, National Library of Medicine, NIH, Bethesda MD 20894, USA
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48
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Petukhov AE, Petrykina EA, Tereshkina OI, Ramenskaya GV, Antipova OM, Turashev AD, Zav’yalova EG, Golovin AV, Pavlova GV, Kopylov AM. Standardization of Thrombaptanib Drug Substance for Residual Organic Solvents. Pharm Chem J 2018. [DOI: 10.1007/s11094-018-1823-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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49
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Kim YJ, Kim HS, Chon JW, Kim DH, Hyeon JY, Seo KH. New colorimetric aptasensor for rapid on-site detection of Campylobacter jejuni and Campylobacter coli in chicken carcass samples. Anal Chim Acta 2018; 1029:78-85. [PMID: 29907294 DOI: 10.1016/j.aca.2018.04.059] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 04/19/2018] [Indexed: 12/23/2022]
Abstract
Campylobacter is the most common cause of infectious intestinal disease, with nearly all cases caused by two species: C. jejuni and C. coli. We recently reported a gold nanoparticle-based two-stage aptasensing platform, which was improved in the present study for the rapid and on-site detection of both C. jejuni and C. coli in food samples. Compared to the previous platform, the improved platform yielded a more obvious colour change from red to purple due to the aggregation of gold nanoparticles, and does not require additional time or a pH optimization step for the aptamers to be adsorbed onto the gold nanoparticles. Using a highly specific aptamer that binds to live C. jejuni and C. coli, the improved aptasensor was highly effective for testing pure culture samples. The accuracy of the newly developed platform was comparable (p = 0.688) to that of the gold-standard detection method of tazobactam-supplemented culture, whereas it was superior to the official agar-based detection method (p = 0.016) in a validation study with 50 naturally contaminated chicken carcass samples. This is the first study on a colorimetric sensor that targets both live C. coli and C. jejuni in naturally contaminated samples. In addition, we provide the first evidence that both morphological status and the amount of Campylobacter present play key roles in the effectiveness of colorimetric detection. Thus, suitable selection of an antibody or aptamer with consideration of the morphological status of pathogens in samples is essential for direct detection without enrichment. Our data suggest that the sensor developed in this study can provide an excellent screening method, with a reduction in the detection time from 48 h to 30 min after enrichment, thus saving time, labour, and cost.
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Affiliation(s)
- Young-Ji Kim
- Center for One Health, College of Veterinary Medicine, Konkuk University, Seoul, South Korea
| | - Hong-Seok Kim
- Center for One Health, College of Veterinary Medicine, Konkuk University, Seoul, South Korea.
| | - Jung-Whan Chon
- Center for One Health, College of Veterinary Medicine, Konkuk University, Seoul, South Korea
| | - Dong-Hyeon Kim
- Center for One Health, College of Veterinary Medicine, Konkuk University, Seoul, South Korea
| | - Ji-Yeon Hyeon
- Center for One Health, College of Veterinary Medicine, Konkuk University, Seoul, South Korea
| | - Kun-Ho Seo
- Center for One Health, College of Veterinary Medicine, Konkuk University, Seoul, South Korea.
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50
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Li K, Deng J, Jin H, Yang X, Fan X, Li L, Zhao Y, Guan Z, Wu Y, Zhang L, Yang Z. Chemical modification improves the stability of the DNA aptamer GBI-10 and its affinity towards tenascin-C. Org Biomol Chem 2018; 15:1174-1182. [PMID: 28084479 DOI: 10.1039/c6ob02577c] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Aptamers are useful tools in molecular imaging due to their numerous attractive properties, such as excellent affinity and selectivity to diverse types of target molecules and biocompatibility. We carried out structure-activity relationship studies with the tenascin-C (TN-C) binding aptamer GBI-10, which is a promising candidate in tumor imaging. To increase the tumor targeting ability and nuclease resistance under physiological conditions, systematic modifications of GBI-10 with single and multiple 2'-deoxyinosine (2'-dI) or d-/l-isonucleoside (d-/l-isoNA) were performed. Results indicated that sector 3 of the proposed secondary structure is the most important region for specific binding with TN-C. By correlating the affinity of eighty-four GBI-10 derivatives with their predicted secondary structure by Zuker Mfold, we first validated the preferred secondary structure at 37 °C. We found that d-/l-isoNA modified GBI-10 derivatives exhibited improved affinity to the target as well as plasma stability. Affinity measurement and confocal imaging analysis highlighted one potent compound: 4AL/26TL/32TL, which possessed a significantly increased targeting ability to tumor cells. These results revealed the types of modified nucleotides, and the position and number of substituents in GBI-10 that were critical to the TN-C binding ability. Stabilized TN-C-binding DNA aptamers were prepared and they could be further developed for tumor imaging. Our strategy to introduce 2'-dI and d-/l-isoNA modifications after the selection process is likely to be generally applicable to improve the in vivo stability of aptamers without compromising their binding ability.
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Affiliation(s)
- Kunfeng Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Jiali Deng
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Hongwei Jin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Xiantao Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Xinmeng Fan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Liyu Li
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Yi Zhao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Zhu Guan
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Yun Wu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Lihe Zhang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
| | - Zhenjun Yang
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China. # #
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