1
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Cox CA, Ogorek AN, Habumugisha JP, Martell JD. Switchable DNA Photocatalysts for Radical Polymerization Controlled by Chemical Stimuli. J Am Chem Soc 2023; 145:1818-1825. [PMID: 36629375 DOI: 10.1021/jacs.2c11199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Polymerization catalysts that activate in response to specific chemical triggers offer spatial and temporal control over polymer synthesis, facilitating the development of responsive materials and custom polymer coatings. However, existing catalysts switch their activity through mechanisms that are not generalizable to chemically diverse stimuli. To approach the level of control exhibited in biological polymer synthesis, switchable polymerization catalysts need to be configurable for activation in response to diverse chemical stimuli. Here, we combine synthetic photocatalysts with conformation-switching DNA aptamers to create polymerization catalysts that respond to diverse chemical stimuli. We use the secondary structure of DNA to bring a photocatalyst and quencher dye into proximity, turning off photocatalysis. The DNA structure can be precisely designed to change conformation in response to a molecular trigger, moving the photocatalyst far from the quencher and activating photocatalysis. We show these photocatalysts can initiate free-radical polymerization to form bulk hydrogels in response to complementary DNA, a metal ion (Zn2+), or small molecules (glucose and hydrocortisone). We demonstrate the biocompatibility of these switchable photocatalysts by triggering their activation on the surface of yeast cells. Finally, we perform reversible-deactivation radical polymerization through photoinduced electron/energy transfer reversible addition-fragmentation chain-transfer in a dual-stimulus manner, in which catalytic activity is regulated reversibly by photoirradiation and the conformational state of the DNA catalyst. These results demonstrate that DNA conformational changes triggered by chemically diverse stimuli can regulate the activity of radical polymerization photocatalysts. This platform offers new capabilities in spatially and temporally controlled polymer synthesis, with potential applications in diagnostics, sensing, and environmentally responsive materials.
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Affiliation(s)
- Caleb A Cox
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ashley N Ogorek
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jean Paul Habumugisha
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Jeffrey D Martell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705, United States
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2
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Babaei A, Pouremamali A, Rafiee N, Sohrabi H, Mokhtarzadeh A, de la Guardia M. Genosensors as an alternative diagnostic sensing approaches for specific detection of various certain viruses: a review of common techniques and outcomes. Trends Analyt Chem 2022; 155:116686. [PMID: 35611316 PMCID: PMC9119280 DOI: 10.1016/j.trac.2022.116686] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 05/08/2022] [Accepted: 05/15/2022] [Indexed: 12/19/2022]
Abstract
Viral infections are responsible for the deaths of millions of people throughout the world. Since outbreak of highly contagious and mutant viruses such as contemporary sars-cov-2 pandemic, has challenged the conventional diagnostic methods, the entity of a thoroughly sensitive, specific, rapid and inexpensive detecting technique with minimum level of false-positivity or -negativity, is desperately needed more than any time in the past decades. Biosensors as minimized devices could detect viruses in simple formats. So far, various nucleic acid, immune- and protein-based biosensors were designed and tested for recognizing the genome, antigen, or protein level of viruses, respectively; however, nucleic acid-based sensing techniques, which is the foundation of constructing genosensors, are preferred not only because of their ultra-sensitivity and applicability in the early stages of infections but also for their ability to differentiate various strains of the same virus. To date, the review articles related to genosensors are just confined to particular pathogenic diseases; In this regard, the present review covers comprehensive information of the research progress of the electrochemical, optical, and surface plasmon resonance (SPR) genosensors that applied for human viruses' diseases detection and also provides a well description of viruses' clinical importance, the conventional diagnosis approaches of viruses and their disadvantages. This review would address the limitations in the current developments as well as the future challenges involved in the successful construction of sensing approaches with the functionalized nanomaterials and also allow exploring into core-research works regarding this area.
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Affiliation(s)
- Abouzar Babaei
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Amir Pouremamali
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Nastaran Rafiee
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hessamaddin Sohrabi
- Department of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz, Iran
| | - Ahad Mokhtarzadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Miguel de la Guardia
- Department of Analytical Chemistry, University of Valencia, Dr. Moliner 50, 46100, Burjassot, Valencia, Spain
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3
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Li Y, Bao Q, Yang S, Yang M, Mao C. Bionanoparticles in cancer imaging, diagnosis, and treatment. VIEW 2022. [DOI: 10.1002/viw.20200027] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Yan Li
- Institute of Applied Bioresource Research College of Animal Science Zhejiang University Hangzhou Zhejiang China
| | - Qing Bao
- School of Materials Science and Engineering Zhejiang University Hangzhou Zhejiang China
| | - Shuxu Yang
- Department of Neurosurgery Sir Run Run Shaw Hospital School of Medicine Zhejiang University Hangzhou Zhejiang China
| | - Mingying Yang
- Institute of Applied Bioresource Research College of Animal Science Zhejiang University Hangzhou Zhejiang China
| | - Chuanbin Mao
- School of Materials Science and Engineering Zhejiang University Hangzhou Zhejiang China
- Department of Chemistry and Biochemistry Stephenson Life Science Research Center University of Oklahoma Norman Oklahoma USA
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4
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Aptamers in Virology-A Consolidated Review of the Most Recent Advancements in Diagnosis and Therapy. Pharmaceutics 2021; 13:pharmaceutics13101646. [PMID: 34683938 PMCID: PMC8540715 DOI: 10.3390/pharmaceutics13101646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/28/2021] [Accepted: 10/01/2021] [Indexed: 01/05/2023] Open
Abstract
The use of short oligonucleotide or peptide molecules as target-specific aptamers has recently garnered substantial attention in the field of the detection and treatment of viral infections. Based on their high affinity and high specificity to desired targets, their use is on the rise to replace antibodies for the detection of viruses and viral antigens. Furthermore, aptamers inhibit intracellular viral transcription and translation, in addition to restricting viral entry into host cells. This has opened up a plethora of new targets for the research and development of novel vaccines against viruses. Here, we discuss the advances made in aptamer technology for viral diagnosis and therapy in the past decade.
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5
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Selection and applications of functional nucleic acids for infectious disease detection and prevention. Anal Bioanal Chem 2021; 413:4563-4579. [PMID: 33506341 PMCID: PMC7840224 DOI: 10.1007/s00216-020-03124-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 11/30/2020] [Accepted: 12/14/2020] [Indexed: 02/07/2023]
Abstract
Infectious diseases caused by pathogenic microorganisms such as viruses and bacteria pose a great threat to human health. Although a significant progress has been obtained in the diagnosis and prevention of infectious diseases, it still remains challenging to develop rapid and cost-effective detection approaches and overcome the side effects of therapeutic agents and pathogen resistance. Functional nucleic acids (FNAs), especially the most widely used aptamers and DNAzymes, hold the advantages of high stability and flexible design, which make them ideal molecular recognition tools for bacteria and viruses, as well as potential therapeutic drugs for infectious diseases. This review summarizes important advances in the selection and detection of bacterial- and virus-associated FNAs, along with their potential prevention ability of infectious disease in recent years. Finally, the challenges and future development directions are concluded.
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6
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Xi H, Juhas M, Zhang Y. G-quadruplex based biosensor: A potential tool for SARS-CoV-2 detection. Biosens Bioelectron 2020; 167:112494. [PMID: 32791468 PMCID: PMC7403137 DOI: 10.1016/j.bios.2020.112494] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 07/26/2020] [Accepted: 07/31/2020] [Indexed: 12/29/2022]
Abstract
G-quadruplex is a non-canonical nucleic acid structure formed by the folding of guanine rich DNA or RNA. The conformation and function of G-quadruplex are determined by a number of factors, including the number and polarity of nucleotide strands, the type of cations and the binding targets. Recent studies led to the discovery of additional advantageous attributes of G-quadruplex with the potential to be used in novel biosensors, such as improved ligand binding and unique folding properties. G-quadruplex based biosensor can detect various substances, such as metal ions, organic macromolecules, proteins and nucleic acids with improved affinity and specificity compared to standard biosensors. The recently developed G-quadruplex based biosensors include electrochemical and optical biosensors. A novel G-quadruplex based biosensors also show better performance and broader applications in the detection of a wide spectrum of pathogens, including SARS-CoV-2, the causative agent of COVID-19 disease. This review highlights the latest developments in the field of G-quadruplex based biosensors, with particular focus on the G-quadruplex sequences and recent applications and the potential of G-quadruplex based biosensors in SARS-CoV-2 detection.
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Affiliation(s)
- Hui Xi
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, 518055, China
| | - Mario Juhas
- Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Yang Zhang
- College of Science, Harbin Institute of Technology (Shenzhen), Shenzhen, Guangdong, 518055, China.
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7
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Ebrahimi SB, Samanta D, Mirkin CA. DNA-Based Nanostructures for Live-Cell Analysis. J Am Chem Soc 2020; 142:11343-11356. [DOI: 10.1021/jacs.0c04978] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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8
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Samanta D, Ebrahimi SB, Mirkin CA. Nucleic-Acid Structures as Intracellular Probes for Live Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1901743. [PMID: 31271253 PMCID: PMC6942251 DOI: 10.1002/adma.201901743] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/08/2019] [Indexed: 05/02/2023]
Abstract
The chemical composition of cells at the molecular level determines their growth, differentiation, structure, and function. Probing this composition is powerful because it provides invaluable insight into chemical processes inside cells and in certain cases allows disease diagnosis based on molecular profiles. However, many techniques analyze fixed cells or lysates of bulk populations, in which information about dynamics and cellular heterogeneity is lost. Recently, nucleic-acid-based probes have emerged as a promising platform for the detection of a wide variety of intracellular analytes in live cells with single-cell resolution. Recent advances in this field are described and common strategies for probe design, types of targets that can be identified, current limitations, and future directions are discussed.
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Affiliation(s)
- Devleena Samanta
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Sasha B Ebrahimi
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Chad A Mirkin
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
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9
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Moutsiopoulou A, Broyles D, Dikici E, Daunert S, Deo SK. Molecular Aptamer Beacons and Their Applications in Sensing, Imaging, and Diagnostics. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1902248. [PMID: 31313884 PMCID: PMC6715520 DOI: 10.1002/smll.201902248] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 05/31/2019] [Indexed: 05/07/2023]
Abstract
The ability to monitor types, concentrations, and activities of different biomolecules is essential to obtain information about the molecular processes within cells. Successful monitoring requires a sensitive and selective tool that can respond to these molecular changes. Molecular aptamer beacon (MAB) is a molecular imaging and detection tool that enables visualization of small or large molecules by combining the selectivity and sensitivity of molecular beacon and aptamer technologies. MAB design leverages structure switching and specific recognition to yield an optical on/off switch in the presence of the target. Various donor-quencher pairs such as fluorescent dyes, quantum dots, carbon-based materials, and metallic nanoparticles have been employed in the design of MABs. In this work, the diverse biomedical applications of MAB technology are focused on. Different conjugation strategies for the energy donor-acceptor pairs are addressed, and the overall sensitivities of each detection system are discussed. The future potential of this technology in the fields of biomedical research and diagnostics is also highlighted.
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Affiliation(s)
- Angeliki Moutsiopoulou
- Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA
- Dr. J. T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, USA
- Department of Chemistry Coral Gables, University of Miami, FL, 33146, USA
| | - David Broyles
- Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA
- Dr. J. T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, USA
| | - Emre Dikici
- Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA
- Dr. J. T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, USA
| | - Sylvia Daunert
- Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA
- Dr. J. T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, USA
- University of Miami Clinical and Translational Science Institute, Miami, FL, 33136, USA
| | - Sapna K Deo
- Leonard M. Miller School of Medicine, Department of Biochemistry and Molecular Biology, University of Miami, Miami, FL, 33136, USA
- Dr. J. T. Macdonald Foundation Biomedical Nanotechnology Institute, University of Miami, Miami, FL, 33136, USA
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10
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Farzin L, Shamsipur M, Samandari L, Sheibani S. HIV biosensors for early diagnosis of infection: The intertwine of nanotechnology with sensing strategies. Talanta 2019; 206:120201. [PMID: 31514868 DOI: 10.1016/j.talanta.2019.120201] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/30/2019] [Accepted: 07/30/2019] [Indexed: 12/20/2022]
Abstract
Human immunodeficiency virus (HIV) is a lentivirus that leads to acquired immunodeficiency syndrome (AIDS). With increasing awareness of AIDS emerging as a global public health threat, different HIV testing kits have been developed to detect antibodies (Ab) directed toward different parts of HIV. A great limitation of these tests is that they can not detect HIV antibodies during early virus infection. Therefore, to overcome this challenge, a wide range of biosensors have been developed for early diagnosis of HIV infection. A significant amount of these studies have been focused on the application of nanomaterials for improving the sensitivity and accuracy of the sensing methods. Following an introduction into this field, a first section of this review covers the synthesis and applicability of such nanomaterials as metal nanoparticles (NPs), quantum dots (QDs), carbon-based nanomaterials and metal nanoclusters (NCs). A second larger section covers the latest developments concerning nanomaterial-based biosensors for HIV diagnosis, with paying a special attention to the determination of CD4+ cells as a hall mark of HIV infection, HIV gene, HIV p24 core protein, HIV p17 peptide, HIV-1 virus-like particles (VLPs) and HIV related enzymes, particularly those that are passed on from the virus to the CD4+ T lymphocytes and are necessary for viral reproduction within the host cell. These studies are described in detail along with their diverse principles/mechanisms (e.g. electrochemistry, fluorescence, electromagnetic-piezoelectric, surface plasmon resonance (SPR), surface enhanced Raman spectroscopy (SERS) and colorimetry). Despite the significant progress in HIV biosensing in the last years, there is a great need for the development of point-of-care (POC) technologies which are affordable, robust, easy to use, portable, and possessing sufficient quantitative accuracy to enable clinical decision making. In the final section, the focus is on the portable sensing devices as a new standard of POC and personalized diagnostics.
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Affiliation(s)
- Leila Farzin
- Radiation Application Research School, Nuclear Science and Technology Research Institute, P.O. Box, 11365-3486, Tehran, Iran.
| | - Mojtaba Shamsipur
- Department of Chemistry, Razi University, P.O. Box, 67149-67346, Kermanshah, Iran
| | - Leila Samandari
- Department of Chemistry, Razi University, P.O. Box, 67149-67346, Kermanshah, Iran
| | - Shahab Sheibani
- Radiation Application Research School, Nuclear Science and Technology Research Institute, P.O. Box, 11365-3486, Tehran, Iran
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11
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Fatin MF, Rahim Ruslinda A, Gopinath SCB, Arshad MKM. High-performance interactive analysis of split aptamer and HIV-1 Tat on multiwall carbon nanotube-modified field-effect transistor. Int J Biol Macromol 2018; 125:414-422. [PMID: 30529550 DOI: 10.1016/j.ijbiomac.2018.12.066] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Revised: 12/04/2018] [Accepted: 12/06/2018] [Indexed: 12/27/2022]
Abstract
Interaction between split RNA aptamer and the clinically important target, HIV-1 Tat was investigated on a biosensing surface transduced by functionally choreographed multiwall carbon nanotubes (MWCNTs). Acid oxidation was performed to functionalize MWCNTs with carboxyl functional groups. X-ray photoelectron spectroscopy analysis had profound ~2.91% increment in overall oxygen group and ~1% increment was noticed with a specific carboxyl content owing to CO and OCO bonding. The interaction between split RNA aptamer and HIV-1 Tat protein was quantified by electrical measurements with the current signal (Ids) over a gate voltage (Vgs). Initially, 34.4 mV gate voltage shift was observed by the immobilization of aptamer on MWCNT. With aptamer and HIV-1 Tat interaction, the current flow was decreased with the concomitant gate voltage shift of 23.5 mV. The attainment of sensitivity with split aptamer and HIV-1 Tat interaction on the fabricated device was 600 pM. To ensure the genuine interaction of aptamer with HIV-1 Tat, other HIV-1 proteins, Nef and p24 were interacted with aptamer and they displayed the negligible interferences with gate voltage shift of 3.5 mV and 5.7 mV, which shows 4 and 2.5 folds lesser than HIV-1 Tat interaction, respectively.
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Affiliation(s)
- M F Fatin
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, Kangar 01000, Perlis, Malaysia
| | - A Rahim Ruslinda
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, Kangar 01000, Perlis, Malaysia.
| | - Subash C B Gopinath
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, Kangar 01000, Perlis, Malaysia; School of Bioprocess Engineering, Universiti Malaysia Perlis, 02600 Arau, Perlis, Malaysia
| | - M K Md Arshad
- Institute of Nano Electronic Engineering, Universiti Malaysia Perlis, Kangar 01000, Perlis, Malaysia; School of Microelectronic Engineering, Universiti Malaysia Perlis, 02600 Arau, Pauh putra, Perlis, Malaysia
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12
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Stewart MP, Langer R, Jensen KF. Intracellular Delivery by Membrane Disruption: Mechanisms, Strategies, and Concepts. Chem Rev 2018; 118:7409-7531. [PMID: 30052023 PMCID: PMC6763210 DOI: 10.1021/acs.chemrev.7b00678] [Citation(s) in RCA: 382] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Intracellular delivery is a key step in biological research and has enabled decades of biomedical discoveries. It is also becoming increasingly important in industrial and medical applications ranging from biomanufacture to cell-based therapies. Here, we review techniques for membrane disruption-based intracellular delivery from 1911 until the present. These methods achieve rapid, direct, and universal delivery of almost any cargo molecule or material that can be dispersed in solution. We start by covering the motivations for intracellular delivery and the challenges associated with the different cargo types-small molecules, proteins/peptides, nucleic acids, synthetic nanomaterials, and large cargo. The review then presents a broad comparison of delivery strategies followed by an analysis of membrane disruption mechanisms and the biology of the cell response. We cover mechanical, electrical, thermal, optical, and chemical strategies of membrane disruption with a particular emphasis on their applications and challenges to implementation. Throughout, we highlight specific mechanisms of membrane disruption and suggest areas in need of further experimentation. We hope the concepts discussed in our review inspire scientists and engineers with further ideas to improve intracellular delivery.
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Affiliation(s)
- Martin P. Stewart
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Robert Langer
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Klavs F. Jensen
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
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13
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Li P, Yu Q, Zhou L, Dong D, Wei S, Ya H, Chen B, Qin Q. Probing and characterizing the high specific sequences of ssDNA aptamer against SGIV-infected cells. Virus Res 2018; 246:46-54. [PMID: 29341876 DOI: 10.1016/j.virusres.2018.01.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2017] [Revised: 12/07/2017] [Accepted: 01/12/2018] [Indexed: 12/15/2022]
Abstract
As the major viral pathogen of grouper aquaculture, Singapore grouper iridovirus (SGIV) has caused great economic losses in China and Southeast Asia. In the previous study, we have generated highly specific ssDNA aptamers against SGIV-infected grouper spleen cells (GS) by Systematic Evolution of Ligands by Exponential Enrichment technology (SELEX), in which Q2 had the highest binding affinity of 16.43 nM. In this study, we would try to identify the specific sequences in the aptamer Q2 that exhibited the high binding affinity to SGIV-infected cells by truncating the original Q2 into some different specific segments. We first evaluated the specificity and binding affinity of these truncated aptamers to SGIV-infected cells by flow cytometry, fluorescent imaging of cells and aptamer-based enzyme-linked apta-sorbent assay (ELASA). We then performed cytotoxicity analysis, assessment of the inhibitory effects upon SGIV infection and the celluar internalization kinetics of each truncated aptamer. Compared to the initial Q2, one of the truncated aptamer Q2-C5 showed a 3-fold increase in the binding affinity for SGIV-infected cells, and held more effective inhibitory effects, higher internalization kinetics and stability. Hence, the aptamer's truncated methods could be applied in the research of identifying aptamer's key sequences. The shorter, structure optimizing aptamer showed more excellent performance over the originally selected aptamer, which could potentially be applied in developing commercial detection probes for the early and rapid diagnosis of SGIV infection, and highly specific therapeutic drugs against SGIV infection.
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Affiliation(s)
- Pengfei Li
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Sciences, Nanning 530007, China
| | - Qing Yu
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Sciences, Nanning 530007, China
| | - Lingli Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha 410081, China
| | - Dexin Dong
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Sciences, Nanning 530007, China
| | - Shina Wei
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Hanzheng Ya
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Sciences, Nanning 530007, China
| | - Bo Chen
- Guangxi Key Laboratory of Marine Environmental Science, Guangxi Academy of Sciences, Nanning 530007, China
| | - Qiwei Qin
- College of Marine Sciences, South China Agricultural University, Guangzhou 510642, China.
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14
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Functional nucleic acids as in vivo metabolite and ion biosensors. Biosens Bioelectron 2017; 94:94-106. [DOI: 10.1016/j.bios.2017.02.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 02/20/2017] [Accepted: 02/20/2017] [Indexed: 12/27/2022]
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15
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Li P, Zhou L, Wei J, Yu Y, Yang M, Wei S, Qin Q. Development and characterization of aptamer-based enzyme-linked apta-sorbent assay for the detection of Singapore grouper iridovirus infection. J Appl Microbiol 2016; 121:634-43. [PMID: 27124762 DOI: 10.1111/jam.13161] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 01/31/2016] [Accepted: 02/21/2016] [Indexed: 01/18/2023]
Abstract
AIMS Singapore grouper iridovirus (SGIV) is a devastating aquaculture virus responsible for heavy economic losses to grouper, Epinephelus sp. aquaculture. The aim of this study was to develop a rapid and sensitive detection method for SGIV infections in infected groupers. METHODS AND RESULTS We previously generated DNA aptamers against SGIV-infected cells. In this study, we established and characterized a novel aptamer (Q3)-based enzyme-linked apta-sorbent assay (ELASA) for the detection of SGIV infection in Epinephelus coioides. The Q3-based ELASA could detect SGIV infection rapidly in vitro and in vivo, with high specificity and stability. Q3-based ELASA specifically recognized SGIV-infected cells, but not other-virus-infected cells or uninfected cells. Q3-based ELASA detected SGIV infection in a dose-dependent manner at Q3 concentrations as low as 125 nmol l(-1) . The results in relation to SGIV-infected cells (5 × 10(4) ), incubation time (1 min) and incubation temperature (37°C) demonstrated that Q3-based ELASA could detect SGIV infection quickly and stably, superior to antibody-based enzyme-linked immunosorbent assay. Q3-based ELASA could detect the presence of SGIV infection in kidney, liver and spleen samples in vivo, at dilutions of 1/50, 1/100 and 1/50 respectively. The complete detection process took 1-2 h. CONCLUSIONS Q3-based ELASA could be a useful tool for diagnosing SGIV infection. SIGNIFICANCE AND IMPACT OF THE STUDY This is the first developed aptamer-based ELASA for detecting SGIV infection, and is widely applicable in grouper aquaculture industry in light of its rapidity, and high specificity and stability.
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Affiliation(s)
- P Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - L Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - J Wei
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Y Yu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,University of Chinese Academy of Sciences, Beijing, China
| | - M Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - S Wei
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China
| | - Q Qin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, China.,College of Marine Sciences, South China Agricultural University, Guangzhou, China
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16
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Li P, Zhou L, Yu Y, Yang M, Ni S, Wei S, Qin Q. Characterization of DNA aptamers generated against the soft-shelled turtle iridovirus with antiviral effects. BMC Vet Res 2015; 11:245. [PMID: 26419355 PMCID: PMC4588899 DOI: 10.1186/s12917-015-0559-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Accepted: 09/22/2015] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Soft-shelled turtle iridovirus (STIV) causes severe systemic disease in farmed soft-shelled turtles (Trionyx sinensis). More efficient methods of controlling and detecting STIV infections are urgently needed. METHODS In this study, we generated eight single-stranded DNA (ssDNA) aptamers against STIV using systematic evolution of ligands by exponential enrichment (SELEX). RESULTS The aptamers formed representative stem-loop secondary structures. Electrophoretic mobility shift assays and fluorescent localization showed that the selected aptamers had high binding affinity for STIV. Aptamer QA-36 had the highest calculated binding affinity (K d ) of 53.8 nM. Flow cytometry and fluorescence microscopy of cell-aptamer interactions demonstrated that QA-12 was able to recognize both STIV-infected cells and tissues with a high level of specificity. Moreover, the selected aptamers inhibited STIV infection in vitro and in vivo, with aptamer QA-36 demonstrating the greatest protective effect against STIV and inhibiting STIV infection in a dose-dependent manner. DISCUSSION We generated DNA aptamers that bound STIV with a high level of specificity, providing an alternative means for investigating STIV pathogenesis, drug development, and medical therapies for STIV infection. CONCLUSIONS These DNA aptamers may thus be suitable antiviral candidates for the control of STIV infections.
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Affiliation(s)
- Pengfei Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Lingli Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Yepin Yu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Min Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China
| | - Songwei Ni
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China
| | - Shina Wei
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China.
| | - Qiwei Qin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou, 510301, China. .,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing, 100049, China.
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17
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Li P, Wei S, Zhou L, Yang M, Yu Y, Wei J, Jiang G, Qin Q. Selection and characterization of novel DNA aptamers specifically recognized by Singapore grouper iridovirus-infected fish cells. J Gen Virol 2015; 96:3348-3359. [PMID: 26310792 DOI: 10.1099/jgv.0.000270] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Singapore grouper iridovirus (SGIV) is a major viral pathogen of grouper aquaculture, and has caused heavy economic losses in China and South-east Asia. In this study, we generated four ssDNA aptamers against SGIV-infected grouper spleen (GS) cells using SELEX (systematic evolution of ligands by exponential enrichment) technology. Four aptamers exhibited high affinity to SGIV-infected GS cells, in particular the Q2 aptamer. Q2 had a binding affinity of 12.09 nM, the highest of the four aptamers. These aptamers also recognized SGIV-infected tissues with high levels of specificity. Protease treatment and flow cytometry analysis of SGIV-infected cells revealed that the target molecules of the Q3, Q4 and Q5 aptamers were trypsin-sensitive proteins, whilst the target molecules of Q2 might be membrane lipids or surface proteins that were not trypsin-sensitive. The generated aptamers appeared to inhibit SGIV infection in vitro. Aptamer Q2 conferred the highest levels of protection against SGIV and was able to inhibit SGIV infection in a dose-dependent manner. In addition, Q2 was efficiently internalized by SGIV-infected GS cells and localized at the viral assembly sites. Our results demonstrated that the four novel aptamers we generated were specific for SGIV-infected cells and could potentially be applied as rapid molecular diagnostic test reagents or therapeutic drugs targeting SGIV.
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Affiliation(s)
- Pengfei Li
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, PR China
| | - Shina Wei
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China
| | - Lingli Zhou
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, PR China
| | - Min Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China
| | - Yepin Yu
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, PR China
| | - Jingguang Wei
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China
| | - Guohua Jiang
- Analytical and Testing Center, Beijing Normal University, Xinjiekouwai Street, Beijing 100875, PR China
| | - Qiwei Qin
- Key Laboratory of Tropical Marine Bio-resources and Ecology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 164 West Xingang Road, Guangzhou 510301, PR China.,University of Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100049, PR China
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18
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Davydova A, Vorobjeva M, Pyshnyi D, Altman S, Vlassov V, Venyaminova A. Aptamers against pathogenic microorganisms. Crit Rev Microbiol 2015; 42:847-65. [PMID: 26258445 PMCID: PMC5022137 DOI: 10.3109/1040841x.2015.1070115] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
An important current issue of modern molecular medicine and biotechnology is the search for new approaches to early diagnostic assays and adequate therapy of infectious diseases. One of the promising solutions to this problem might be a development of nucleic acid aptamers capable of interacting specifically with bacteria, protozoa, and viruses. Such aptamers can be used for the specific recognition of infectious agents as well as for blocking of their functions. The present review summarizes various modern SELEX techniques used in this field, and of several currently identified aptamers against viral particles and unicellular organisms, and their applications. The prospects of applying nucleic acid aptamers for the development of novel detection systems and antibacterial and antiviral drugs are discussed.
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Affiliation(s)
- Anna Davydova
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Maria Vorobjeva
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Dmitrii Pyshnyi
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Sidney Altman
- b Department of Molecular, Cellular and Developmental Biology , Yale University , New Haven , CT , USA
| | - Valentin Vlassov
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
| | - Alya Venyaminova
- a Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences , Novosibirsk , Russia and
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19
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Saberian-Borujeni M, Johari-Ahar M, Hamzeiy H, Barar J, Omidi Y. Nanoscaled aptasensors for multi-analyte sensing. ACTA ACUST UNITED AC 2014; 4:205-15. [PMID: 25671177 PMCID: PMC4298712 DOI: 10.15171/bi.2014.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 09/03/2014] [Accepted: 11/08/2014] [Indexed: 12/21/2022]
Abstract
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Introduction: Nanoscaled aptamers (Aps), as short single-stranded DNA or RNA oligonucleotides, are able to bind to their specific targets with high affinity, upon which they are considered as powerful diagnostic and analytical sensing tools (the so-called "aptasensors"). Aptamers are selected from a random pool of oligonucleotides through a procedure known as "systematic evolution of ligands by exponential enrichment".
Methods: In this work, the most recent studies in the field of aptasensors are reviewed and discussed with a main focus on the potential of aptasensors for the multianalyte detection(s).
Results: Due to the specific folding capability of aptamers in the presence of analyte, aptasensors have substantially successfully been exploited for the detection of a wide range of small and large molecules (e.g., drugs and their metabolites, toxins, and associated biomarkers in various diseases) at very low concentrations in the biological fluids/samples even in presence of interfering species.
Conclusion: Biological samples are generally considered as complexes in the real biological media. Hence, the development of aptasensors with capability to determine various targets simultaneously within a biological matrix seems to be our main challenge. To this end, integration of various key scientific dominions such as bioengineering and systems biology with biomedical researches are inevitable.
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Affiliation(s)
- Mehdi Saberian-Borujeni
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Johari-Ahar
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Hamzeiy
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Jaleh Barar
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Yadollah Omidi
- Research Center for Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran
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20
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Métifiot M, Amrane S, Litvak S, Andreola ML. G-quadruplexes in viruses: function and potential therapeutic applications. Nucleic Acids Res 2014; 42:12352-66. [PMID: 25332402 PMCID: PMC4227801 DOI: 10.1093/nar/gku999] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 09/26/2014] [Accepted: 10/06/2014] [Indexed: 12/15/2022] Open
Abstract
G-rich nucleic acids can form non-canonical G-quadruplex structures (G4s) in which four guanines fold in a planar arrangement through Hoogsteen hydrogen bonds. Although many biochemical and structural studies have focused on DNA sequences containing successive, adjacent guanines that spontaneously fold into G4s, evidence for their in vivo relevance has recently begun to accumulate. Complete sequencing of the human genome highlighted the presence of ∼300,000 sequences that can potentially form G4s. Likewise, the presence of putative G4-sequences has been reported in various viruses genomes [e.g., Human immunodeficiency virus (HIV-1), Epstein-Barr virus (EBV), papillomavirus (HPV)]. Many studies have focused on telomeric G4s and how their dynamics are regulated to enable telomere synthesis. Moreover, a role for G4s has been proposed in cellular and viral replication, recombination and gene expression control. In parallel, DNA aptamers that form G4s have been described as inhibitors and diagnostic tools to detect viruses [e.g., hepatitis A virus (HAV), EBV, cauliflower mosaic virus (CaMV), severe acute respiratory syndrome virus (SARS), simian virus 40 (SV40)]. Here, special emphasis will be given to the possible role of these structures in a virus life cycle as well as the use of G4-forming oligonucleotides as potential antiviral agents and innovative tools.
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Affiliation(s)
- Mathieu Métifiot
- CNRS UMR-5234, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Samir Amrane
- INSERM, U869, IECB, ARNA laboratory, Université de Bordeaux, 2 Rue Robert Escarpit 33600 Pessac, France
| | - Simon Litvak
- CNRS UMR-5234, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
| | - Marie-Line Andreola
- CNRS UMR-5234, Université de Bordeaux, 146 Rue Léo Saignat, 33076 Bordeaux, France
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21
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Mbita Z, Hull R, Dlamini Z. Human immunodeficiency virus-1 (HIV-1)-mediated apoptosis: new therapeutic targets. Viruses 2014; 6:3181-227. [PMID: 25196285 PMCID: PMC4147692 DOI: 10.3390/v6083181] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2014] [Revised: 06/12/2014] [Accepted: 07/08/2014] [Indexed: 12/18/2022] Open
Abstract
HIV has posed a significant challenge due to the ability of the virus to both impair and evade the host’s immune system. One of the most important mechanisms it has employed to do so is the modulation of the host’s native apoptotic pathways and mechanisms. Viral proteins alter normal apoptotic signaling resulting in increased viral load and the formation of viral reservoirs which ultimately increase infectivity. Both the host’s pro- and anti-apoptotic responses are regulated by the interactions of viral proteins with cell surface receptors or apoptotic pathway components. This dynamic has led to the development of therapies aimed at altering the ability of the virus to modulate apoptotic pathways. These therapies are aimed at preventing or inhibiting viral infection, or treating viral associated pathologies. These drugs target both the viral proteins and the apoptotic pathways of the host. This review will examine the cell types targeted by HIV, the surface receptors exploited by the virus and the mechanisms whereby HIV encoded proteins influence the apoptotic pathways. The viral manipulation of the hosts’ cell type to evade the immune system, establish viral reservoirs and enhance viral proliferation will be reviewed. The pathologies associated with the ability of HIV to alter apoptotic signaling and the drugs and therapies currently under development that target the ability of apoptotic signaling within HIV infection will also be discussed.
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Affiliation(s)
- Zukile Mbita
- College of Agriculture and Environmental Sciences, University of South Africa, Florida Science Campus, C/o Christiaan de Wet and Pioneer Avenue P/Bag X6, Johannesburg 1710, South Africa.
| | - Rodney Hull
- College of Agriculture and Environmental Sciences, University of South Africa, Florida Science Campus, C/o Christiaan de Wet and Pioneer Avenue P/Bag X6, Johannesburg 1710, South Africa.
| | - Zodwa Dlamini
- College of Agriculture and Environmental Sciences, University of South Africa, Florida Science Campus, C/o Christiaan de Wet and Pioneer Avenue P/Bag X6, Johannesburg 1710, South Africa.
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22
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Toga T, Kuraoka I, Yasui A, Iwai S. A transfection reporter for the prevention of false-negative results in molecular beacon experiments. Anal Biochem 2013; 440:9-11. [PMID: 23685051 DOI: 10.1016/j.ab.2013.04.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 04/30/2013] [Indexed: 11/26/2022]
Abstract
We previously developed a molecular beacon-type probe to detect the strand scission in cellular base excision repair and found that the phosphodiester linkages in the fluorophore/quencher linkers were cleaved. This reaction was applied to a transfection reporter, which contained the unmodified phosphodiester in the linker to another type of fluorophore. After cotransfection of cells with the probe and the reporter, the signals were used to detect the incision and to confirm the proper transfection, respectively. This method will contribute to the prevention of false-negative results in experiments using molecular beacon-type probes.
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Affiliation(s)
- Tatsuya Toga
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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23
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Oligonucleotide optical switches for intracellular sensing. Anal Bioanal Chem 2013; 405:6181-96. [PMID: 23793395 DOI: 10.1007/s00216-013-7086-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 05/16/2013] [Accepted: 05/17/2013] [Indexed: 12/16/2022]
Abstract
Fluorescence imaging coupled with nanotechnology is making possible the development of powerful tools in the biological field for applications such as cellular imaging and intracellular messenger RNA monitoring and detection. The delivery of fluorescent probes into cells and tissues is currently receiving growing interest because such molecules, often coupled to nanodimensional materials, can conveniently allow the preparation of small tools to spy on cellular mechanisms with high specificity and sensitivity. The purpose of this review is to provide an exhaustive overview of current research in oligonucleotide optical switches for intracellular sensing with a focus on the engineering methods adopted for these oligonucleotides and the more recent and fascinating techniques for their internalization into living cells. Oligonucleotide optical switches can be defined as specifically designed short nucleic acid molecules capable of turning on or modifying their light emission on molecular interaction with well-defined molecular targets. Molecular beacons, aptamer beacons, hybrid molecular probes, and simpler linear oligonucleotide switches are the most promising optical nanosensors proposed in recent years. The intracellular targets which have been considered for sensing are a plethora of messenger-RNA-expressing cellular proteins and enzymes, or, directly, proteins or small molecules in the case of sensing through aptamer-based switches. Engineering methods, including modification of the oligonucleotide itself with locked nucleic acids, peptide nucleic acids, or L-DNA nucleotides, have been proposed to enhance the stability of nucleases and to prevent false-negative and high background optical signals. Conventional delivery techniques are treated here together with more innovative methods based on the coupling of the switches with nano-objects.
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Zhang H, Li F, Dever B, Li XF, Le XC. DNA-mediated homogeneous binding assays for nucleic acids and proteins. Chem Rev 2012; 113:2812-41. [PMID: 23231477 DOI: 10.1021/cr300340p] [Citation(s) in RCA: 339] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hongquan Zhang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
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Abstract
Molecular imaging has greatly advanced basic biology and translational medicine through visualization and quantification of single/multiple molecular events temporally and spatially in a cellular context and in living organisms. Aptamers, short single-stranded nucleic acids selected in vitro to bind a broad range of target molecules avidly and specifically, are ideal molecular recognition elements for probe development in molecular imaging. This review summarizes the current state of aptamer-based biosensor development (probe design and imaging modalities) and their application in imaging small molecules, nucleic acids and proteins mostly in a cellular context with some animal studies. The article is concluded with a brief discussion on the perspective of aptamer-based molecular imaging.
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Affiliation(s)
- Tianjiao Wang
- Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA.
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Deal RB. Grand Challenge: Accelerating Discovery through Technology Development. FRONTIERS IN PLANT SCIENCE 2011; 2:41. [PMID: 22629262 PMCID: PMC3355533 DOI: 10.3389/fpls.2011.00041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 08/02/2011] [Indexed: 05/04/2023]
Affiliation(s)
- Roger B. Deal
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattle, WA, USA
- *Correspondence:
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