1
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Fluorescent Platforms for RNA Chemical Biology Research. Genes (Basel) 2022; 13:genes13081348. [PMID: 36011259 PMCID: PMC9407474 DOI: 10.3390/genes13081348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/21/2022] [Accepted: 07/22/2022] [Indexed: 12/03/2022] Open
Abstract
Efficient detection and observation of dynamic RNA changes remain a tremendous challenge. However, the continuous development of fluorescence applications in recent years enhances the efficacy of RNA imaging. Here we summarize some of these developments from different aspects. For example, single-molecule fluorescence in situ hybridization (smFISH) can detect low abundance RNA at the subcellular level. A relatively new aptamer, Mango, is widely applied to label and track RNA activities in living cells. Molecular beacons (MBs) are valid for quantifying both endogenous and exogenous mRNA and microRNA (miRNA). Covalent binding enzyme labeling fluorescent group with RNA of interest (ROI) partially overcomes the RNA length limitation associated with oligonucleotide synthesis. Forced intercalation (FIT) probes are resistant to nuclease degradation upon binding to target RNA and are used to visualize mRNA and messenger ribonucleoprotein (mRNP) activities. We also summarize the importance of some fluorescence spectroscopic techniques in exploring the function and movement of RNA. Single-molecule fluorescence resonance energy transfer (smFRET) has been employed to investigate the dynamic changes of biomolecules by covalently linking biotin to RNA, and a focus on dye selection increases FRET efficiency. Furthermore, the applications of fluorescence assays in drug discovery and drug delivery have been discussed. Fluorescence imaging can also combine with RNA nanotechnology to target tumors. The invention of novel antibacterial drugs targeting non-coding RNAs (ncRNAs) is also possible with steady-state fluorescence-monitored ligand-binding assay and the T-box riboswitch fluorescence anisotropy assay. More recently, COVID-19 tests using fluorescent clustered regularly interspaced short palindromic repeat (CRISPR) technology have been demonstrated to be efficient and clinically useful. In summary, fluorescence assays have significant applications in both fundamental and clinical research and will facilitate the process of RNA-targeted new drug discovery, therefore deserving further development and updating.
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2
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Bustamante-Jaramillo LF, Fingal J, Blondot ML, Rydell GE, Kann M. Imaging of Hepatitis B Virus Nucleic Acids: Current Advances and Challenges. Viruses 2022; 14:v14030557. [PMID: 35336964 PMCID: PMC8950347 DOI: 10.3390/v14030557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/30/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022] Open
Abstract
Hepatitis B virus infections are the main reason for hepatocellular carcinoma development. Current treatment reduces the viral load but rarely leads to virus elimination. Despite its medical importance, little is known about infection dynamics on the cellular level not at least due to technical obstacles. Regardless of infections leading to extreme viral loads, which may reach 1010 virions per mL serum, hepatitis B viruses are of low abundance and productivity in individual cells. Imaging of the infections in cells is thus a particular challenge especially for cccDNA that exists only in a few copies. The review describes the significance of microscopical approaches on genome and transcript detection for understanding hepatitis B virus infections, implications for understanding treatment outcomes, and recent microscopical approaches, which have not been applied in HBV research.
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Affiliation(s)
- Luisa F. Bustamante-Jaramillo
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden; (L.F.B.-J.); (J.F.); (G.E.R.)
| | - Joshua Fingal
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden; (L.F.B.-J.); (J.F.); (G.E.R.)
| | - Marie-Lise Blondot
- Microbiologie Fondamentale et Pathogénicité (MFP), CNRS UMR 5234, University of Bordeaux, 33076 Bordeaux, France;
| | - Gustaf E. Rydell
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden; (L.F.B.-J.); (J.F.); (G.E.R.)
| | - Michael Kann
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden; (L.F.B.-J.); (J.F.); (G.E.R.)
- Region Västra Götaland, Department of Clinical Microbiology, Sahlgrenska University Hospital, 405 30 Gothenburg, Sweden
- Correspondence:
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3
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Mao S, Ying Y, Wu R, Chen AK. Recent Advances in the Molecular Beacon Technology for Live-Cell Single-Molecule Imaging. iScience 2020; 23:101801. [PMID: 33299972 PMCID: PMC7702005 DOI: 10.1016/j.isci.2020.101801] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Nucleic acids, aside from being best known as the carrier of genetic information, are versatile biomaterials for constructing nanoscopic devices for biointerfacing, owing to their unique properties such as specific base pairing and predictable structure. For live-cell analysis of native RNA transcripts, the most widely used nucleic acid-based nanodevice has been the molecular beacon (MB), a class of stem-loop-forming probes that is activated to fluoresce upon hybridization with target RNA. Here, we overview efforts that have been made in developing MB-based bioassays for sensitive intracellular analysis, particularly at the single-molecule level. We also describe challenges that are currently limiting the widespread use of MBs and provide possible solutions. With continued refinement of MBs in terms of labeling specificity and detection accuracy, accompanied by new development in imaging platforms with unprecedented sensitivity, the application of MBs is envisioned to expand in various biological research fields.
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Affiliation(s)
- Shiqi Mao
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Yachen Ying
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Ruonan Wu
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
| | - Antony K. Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, No. 5 Yiheyuan Road, Haidian District, Beijing 100871, China
- Corresponding author
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4
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Li H, Li Y, Xiao Y, Zhang B, Cheng Z, Shi J, Xiong J, Li Z, Zhang K. Well-Defined DNA-Polymer Miktoarm Stars for Enzyme-Resistant Nanoflares and Carrier-Free Gene Regulation. Bioconjug Chem 2020; 31:530-536. [PMID: 32041403 DOI: 10.1021/acs.bioconjchem.0c00017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Herein, we report a star-architectured poly(ethylene glycol) (PEG)-oligonucleotide nanoconjugate of a well-defined molecular structure. Based upon fullerene C60 cores, each star bears precisely 1 DNA strand and 11 polymer chains. The elevated PEG density provides the DNA with steric selectivity: the DNA is significantly more resistant to nuclease digestion while remaining able to hybridize with a complementary sequence. The degree of resistance increases as the centers of mass for the DNA and fullerene are closer together. Such steric selectivity reduces protein-related background signals of the nanoflares synthesized from these miktoarm star polymers. Importantly, the stars improve cellular uptake and regulate gene expression as a non-cytotoxic, single-entity antisense agent without the need for a transfection carrier.
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Affiliation(s)
- Hui Li
- Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Yang Li
- Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Yue Xiao
- Institute of Chemical Biology and Clinical Application at the First Affiliated Hospital, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China.,Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Bohan Zhang
- Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Zehong Cheng
- Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Jianqiao Shi
- Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Jing Xiong
- Institute of Chemical Biology and Nanomedicine, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, P. R. China
| | - Zhaohui Li
- Institute of Chemical Biology and Clinical Application at the First Affiliated Hospital, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China
| | - Ke Zhang
- Institute of Chemical Biology and Clinical Application at the First Affiliated Hospital, Henan Joint International Research Laboratory of Green Construction of Functional Molecules and Their Bioanalytical Applications, College of Chemistry, Zhengzhou University, Zhengzhou 450001, P. R. China.,Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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5
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Feng X, Kang W, Wu X, Wang S, Liu F. Quantitative Detection and Real-Time Monitoring of Endogenous mRNA at the Single Live Cell Level Using a Ratiometric Molecular Beacon. ACS APPLIED MATERIALS & INTERFACES 2019; 11:28752-28761. [PMID: 31329405 DOI: 10.1021/acsami.9b12394] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Messenger ribonucleic acid (mRNA) plays an important role in various cellular processes. however, traditional techniques cannot realize mRNA detections in live cells as they rely on mRNA purification or cell fixation. To achieve real-time and quantitative mRNA detections at a single live cell level, a single-strand stem-loop-structured ratiometric molecular beacon (RMB) composed of the phosphorothioate-modified loop domain on the 2'-O-methyl RNA backbone with a reporter dye, quencher, and reference dye is proposed to detect the Hsp27 mRNA as a modeled endogenous mRNA. When the RMB hybridizes with the target, the stem-loop structure opens, causing separation of the reporter dye and the quencher and restores the reporter fluorescent signals; therefore, the Hsp27 mRNA can be quantitatively detected according to the ratio of the reporter fluorescent signal to the reference fluorescent signal. Both the phosphorothioate and 2'-O-methyl RNA modifications obviously reduce the nonspecific opening, and the additional reference dye ensures the detection precision using co-localization analysis. Not only does this remove the false-positive signal caused by the nuclease degradation-generated RMB fragment, but it also corrects variations caused by direct measurement of reporter fluorescence intensities at a single cell level owing to inhomogeneity in probe delivery. The designed RMB could detect the Hsp27 mRNA with high signal-to-noise ratio and sensitivity as well as excellent specificity and antidegradation capability proved in vitro and in live cells. Furthermore, it was successfully adopted in subcellular localization, quantitative copy number measurements, and even real-time monitoring of Hsp27 mRNA in live cells, demonstrating that the proposed RMB can be a potential quantitative endogenous mRNA detection tool, especially at a single live cell level.
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Affiliation(s)
- Xufei Feng
- Joint International Research Laboratory of Animal Health and Food Safety & Single Molecule Nanometry Laboratory (Sinmolab) , Nanjing Agricultural University , Nanjing 210095 , China
| | - Wenjie Kang
- Joint International Research Laboratory of Animal Health and Food Safety & Single Molecule Nanometry Laboratory (Sinmolab) , Nanjing Agricultural University , Nanjing 210095 , China
| | - Xuping Wu
- The Second Hospital of Nanjing , Nanjing University of Chinese Medicine , Nanjing 210003 , China
| | - Shouyu Wang
- Joint International Research Laboratory of Animal Health and Food Safety & Single Molecule Nanometry Laboratory (Sinmolab) , Nanjing Agricultural University , Nanjing 210095 , China
- Computational Optics Laboratory, School of Science , Jiangnan University , Wuxi , Jiangsu 214122 , China
| | - Fei Liu
- Joint International Research Laboratory of Animal Health and Food Safety & Single Molecule Nanometry Laboratory (Sinmolab) , Nanjing Agricultural University , Nanjing 210095 , China
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6
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Wu X, Mao S, Yang Y, Rushdi MN, Krueger CJ, Chen AK. A CRISPR/molecular beacon hybrid system for live-cell genomic imaging. Nucleic Acids Res 2019; 46:e80. [PMID: 29718399 PMCID: PMC6061827 DOI: 10.1093/nar/gky304] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 04/12/2018] [Indexed: 12/20/2022] Open
Abstract
The clustered regularly interspersed short palindromic repeat (CRISPR) gene-editing system has been repurposed for live-cell genomic imaging, but existing approaches rely on fluorescent protein reporters, making sensitive and continuous imaging difficult. Here, we present a fluorophore-based live-cell genomic imaging system that consists of a nuclease-deactivated mutant of the Cas9 protein (dCas9), a molecular beacon (MB), and an engineered single-guide RNA (sgRNA) harboring a unique MB target sequence (sgRNA-MTS), termed CRISPR/MB. Specifically, dCas9 and sgRNA-MTS are first co-expressed to target a specific locus in cells, followed by delivery of MBs that can then hybridize to MTS to illuminate the target locus. We demonstrated the feasibility of this approach for quantifying genomic loci, for monitoring chromatin dynamics, and for dual-color imaging when using two orthogonal MB/MTS pairs. With flexibility in selecting different combinations of fluorophore/quencher pairs and MB/MTS sequences, our CRISPR/MB hybrid system could be a promising platform for investigating chromatin activities.
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Affiliation(s)
- Xiaotian Wu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.,School of Life Sciences, Peking University, Beijing 100871, China
| | - Shiqi Mao
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Yantao Yang
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Muaz N Rushdi
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.,Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Christopher J Krueger
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.,Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
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7
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Mach KE, Kaushik AM, Hsieh K, Wong PK, Wang TH, Liao JC. Optimizing peptide nucleic acid probes for hybridization-based detection and identification of bacterial pathogens. Analyst 2019; 144:1565-1574. [PMID: 30656297 PMCID: PMC7039532 DOI: 10.1039/c8an02194e] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Point-of-care (POC) diagnostics for infectious diseases have the potential to improve patient care and antibiotic stewardship. Nucleic acid hybridization is at the core of many amplification-free molecular diagnostics and detection probe configuration is key to diagnostic performance. Modified nucleic acids such as peptide nucleic acid (PNA) offer advantages compared to conventional DNA probes allowing for faster hybridization, better stability and minimal sample preparation for direct detection of pathogens. Probes with tethered fluorophore and quencher allow for solution-based assays and eliminate the need for washing steps thereby facilitating integration into microfluidic devices. Here, we compared the sensitivity and specificity of double stranded PNA probes (dsPNA) and PNA molecular beacons targeting E. coli and P. aeruginosa for direct detection of bacterial pathogens. In bulk fluid assays, the dsPNAs had an overall higher fluorescent signal and better sensitivity and specificity than the PNA beacons for pathogen detection. We further designed and tested an expanded panel of dsPNA probes for detection of a wide variety of pathogenic bacteria including probes for universal detection of eubacteria, Enterobacteriaceae family, and P. mirablis. To confirm that the advantage translated to other assay types we compared the PNA beacon and dsPNA in a prototype droplet microfluidic device. Beyond the bulk fluid assay and droplet devices, use of dsPNA probes may be advantageous in a wide variety of assays that employ homogenous nucleic acid hybridization.
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Affiliation(s)
- Kathleen E Mach
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA.
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8
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Chen M, Mao S, Wu X, Ma Z, Yang Y, Krueger CJ, Chen AK. Single-Molecule Analysis of RNA Dynamics in Living Cells Using Molecular Beacons. Methods Mol Biol 2019; 1870:23-39. [PMID: 30539544 DOI: 10.1007/978-1-4939-8808-2_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Over the past decade, emerging evidence has indicated that long intergenic noncoding RNAs (lincRNAs), a class of RNA transcripts greater than 200 nt in length, function as key regulators of gene expression in cellular physiology and pathogenesis. Greater understanding of lincRNA activities, particularly in the context of subcellular localization and dynamic regulation at the single-molecule level, is expected to provide in-depth understanding of molecular mechanisms that regulate cell behavior and disease evolution. We have recently developed a fluorescence-imaging approach to investigate RNA dynamics in living cells at the single-molecule level. This approach entails the use of molecular beacons (MBs), which are a class of stem-loop forming oligonculeotide-based probes that emit detectable fluorescence upon binding to target sequence, and tandem repeats of MB target sequences integrated to the target RNA sequence. Binding of the MBs to the tandem repeats could illuminate the target RNA as a bright spot when imaged by conventional fluorescence microscopy, making the MB-based imaging approach a versatile tool for RNA analysis across laboratories. In this chapter, we describe the development of the MB-based approach and its application for imaging single NEAT1 lincRNA transcripts in living cells.
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Affiliation(s)
- Mingming Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
| | - Shiqi Mao
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Xiaotian Wu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Zhao Ma
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Yantao Yang
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
| | - Christopher J Krueger
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China
- Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, China.
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9
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Chamiolo J, Fang GM, Hövelmann F, Friedrich D, Knoll A, Loewer A, Seitz O. Comparing Agent-Based Delivery of DNA and PNA Forced Intercalation (FIT) Probes for Multicolor mRNA Imaging. Chembiochem 2018; 20:595-604. [PMID: 30326174 PMCID: PMC6470956 DOI: 10.1002/cbic.201800526] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Indexed: 12/19/2022]
Abstract
Fluorogenic oligonucleotide probes allow mRNA imaging in living cells. A key challenge is the cellular delivery of probes. Most delivery agents, such as cell‐penetrating peptides (CPPs) and pore‐forming proteins, require interactions with the membrane. Charges play an important role. To explore the influence of charge on fluorogenic properties and delivery efficiency, we compared peptide nucleic acid (PNA)‐ with DNA‐based forced intercalation (FIT) probes. Perhaps counterintuitively, fluorescence signaling by charged DNA FIT probes proved tolerant to CPP conjugation, whereas CPP–FIT PNA conjugates were affected. Live‐cell imaging was performed with a genetically engineered HEK293 cell line to allow the inducible expression of a specific mRNA target. Blob‐like features and high background were recurring nuisances of the tested CPP and lipid conjugates. By contrast, delivery by streptolysin‐O provided high enhancements of the fluorescence of the FIT probe upon target induction. Notably, DNA‐based FIT probes were brighter and more responsive than PNA‐based FIT probes. Optimized conditions enabled live‐cell multicolor imaging of three different mRNA target sequences.
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Affiliation(s)
- Jasmine Chamiolo
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany
| | - Ge-Min Fang
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany.,Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, P.R. China
| | - Felix Hövelmann
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany
| | - Dhana Friedrich
- Max Delbrück Centrum für Molekulare Medizin, Robert Rössle Strasse 10, 13125, Berlin, Germany.,Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 13, 64287, Darmstadt, Germany
| | - Andrea Knoll
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany
| | - Alexander Loewer
- Max Delbrück Centrum für Molekulare Medizin, Robert Rössle Strasse 10, 13125, Berlin, Germany.,Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 13, 64287, Darmstadt, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany
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10
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Abstract
Conventional molecular beacons (MBs) have been used extensively for imaging specific endogenous RNAs in living cells, but their tendency to generate false-positive signals as a result of nuclease degradation and/or nonspecific binding limits sensitive and accurate imaging of intracellular RNAs. In an attempt to overcome this limitation, MBs have been synthesized with various chemically modified oligonucleotide backbones to confer greater biostability. We have recently developed a new MB architecture composed of 2'-O-methyl RNA (2Me), a fully phosphorothioate (PS) modified loop domain and a phosphodiester stem (2Me/PSLOOP MB). We showed that this new MB exhibits a marginal level of false-positive signals and enables accurate single-molecule imaging of target RNA in living cells. In this chapter, we describe detailed methods that led us to conclude that, among various PS-modified configurations, the 2Me/PSLOOP MB is an optimal design for intracellular RNA analysis.
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11
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Real-Hohn A, Provance DW, Gonçalves RB, Denani CB, de Oliveira AC, Salerno VP, Oliveira Gomes AM. Impairing the function of MLCK, myosin Va or myosin Vb disrupts Rhinovirus B14 replication. Sci Rep 2017; 7:17153. [PMID: 29215055 PMCID: PMC5719429 DOI: 10.1038/s41598-017-17501-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 11/27/2017] [Indexed: 12/19/2022] Open
Abstract
Together, the three human rhinovirus (RV) species are the most frequent cause of the common cold. Because of their high similarity with other viral species of the genus Enterovirus, within the large family Picornaviridae, studies on RV infectious activities often offer a less pathogenic model for more aggressive enteroviruses, e.g. poliovirus or EV71. Picornaviruses enter via receptor mediated endocytosis and replicate in the cytosol. Most of them depend on functional F-actin, Rab proteins, and probably motor proteins. To assess the latter, we evaluated the role of myosin light chain kinase (MLCK) and two myosin V isoforms (Va and Vb) in RV-B14 infection. We report that ML-9, a very specific MLCK inhibitor, dramatically reduced RV-B14 entry. We also demonstrate that RV-B14 infection in cells expressing dominant-negative forms of myosin Va and Vb was impaired after virus entry. Using immunofluorescent localization and immunoprecipitation, we show that myosin Va co-localized with RV-B14 exclusively after viral entry (15 min post infection) and that myosin Vb was present in the clusters of newly synthesized RNA in infected cells. These clusters, observed at 180 min post infection, are reminiscent of replication sites. Taken together, these results identify myosin light chain kinase, myosin Va and myosin Vb as new players in RV-B14 infection that participate directly or indirectly in different stages of the viral cycle.
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Affiliation(s)
- Antonio Real-Hohn
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Departamento de Biociências da Atividade Física, Escola de Educação Física e Desportos, Universidade Federal Rio do Janeiro, Rio de Janeiro, Brazil.,Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Rio de Janeiro, RJ, Brazil
| | - D William Provance
- Center for Technological Development in Health, National Institute of Science and Technology for Innovation in Diseases of Neglected Populations, Oswaldo Cruz Foundation/Fiocruz, Rio de Janeiro, Brazil
| | - Rafael Braga Gonçalves
- Departamento de Bioquímica, Instituto Biomédico, Universidade Federal do Estado do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Rio de Janeiro, RJ, Brazil
| | - Caio Bidueira Denani
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Rio de Janeiro, RJ, Brazil
| | - Andréa Cheble de Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Rio de Janeiro, RJ, Brazil
| | - Verônica P Salerno
- Departamento de Biociências da Atividade Física, Escola de Educação Física e Desportos, Universidade Federal Rio do Janeiro, Rio de Janeiro, Brazil
| | - Andre Marco Oliveira Gomes
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil. .,Instituto Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem, Rio de Janeiro, RJ, Brazil.
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12
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Gupta SD, Sachs Z. Novel single-cell technologies in acute myeloid leukemia research. Transl Res 2017; 189:123-135. [PMID: 28802867 PMCID: PMC6584944 DOI: 10.1016/j.trsl.2017.07.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/18/2017] [Accepted: 07/20/2017] [Indexed: 12/29/2022]
Abstract
Acute myeloid leukemia (AML) is a lethal malignancy because patients who initially respond to chemotherapy eventually relapse with treatment refractory disease. Relapse is caused by leukemia stem cells (LSCs) that reestablish the disease through self-renewal. Self-renewal is the ability of a stem cell to produce copies of itself and give rise to progeny cells. Therefore, therapeutic strategies eradicating LSCs are essential to prevent relapse and achieve long-term remission in AML. AML is a heterogeneous disease both at phenotypic and genotypic levels, and this heterogeneity extends to LSCs. Classical studies in AML have aimed at characterization of the bulk tumor population, thereby masking cellular heterogeneity. Single-cell approaches provide a novel opportunity to elucidate molecular mechanisms in heterogeneous diseases such as AML. In recent years, major advancements in single-cell measurement systems have revolutionized our understanding of the pathophysiology of AML and enabled the characterization of LSCs. Identifying the molecular mechanisms critical to AML LSCs will aid in the development of targeted therapeutic strategies to combat this deadly disease.
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Affiliation(s)
- Soumyasri Das Gupta
- Division of Hematology, Oncology, and Transplantation, Department Medicine, University of Minnesota, Minneapolis, Minn
| | - Zohar Sachs
- Division of Hematology, Oncology, and Transplantation, Department Medicine, University of Minnesota, Minneapolis, Minn; Masonic Cancer Center, University of Minnesota, Minneapolis, Minn.
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13
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Jin C, Fu T, Wang R, Liu H, Zou J, Zhao Z, Ye M, Zhang X, Tan W. Fluorinated molecular beacons as functional DNA nanomolecules for cellular imaging. Chem Sci 2017; 8:7082-7086. [PMID: 29147537 PMCID: PMC5637457 DOI: 10.1039/c7sc02819a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 08/21/2017] [Indexed: 01/16/2023] Open
Abstract
Molecular beacons (MBs) are simple, but practical, fluorescent nanoprobes widely used to detect small molecules, nucleic acids and proteins. However, some challenges still remain when MBs are employed in complex biological environments, such as instability and non-target interference. To meet such challenges, we have designed and synthesized fluorinated molecular beacons (FMBs) as functional DNA nanomolecules for cellular imaging, in which the stem sequence is simply composed of artificial nucleotides with 3,5-bis(trifluoromethyl)benzene (F) as the surrogate base of natural A, T, C and G bases. The introduction of F base into MBs significantly increases their hydrophobicity, and the stem is formed by the assembly of self-complementary base F nucleotides through hydrophobic interactions. Fluorescence studies revealed that FMBs confer improved stability over conventional MBs. To demonstrate the application of FMBs for cellular imaging, we constructed an FMB to detect mRNA in MCF-7 cells, and the FMB was proven to be a practical nanoprobe for cellular imaging of mRNA.
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Affiliation(s)
- Cheng Jin
- Molecular Science and Biomedicine Laboratory , State Key Laboratory of Chemo/Bio-Sensing and Chemometrics , College of Chemistry and Chemical Engineering , College of Life Sciences , Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China . ;
| | - Ting Fu
- Molecular Science and Biomedicine Laboratory , State Key Laboratory of Chemo/Bio-Sensing and Chemometrics , College of Chemistry and Chemical Engineering , College of Life Sciences , Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China . ;
| | - Ruowen Wang
- Molecular Science and Biomedicine Laboratory , State Key Laboratory of Chemo/Bio-Sensing and Chemometrics , College of Chemistry and Chemical Engineering , College of Life Sciences , Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China . ;
- Department of Chemistry , Department of 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 32611-7200 , USA
- Department of Biotechnology and Biomedicine , Yangtze Delta Region Institute of Tsinghua University , Zhejiang 314006 , China
| | - Hui Liu
- Molecular Science and Biomedicine Laboratory , State Key Laboratory of Chemo/Bio-Sensing and Chemometrics , College of Chemistry and Chemical Engineering , College of Life Sciences , Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China . ;
| | - Jianmei Zou
- Molecular Science and Biomedicine Laboratory , State Key Laboratory of Chemo/Bio-Sensing and Chemometrics , College of Chemistry and Chemical Engineering , College of Life Sciences , Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China . ;
| | - Zilong Zhao
- Molecular Science and Biomedicine Laboratory , State Key Laboratory of Chemo/Bio-Sensing and Chemometrics , College of Chemistry and Chemical Engineering , College of Life Sciences , Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China . ;
| | - Mao Ye
- Molecular Science and Biomedicine Laboratory , State Key Laboratory of Chemo/Bio-Sensing and Chemometrics , College of Chemistry and Chemical Engineering , College of Life Sciences , Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China . ;
| | - Xiaobing Zhang
- Molecular Science and Biomedicine Laboratory , State Key Laboratory of Chemo/Bio-Sensing and Chemometrics , College of Chemistry and Chemical Engineering , College of Life Sciences , Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China . ;
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory , State Key Laboratory of Chemo/Bio-Sensing and Chemometrics , College of Chemistry and Chemical Engineering , College of Life Sciences , Aptamer Engineering Center of Hunan Province , Hunan University , Changsha , Hunan 410082 , China . ;
- Department of Chemistry , Department of 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 32611-7200 , USA
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14
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Ma Z, Wu X, Krueger CJ, Chen AK. Engineering Novel Molecular Beacon Constructs to Study Intracellular RNA Dynamics and Localization. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:279-286. [PMID: 28942262 PMCID: PMC5673673 DOI: 10.1016/j.gpb.2017.04.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 04/08/2017] [Accepted: 04/17/2017] [Indexed: 11/25/2022]
Abstract
With numerous advancements in novel biochemical techniques, our knowledge of the role of RNAs in the regulation of cellular physiology and pathology has grown significantly over the past several decades. Nevertheless, detailed information regarding RNA processing, trafficking, and localization in living cells has been lacking due to technical limitations in imaging single RNA transcripts in living cells with high spatial and temporal resolution. In this review, we discuss techniques that have shown great promise for single RNA imaging, followed by highlights in our recent work in the development of molecular beacons (MBs), a class of nanoscale oligonucleotide-probes, for detecting individual RNA transcripts in living cells. With further refinement of MB design and development of more sophisticated fluorescence microscopy techniques, we envision that MB-based approaches could promote new discoveries of RNA functions and activities.
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Affiliation(s)
- Zhao Ma
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Xiaotian Wu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China
| | - Christopher J Krueger
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China; Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing 100871, China.
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15
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Liu X, Ouyang T, Ouyang H, Ren L. Single particle labeling of RNA virus in live cells. Virus Res 2017; 237:14-21. [PMID: 28506790 DOI: 10.1016/j.virusres.2017.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Revised: 05/10/2017] [Accepted: 05/10/2017] [Indexed: 12/17/2022]
Abstract
Real-time and visual tracking of viral infection is crucial for elucidating the infectious and pathogenesis mechanisms. To track the virus successfully, an efficient labeling method is necessary. In this review, we first discuss the practical labeling techniques for virus tracking in live cells. We then describe the current knowledge of interactions between RNA viruses (especially influenza viruses, immunodeficiency viruses, and Flaviviruses) and host cellular structures, obtained using single particle labeling techniques combined with real-time fluorescence microscopy. Single particle labeling provides an easy system for understanding the RNA virus life cycle.
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Affiliation(s)
- Xiaohui Liu
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, Jilin 130062, China
| | - Ting Ouyang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, Jilin 130062, China
| | - Hongsheng Ouyang
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, Jilin 130062, China
| | - Linzhu Ren
- Jilin Provincial Key Laboratory of Animal Embryo Engineering, College of Animal Sciences, Jilin University, Changchun, Jilin 130062, China.
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16
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Chen M, Ma Z, Wu X, Mao S, Yang Y, Tan J, Krueger CJ, Chen AK. A molecular beacon-based approach for live-cell imaging of RNA transcripts with minimal target engineering at the single-molecule level. Sci Rep 2017; 7:1550. [PMID: 28484218 PMCID: PMC5431543 DOI: 10.1038/s41598-017-01740-1] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 04/18/2017] [Indexed: 12/27/2022] Open
Abstract
Analysis of RNA dynamics and localization at the single-molecule level in living cells has been predominantly achieved by engineering target RNAs with large insertions of tandem repeat sequences that are bound by protein-based or oligonucleotide-based fluorescent probes. Thus, individual RNAs are tagged by multiple fluorescent probes, making them detectable by fluorescence microscopy. Since large insertions may affect RNA processes including trafficking and localization, here we present a strategy to visualize single RNA transcripts in living cells using molecular beacons (MBs) - fluorogenic oligonucleotide probes - with minimal target engineering. The MBs are composed of 2′-O-methyl RNAs with a fully phosphorothioate-modified loop domain (2Me/PSLOOP MBs), an architecture that elicits marginal levels of nonspecific signals in cells. We showed that MBs can detect single transcripts containing as few as 8 target repeat sequences with ~90% accuracy. In both the nucleus and the cytoplasm, mRNAs harboring 8 repeats moved faster than those with 32 repeats, suggesting that intracellular activities are less impeded by smaller engineered insertions. We then report the first MB-based imaging of intracellular dynamics and localization of single long noncoding RNAs (lncRNAs). We envision the proposed minimally-engineered, MB-based technology for live-cell single-molecule RNA imaging could facilitate new discoveries in RNA research.
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Affiliation(s)
- Mingming Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China.,Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.,Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Zhao Ma
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Xiaotian Wu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Shiqi Mao
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Yantao Yang
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Jie Tan
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Christopher J Krueger
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China.,Wallace H Coulter Department of Biomedical Engineering, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China.
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17
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Abraham P, Maliekal TT. Single cell biology beyond the era of antibodies: relevance, challenges, and promises in biomedical research. Cell Mol Life Sci 2017; 74:1177-1189. [PMID: 27714408 PMCID: PMC11107591 DOI: 10.1007/s00018-016-2382-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 01/05/2023]
Abstract
Research of the past two decades has proved the relevance of single cell biology in basic research and translational medicine. Successful detection and isolation of specific subsets is the key to understand their functional heterogeneity. Antibodies are conventionally used for this purpose, but their relevance in certain contexts is limited. In this review, we discuss some of these contexts, posing bottle neck for different fields of biology including biomedical research. With the advancement of chemistry, several methods have been introduced to overcome these problems. Even though microfluidics and microraft array are newer techniques exploited for single cell biology, fluorescence-activated cell sorting (FACS) remains the gold standard technique for isolation of cells for many biomedical applications, like stem cell therapy. Here, we present a comprehensive and comparative account of some of the probes that are useful in FACS. Further, we illustrate how these techniques could be applied in biomedical research. It is postulated that intracellular molecular markers like nucleostemin (GNL3), alkaline phosphatase (ALPL) and HIRA can be used for improving the outcome of cardiac as well as bone regeneration. Another field that could utilize intracellular markers is diagnostics, and we propose the use of specific peptide nucleic acid probes (PNPs) against certain miRNAs for cancer surgical margin prediction. The newer techniques for single cell biology, based on intracellular molecules, will immensely enhance the repertoire of possible markers for the isolation of cell types useful in biomedical research.
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Affiliation(s)
- Parvin Abraham
- Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India
| | - Tessy Thomas Maliekal
- Cancer Research, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala, 695014, India.
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18
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Shigeto H, Nakatsuka K, Ikeda T, Hirota R, Kuroda A, Funabashi H. Continuous Monitoring of Specific mRNA Expression Responses with a Fluorescence Resonance Energy Transfer-Based DNA Nano-tweezer Technique That Does Not Require Gene Recombination. Anal Chem 2016; 88:7894-8. [DOI: 10.1021/acs.analchem.6b02710] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Hajime Shigeto
- Institute
for Sustainable Sciences and Development, Hiroshima University, Higashihiroshima, Hiroshima 739-8511, Japan
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Keisuke Nakatsuka
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Takeshi Ikeda
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Ryuichi Hirota
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Akio Kuroda
- Department
of Molecular Biotechnology, Graduate School of Advanced Sciences of
Matter, Hiroshima University, Higashihiroshima, Hiroshima 739-8530, Japan
| | - Hisakage Funabashi
- Institute
for Sustainable Sciences and Development, Hiroshima University, Higashihiroshima, Hiroshima 739-8511, Japan
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19
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Zhao D, Yang Y, Qu N, Chen M, Ma Z, Krueger CJ, Behlke MA, Chen AK. Single-molecule detection and tracking of RNA transcripts in living cells using phosphorothioate-optimized 2'-O-methyl RNA molecular beacons. Biomaterials 2016; 100:172-83. [PMID: 27261815 DOI: 10.1016/j.biomaterials.2016.05.022] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 05/10/2016] [Accepted: 05/17/2016] [Indexed: 12/11/2022]
Abstract
Molecular Beacons (MBs) composed of 2'-O-methyl RNA (2Me) and phosphorothioate (PS) linkages throughout the backbone (2Me/PSFULL MBs) have enabled long-term imaging of RNA in living cells, but excess PS modification can induce nonspecific binding, causing false-positive signals. In this study, we evaluate the intracellular stability of MBs composed of 2Me with various PS modifications, and found that false-positive signals could be reduced to marginal levels when the MBs possess a fully PS-modified loop domain and a phosphodiester stem (2Me/PSLOOP MB). Additionally, 2Me/PSLOOP MBs exhibited uncompromised hybridization kinetics, prolonged functionality and >88% detection accuracy for single RNA transcripts, and could do so without interfering with gene expression or cell growth. Finally, 2Me/PSLOOP MBs could image the dynamics of single mRNA transcripts in the nucleus and the cytoplasm simultaneously, regardless of whether the MBs targeted the 5'- or the 3'-UTR. Together, these findings demonstrate the effectiveness of loop-domain PS modification in reducing nonspecific signals and the potential for sensitive and accurate imaging of individual RNAs at the single-molecule level. With the growing interest in the role of RNA localization and dynamics in health and disease, 2Me/PSLOOP MBs could enable new discoveries in RNA research.
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Affiliation(s)
- Dan Zhao
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Yantao Yang
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Na Qu
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Mingming Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Zhao Ma
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Christopher J Krueger
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China
| | - Mark A Behlke
- Integrated DNA Technologies Inc., Coralville, IA, 52241, USA
| | - Antony K Chen
- Department of Biomedical Engineering, College of Engineering, Peking University, Beijing, 100871, China.
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20
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Zhang C, Ding C, Xiang D, Li L, Ji X, He Z, Xian Y. DNA Functionalized Fluorescent Quantum Dots for Bioanalytical Applications. CHINESE J CHEM 2016. [DOI: 10.1002/cjoc.201500906] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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21
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Gao K, Huang X, Chiang CL, Wang X, Chang L, Boukany P, Marcucci G, Lee R, Lee LJ. Induced Apoptosis Investigation in Wild-type and FLT3-ITD Acute Myeloid Leukemia Cells by Nanochannel Electroporation and Single-cell qRT-PCR. Mol Ther 2016; 24:956-64. [PMID: 26782640 DOI: 10.1038/mt.2016.6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 01/05/2016] [Indexed: 12/28/2022] Open
Abstract
Nanochannel electroporation (NEP) was applied to deliver precise dosages of myeloid cell leukemia-1 (Mcl-1)-specific siRNA and molecular beacons to two types of acute myeloid leukemia (AML) cells, FMS-like tyrosine kinase-3 wild-type (WT) and internal tandem duplications (ITD) type at the single-cell level. NEP, together with single-cell quantitative reverse transcription PCR, led to an observation showing nearly 20-folds more Mcl-1 siRNA than MCL1 mRNA were required to induce cell death for both cell lines and patient blasts, i.e., ~8,800 siRNAs for ~500 ± 50 mRNAs in ITD cells and ~6,000 siRNAs for ~300 ± 50 mRNAs in WT cells. A time-lapse study revealed that >75% MCL1 mRNA was downregulated within 1 hour after delivery of a small amount of siRNA. However, additional siRNA was required to inhibit the newly transcribed mRNA for >12 hours until the cell lost its ability of self-protection recovery. A multidelivery strategy of low doses and short delivery interval, which require 77% less siRNA and has the potential of lower side effects and clinical cost, was as effective as a single high-dose siRNA delivery. Our method provides a viable analytical tool to investigate gene silencing at the single-cell level for oligonucleotide-based therapy.
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Affiliation(s)
- Keliang Gao
- NSF Nanoscale Science and Engineering Center for Affordable Nanoengineering of Polymeric Biomedical Devices, The Ohio State University, Columbus, Ohio, USA.,College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Xiaomeng Huang
- NSF Nanoscale Science and Engineering Center for Affordable Nanoengineering of Polymeric Biomedical Devices, The Ohio State University, Columbus, Ohio, USA.,Molecular Cellular and Developmental Biology, The Ohio State University, Columbus, Ohio, USA.,Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Chi-Ling Chiang
- NSF Nanoscale Science and Engineering Center for Affordable Nanoengineering of Polymeric Biomedical Devices, The Ohio State University, Columbus, Ohio, USA.,Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Xinmei Wang
- NSF Nanoscale Science and Engineering Center for Affordable Nanoengineering of Polymeric Biomedical Devices, The Ohio State University, Columbus, Ohio, USA
| | - Lingqian Chang
- NSF Nanoscale Science and Engineering Center for Affordable Nanoengineering of Polymeric Biomedical Devices, The Ohio State University, Columbus, Ohio, USA
| | - Pouyan Boukany
- NSF Nanoscale Science and Engineering Center for Affordable Nanoengineering of Polymeric Biomedical Devices, The Ohio State University, Columbus, Ohio, USA
| | - Guido Marcucci
- Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio, USA
| | - Robert Lee
- College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Ly James Lee
- NSF Nanoscale Science and Engineering Center for Affordable Nanoengineering of Polymeric Biomedical Devices, The Ohio State University, Columbus, Ohio, USA.,Molecular Cellular and Developmental Biology, The Ohio State University, Columbus, Ohio, USA.,Department of Chemical and Biomolecular Engineering, The Ohio State University, Columbus, Ohio, USA
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22
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Bridle H, Balharry D, Gaiser B, Johnston H. Exploitation of Nanotechnology for the Monitoring of Waterborne Pathogens: State-of-the-Art and Future Research Priorities. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:10762-77. [PMID: 26301863 DOI: 10.1021/acs.est.5b01673] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Contaminated drinking water is one of the most important environmental contributors to the human disease burden. Monitoring of water for the presence of pathogens is an essential part of ensuring drinking water safety. In order to assess water quality it is essential to have methods available to sample and detect the type, level and viability of pathogens in water which are effective, cheap, quick, sensitive, and where possible high throughput. Nanotechnology has the potential to drastically improve the monitoring of waterborne pathogens when compared to conventional approaches. To date, there have been no reviews that outline the applications of nanotechnology in this area despite increasing exploitation of nanotechnology for this purpose. This review is therefore the first overview of the state-of-the-art in the application of nanotechnology to waterborne pathogen sampling and detection schemes. Research in this field has been centered on the use of engineered nanomaterials. The effectiveness and limitations of nanomaterial-based approaches is outlined. A future outlook of the advances that are likely to emerge in this area, as well as recommendations for areas of further research are provided.
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Affiliation(s)
- Helen Bridle
- Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University , Riccarton, Edinburgh, EH14 4AS, United Kingdom
| | - Dominique Balharry
- School of Life Sciences, Heriot-Watt University , Riccarton, Edinburgh, EH14 4AS, United Kingdom
- Centre for Genomics and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh , Western General Hospital, Crewe Road, Edinburgh, EH4 2XU, United Kingdom
| | - Birgit Gaiser
- School of Life Sciences, Heriot-Watt University , Riccarton, Edinburgh, EH14 4AS, United Kingdom
| | - Helinor Johnston
- School of Life Sciences, Heriot-Watt University , Riccarton, Edinburgh, EH14 4AS, United Kingdom
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23
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Funabashi H, Shigeto H, Nakatsuka K, Kuroda A. A FRET-based DNA nano-tweezer technique for the imaging analysis of specific mRNA. Analyst 2015; 140:999-1003. [PMID: 25529369 DOI: 10.1039/c4an02064b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
A DNA nano-tweezer (DNA-NT) structure-based target mRNA detection probe, which uses fluorescence resonance energy transfer (FRET) as a detection signal and works as a single molecule, has been developed. This FRET-paired fluorescent dye-modified DNA-NT, self-assembled from three single-stranded DNAs, alters its structure from open to closed states and produces a FRET signal in response to in vitro transcripts of Hes-1 mRNA. Our results showed that the FRET-based DNA-NT detected both GLUT1 mRNA as a pre-fixed target mRNA model and Hes-1 mRNA as a model expressed inside a living cell. These results confirm the feasibility of using the FRET-based DNA-NT for imaging analysis of target mRNA.
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Affiliation(s)
- Hisakage Funabashi
- Institute for Sustainable Sciences and Development, Hiroshima University, Higashihiroshima, Hiroshima 739-8511, Japan.
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24
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van Duijnhoven SMJ, Robillard MS, Langereis S, Grüll H. Bioresponsive probes for molecular imaging: concepts and in vivo applications. CONTRAST MEDIA & MOLECULAR IMAGING 2015; 10:282-308. [PMID: 25873263 DOI: 10.1002/cmmi.1636] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 01/24/2015] [Accepted: 02/03/2015] [Indexed: 12/30/2022]
Abstract
Molecular imaging is a powerful tool to visualize and characterize biological processes at the cellular and molecular level in vivo. In most molecular imaging approaches, probes are used to bind to disease-specific biomarkers highlighting disease target sites. In recent years, a new subset of molecular imaging probes, known as bioresponsive molecular probes, has been developed. These probes generally benefit from signal enhancement at the site of interaction with its target. There are mainly two classes of bioresponsive imaging probes. The first class consists of probes that show direct activation of the imaging label (from "off" to "on" state) and have been applied in optical imaging and magnetic resonance imaging (MRI). The other class consists of probes that show specific retention of the imaging label at the site of target interaction and these probes have found application in all different imaging modalities, including photoacoustic imaging and nuclear imaging. In this review, we present a comprehensive overview of bioresponsive imaging probes in order to discuss the various molecular imaging strategies. The focus of the present article is the rationale behind the design of bioresponsive molecular imaging probes and their potential in vivo application for the detection of endogenous molecular targets in pathologies such as cancer and cardiovascular disease.
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Affiliation(s)
- Sander M J van Duijnhoven
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,Department of Minimally Invasive Healthcare, Philips Research, Eindhoven, The Netherlands
| | - Marc S Robillard
- Department of Minimally Invasive Healthcare, Philips Research, Eindhoven, The Netherlands
| | - Sander Langereis
- Department of Minimally Invasive Healthcare, Philips Research, Eindhoven, The Netherlands
| | - Holger Grüll
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands.,Department of Minimally Invasive Healthcare, Philips Research, Eindhoven, The Netherlands
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25
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Abstract
Over the past two decades, cell-penetrating peptides (CPPs) have become increasingly popular both in research and in application. There have been numerous studies on the physiochemical characteristics and behavior of CPPs in various environments; likewise, the mechanisms of entry and delivery capabilities of these peptides have also been extensively researched. Besides the fundamental issues, there is an enormous interest in the delivery capabilities of the peptides as the family of CPPs is a promising and mostly non-toxic delivery vector candidate for numerous medical applications such as gene silencing, transgene delivery, and splice correction. Lately, however, there has been an emerging field of study besides the high-profile gene therapy applications-the use of peptides and CPPs to combat various infections caused by harmful bacteria, fungi, and viruses.In this chapter, we aim to provide a short overview of the history and properties of CPPs which is followed by more thorough descriptions of antimicrobial and antiviral peptides. To achieve this, we analyze the origin of such peptides, give an overview of the mechanisms of action and discuss the various practical applications which are ongoing or have been suggested based on research.
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Affiliation(s)
- Kalle Pärn
- Laboratory of Molecular Biotechnology, Institute of Technology, Tartu University, Nooruse 1/517, Tartu, 50411, Estonia,
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26
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Blackstock D, Chen W. Halo-tag mediated self-labeling of fluorescent proteins to molecular beacons for nucleic acid detection. Chem Commun (Camb) 2014; 50:13735-8. [DOI: 10.1039/c4cc07118b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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27
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Real-time imaging of the epithelial-mesenchymal transition using microRNA-200a sequence-based molecular beacon-conjugated magnetic nanoparticles. PLoS One 2014; 9:e102164. [PMID: 25048580 PMCID: PMC4105468 DOI: 10.1371/journal.pone.0102164] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 06/16/2014] [Indexed: 12/30/2022] Open
Abstract
The epithelial-mesenchymal transition (EMT) plays important roles in tumor progression to metastasis. Thus, the development of an imaging probe that can monitor transient periods of the EMT process in live cells is required for a better understanding of metastatic process. Inspired by the fact that the mRNA expression levels of zinc finger E-box-binding homeobox 1 (ZEB1) increase when cells adopt mesenchyme characteristics and that microRNA-200a (miR-200a) can bind to ZEB1 mRNA, we conjugated molecular beacon (MB) mimicking mature miR-200a to magnetic nanoparticles (miR-200a-MB-MNPs) and devised an imaging method to observe transitional changes in the cells during EMT. Transforming growth factor-β1 treated epithelial cells and breast cancer cell lines representing both epithelial and mesenchymal phenotypes were used for the validation of miR-200a-MB-MNPs as an EMT imaging probe. The real-time imaging of live cells acquired with the induction of EMT revealed an increase in fluorescence signals by miR-200a-MB-MNPs, cell morphology alterations, and the loss of cell-cell adhesion. Our results suggest that miR-200a-MB-MNPs can be used as an imaging probe for the real-time monitoring of the EMT process in live cells.
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Wang K, Huang J, Yang X, He X, Liu J. Recent advances in fluorescent nucleic acid probes for living cell studies. Analyst 2014; 138:62-71. [PMID: 23154215 DOI: 10.1039/c2an35254k] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Living cell studies can offer tremendous opportunities for biological and disease studies. Due to their high sensitivity and selectivity, minimum interference with living biological systems, ease of design and synthesis, fluorescent nucleic acid probes (FNAPs) have been widely used in living cell studies, such as for intracellular detection, cell detection, and cell-to-cell communication. Here, we review the general requirements and the recent developments in FNAPs for living cell studies. We broadly classify these designs as hybridization probes and aptamer probes. For hybridization probes, we describe recently developed designs, such as nanomaterial-based and amplification-based hybridization probes. For aptamer probes, we discuss four general paradigms that have appeared most frequently in the literature: nanomaterial-based, nanomachine-based, cell surface-anchored and activatable aptamer probe designs in vivo. FNAPs promise to open up new and exciting opportunities in biological marks detection for a wide range of biological and medical applications.
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Affiliation(s)
- Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Institute of Biology, Hunan University, Changsha 410082, China.
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Stolz RM, Northrop BH. Experimental and Theoretical Studies of Selective Thiol–Ene and Thiol–Yne Click Reactions Involving N-Substituted Maleimides. J Org Chem 2013; 78:8105-16. [DOI: 10.1021/jo4014436] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Robert M. Stolz
- Department of Chemistry, Wesleyan University, Middletown, Connecticut
06459, United States
| | - Brian H. Northrop
- Department of Chemistry, Wesleyan University, Middletown, Connecticut
06459, United States
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Use of flow cytometry for rapid, quantitative detection of poliovirus-infected cells via TAT peptide-delivered molecular beacons. Appl Environ Microbiol 2012; 79:696-700. [PMID: 23160127 DOI: 10.1128/aem.02429-12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Rapid and efficient detection of viral infection is crucial for the prevention of disease spread during an outbreak and for timely clinical management. In this paper, the utility of Tat peptide-modified molecular beacons (MBs) as a rapid diagnostic tool for the detection of virus-infected cells was demonstrated. The rapid intracellular delivery mediated by the Tat peptide enabled the detection of infected cells within 30 s, reaching saturation in signal in 30 min. This rapid detection scheme was coupled with flow cytometry (FC), resulting in an automated, high-throughput method for the identification of virus-infected cells. Because of the 2-order-of-magnitude difference in fluorescence intensity between infected and uninfected cells, as few as 1% infected cells could be detected. Because of its speed and sensitivity, this approach may be adapted for the practical diagnosis of multiple viral infections.
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Kummer S, Knoll A, Socher E, Bethge L, Herrmann A, Seitz O. PNA FIT-probes for the dual color imaging of two viral mRNA targets in influenza H1N1 infected live cells. Bioconjug Chem 2012; 23:2051-60. [PMID: 22946435 DOI: 10.1021/bc300249f] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fluorogenic hybridization probes that allow RNA imaging provide information as to how the synthesis and transport of particular RNA molecules is orchestrated in living cells. In this study, we explored the peptide nucleic acid (PNA)-based FIT-probes in the simultaneous imaging of two different viral mRNA molecules expressed during the replication cycle of the H1N1 influenza A virus. PNA FIT-probes are non-nucleotidic, nonstructured probes and contain a single asymmetric cyanine dye which serves as a fluorescent base surrogate. The fluorochrome acts as a local intercalator probe and reports hybridization of target DNA/RNA by enhancement of fluorescence. Though multiplexed hybridization probes are expected to facilitate the analysis of RNA expression, there are no previous reports on the dual color imaging of two different viral mRNA targets. In this work, we developed a set of two differently colored PNA FIT-probes that allow the spectrally resolved imaging of mRNA coding for neuraminidase (NA) and matrix protein 1 (M1); proteins which execute distinct functions during the replication of the influenza A virus. The probes are characterized by a wide range of applicable hybridization temperatures. The same probe sequence enabled live-cell RNA imaging (at 37 °C) as well as real-time PCR measurements (at 60 °C annealing temperature). This facilitated a comprehensive analysis of RNA expression by quantitative (qPCR) and qualitative (imaging) means. Confocal laser scanning microscopy showed that the viral-RNA specific PNA FIT-probes neither stained noninfected cells nor cells infected by a control virus. The joint use of differently colored PNA FIT-probes in this feasibility study revealed significant differences in the expression pattern of influenza H1N1 mRNAs coding for NA or M1. These experiments provide evidence for the usefulness of PNA FIT-probes in investigations on the temporal and spatial progression of mRNA synthesis in living cells for two mRNA species.
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Affiliation(s)
- Susann Kummer
- Department of Biology, Humboldt University Berlin, Invalidenstr. 42, D-10115 Berlin, Germany
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32
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Kam Y, Rubinstein A, Nissan A, Halle D, Yavin E. Detection of endogenous K-ras mRNA in living cells at a single base resolution by a PNA molecular beacon. Mol Pharm 2012; 9:685-93. [PMID: 22289057 DOI: 10.1021/mp200505k] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Detection of mRNA alterations is a promising approach for identifying biomarkers as means of differentiating benign from malignant lesions. By choosing the KRAS oncogene as a target gene, two types of molecular beacons (MBs) based on either phosphothioated DNA (PS-DNA-MB) or peptide nucleic acid (TO-PNA-MB, where TO = thiazole orange) were synthesized and compared in vitro and in vivo. Their specificity was examined in wild-type KRAS (HT29) or codon 12 point mutation (Panc-1, SW480) cells. Incubation of both beacons with total RNA extracted from the Panc-1 cell line (fully complementary sequence) showed a fluorescent signal for both beacons. Major differences were observed, however, for single mismatch mRNA transcripts in cell lines HT29 and SW480. PS-DNA-MB weakly discriminated such single mismatches in comparison to TO-PNA-MB, which was profoundly more sensitive. Cell transfection of TO-PNA-MB with the aid of PEI resulted in fluorescence in cells expressing the fully complementary RNA transcript (Panc-1) but undetectable fluorescence in cells expressing the K-ras mRNA that has a single mismatch to the designed TO-PNA-MB (HT29). A weaker fluorescent signal was also detected in SW480 cells; however, these cells express approximately one-fifth of the target mRNA of the designed TO-PNA-MB. In contrast, PS-DNA-MB showed no fluorescence in all cell lines tested post PEI transfection. Based on the fast hybridization kinetics and on the single mismatch discrimination found for TO-PNA-MB we believe that such molecular beacons are promising for in vivo real-time imaging of endogenous mRNA with single nucleotide polymorphism (SNP) resolution.
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Affiliation(s)
- Yossi Kam
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, PO Box 12065, Jerusalem 91120, Israel
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33
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Simultaneous detection of infectious human echoviruses and adenoviruses by an in situ nuclease-resistant molecular beacon-based assay. Appl Environ Microbiol 2011; 78:1584-8. [PMID: 22194298 DOI: 10.1128/aem.05937-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A multiplex methodology using two nuclease-resistant molecular beacons that target specific genomic regions of adenovirus 2 and echovirus 17 during simultaneous infection in A549 cells is presented. Using fluorescence microscopy, visualization of enteroviral and adenoviral replication was possible within 3 h postinfection.
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34
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Hamza IA, Jurzik L, Überla K, Wilhelm M. Methods to detect infectious human enteric viruses in environmental water samples. Int J Hyg Environ Health 2011; 214:424-36. [PMID: 21920815 PMCID: PMC7106513 DOI: 10.1016/j.ijheh.2011.07.014] [Citation(s) in RCA: 91] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 07/24/2011] [Accepted: 07/28/2011] [Indexed: 02/06/2023]
Abstract
Currently, a wide range of analytical methods is available for virus detection in environmental water samples. Molecular methods such as polymerase chain reaction (PCR) and quantitative real time PCR (qPCR) have the highest sensitivity and specificity to investigate virus contamination in water, so they are the most commonly used in environmental virology. Despite great sensitivity of PCR, the main limitation is the lack of the correlation between the detected viral genome and viral infectivity, which limits conclusions regarding the significance for public health. To provide information about the infectivity of the detected viruses, cultivation on animal cell culture is the gold standard. However, cell culture infectivity assays are laborious, time consuming and costly. Also, not all viruses are able to produce cytopathic effect and viruses such as human noroviruses have no available cell line for propagation. In this brief review, we present a summary and critical evaluation of different approaches that have been recently proposed to overcome limitations of the traditional cell culture assay and PCR assay such as integrated cell culture-PCR, detection of genome integrity, detection of capsid integrity, and measurement of oxidative damages on viral capsid protein. Techniques for rapid detection of infectious viruses such as fluorescence microscopy and automated flow cytometry have also been suggested to assess virus infectivity in water samples.
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Affiliation(s)
- Ibrahim Ahmed Hamza
- Department of Hygiene, Social and Environmental Medicine, Ruhr-University Bochum, Germany.
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35
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Monroy-Contreras R, Vaca L. Molecular beacons: powerful tools for imaging RNA in living cells. J Nucleic Acids 2011; 2011:741723. [PMID: 21876785 PMCID: PMC3163130 DOI: 10.4061/2011/741723] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2010] [Revised: 06/14/2011] [Accepted: 06/22/2011] [Indexed: 12/25/2022] Open
Abstract
Recent advances in RNA functional studies highlights the pivotal role of these molecules in cell physiology. Diverse methods have been implemented to measure the expression levels of various RNA species, using either purified RNA or fixed cells. Despite the fact that fixed cells offer the possibility to observe the spatial distribution of RNA, assays with capability to real-time monitoring RNA transport into living cells are needed to further understand the role of RNA dynamics in cellular functions. Molecular beacons (MBs) are stem-loop hairpin-structured oligonucleotides equipped with a fluorescence quencher at one end and a fluorescent dye (also called reporter or fluorophore) at the opposite end. This structure permits that MB in the absence of their target complementary sequence do not fluoresce. Upon binding to targets, MBs emit fluorescence, due to the spatial separation of the quencher and the reporter. Molecular beacons are promising probes for the development of RNA imaging techniques; nevertheless much work remains to be done in order to obtain a robust technology for imaging various RNA molecules together in real time and in living cells. The present work concentrates on the different requirements needed to use successfully MB for cellular studies, summarizing recent advances in this area.
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Affiliation(s)
- Ricardo Monroy-Contreras
- Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, 04510 Mexico, DF, Mexico
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36
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Detection of murine norovirus-1 by using TAT peptide-delivered molecular beacons. Appl Environ Microbiol 2011; 77:5517-20. [PMID: 21652740 DOI: 10.1128/aem.03048-10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A TAT peptide-delivered molecular beacon was developed and utilized to enumerate murine norovirus 1, a human norovirus (NoV) surrogate, in RAW 264.7 cells. This allowed the detection of a single infective virus within 6 h, a 12-fold improvement in time required for viral detection and quantification compared to that required by the conventional plaque assay.
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37
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Sivaraman D, Biswas P, Cella LN, Yates MV, Chen W. Detecting RNA viruses in living mammalian cells by fluorescence microscopy. Trends Biotechnol 2011; 29:307-13. [PMID: 21529975 DOI: 10.1016/j.tibtech.2011.02.006] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 02/20/2011] [Accepted: 02/23/2011] [Indexed: 12/29/2022]
Abstract
Traditional methods that rely on viral isolation and culture techniques continue to be the gold standards used for detection of infectious viral particles. However, new techniques that rely on visualization of live cells can shed light on understanding virus-host interaction for early stage detection and potential drug discovery. Live-cell imaging techniques that incorporate fluorescent probes into viral components provide opportunities for understanding mRNA expression, interaction, and virus movement and localization. Other viral replication events inside a host cell can be exploited for non-invasive detection, such as single-virus tracking, which does not inhibit viral infectivity or cellular function. This review highlights some of the recent advances made using these novel approaches for visualization of viral entry and replication in live cells.
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Affiliation(s)
- Divya Sivaraman
- Department of Chemical Engineering, University of Delaware, Newark, DE 19716, USA
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38
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Urbinati CR, Long RM. Techniques for following the movement of single RNAs in living cells. WILEY INTERDISCIPLINARY REVIEWS-RNA 2011; 2:601-9. [PMID: 21957047 DOI: 10.1002/wrna.83] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The ability to investigate gene expression has evolved from static approaches that analyze a population of cells to dynamic approaches that analyze individual living cells. During the last decade, a number of different fluorescent methods have been developed for monitoring the dynamics of single RNAs in living cells. Spatial-temporal analyses of single RNAs in living cells have provided novel insight into nuclear transport, RNA localization, and decay. Technical advances with these approaches allow for single molecule detection, providing an unprecedented view of RNA movement. In this article, we discuss the methods for observing single RNAs in living cells, highlighting the advantages and limitations of each method.
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Affiliation(s)
- Carl R Urbinati
- Department of Biology, Loyola Marymount University, Los Angeles, CA, USA
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39
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Harry SR, Hicks DJ, Amiri KI, Wright DW. Hairpin DNA coated gold nanoparticles as intracellular mRNA probes for the detection of tyrosinase gene expression in melanoma cells. Chem Commun (Camb) 2010; 46:5557-9. [PMID: 20526488 DOI: 10.1039/c001969k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new intracellular mRNA imaging probe has been developed that incorporates thiol-terminated hairpin oligonucleotides covalently bound to the surface of citrate-capped gold nanoparticles. The hairpin DNA-coated gold nanoparticles (hAuNPs) positively identifies tyrosinase mRNA in cultured melanoma cells.
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Affiliation(s)
- S Reese Harry
- Department of Chemistry, Vanderbilt University, Station B351822, Nashville, TN 37235, USA
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40
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Chen AK, Davydenko O, Behlke MA, Tsourkas A. Ratiometric bimolecular beacons for the sensitive detection of RNA in single living cells. Nucleic Acids Res 2010; 38:e148. [PMID: 20507905 PMCID: PMC2919734 DOI: 10.1093/nar/gkq436] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Numerous studies have utilized molecular beacons (MBs) to image RNA expression in living cells; however, there is growing evidence that the sensitivity of RNA detection is significantly hampered by their propensity to emit false-positive signals. To overcome these limitations, we have developed a new RNA imaging probe called ratiometric bimolecular beacon (RBMB), which combines functional elements of both conventional MBs and siRNA. Analogous to MBs, RBMBs elicit a fluorescent reporter signal upon hybridization to complementary RNA. In addition, an siRNA-like double-stranded domain is used to facilitate nuclear export. Accordingly, live-cell fluorescent imaging showed that RBMBs are localized predominantly in the cytoplasm, whereas MBs are sequestered into the nucleus. The retention of RBMBs within the cytoplasmic compartment led to >15-fold reduction in false-positive signals and a significantly higher signal-to-background compared with MBs. The RBMBs were also designed to possess an optically distinct reference fluorophore that remains unquenched regardless of probe confirmation. This reference dye not only provided a means to track RBMB localization, but also allowed single cell measurements of RBMB fluorescence to be corrected for variations in probe delivery. Combined, these attributes enabled RBMBs to exhibit an improved sensitivity for RNA detection in living cells.
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Affiliation(s)
- Antony K Chen
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA
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41
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Yeh HY, Yates MV, Mulchandani A, Chen W. Molecular beacon-quantum dot-Au nanoparticle hybrid nanoprobes for visualizing virus replication in living cells. Chem Commun (Camb) 2010; 46:3914-6. [PMID: 20419176 DOI: 10.1039/c001553a] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we describe a new hybrid fluorescent nanoprobe composed of a nuclease-resistant molecular beacon (MB) backbone, CdSe-ZnS core-shell quantum dots (QDs) as donors, and gold nanoparticles (Au NPs) as quenchers, for the real-time visualization of virus replication in living cells. By using a Au NP-MB to QD ratio of 6 : 1, a 7.3-fold increase in fluorescent signal was achieved upon target binding. For living cell experiments, a hexahistidine-appended Tat peptide was self-assembled onto the QD surface to provide nearly 100% non-invasive delivery of the QD-MB-Au NP probes within 2 h. By directly visualizing the fluorescent complexes formed with the newly synthesized viral RNA, this QD-MB-Au NP probe provided sensitive and real-time detection of infectious viruses as well as the real-time visualization of cell-to-cell virus spreading.
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Affiliation(s)
- Hsiao-Yun Yeh
- Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521, USA
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42
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Kersemans V, Cornelissen B. Targeting the Tumour: Cell Penetrating Peptides for Molecular Imaging and Radiotherapy. Pharmaceuticals (Basel) 2010; 3:600-620. [PMID: 27713270 PMCID: PMC4033971 DOI: 10.3390/ph3030600] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2009] [Revised: 02/02/2010] [Accepted: 03/10/2010] [Indexed: 11/16/2022] Open
Abstract
Over the last couple of years, the number of original papers and reviews discussing various applications of cell penetrating peptides (CPPs) has grown exponentially. This is not remarkable since CPPs are capable of transporting the most varying cargo across cell membranes which is one of the biggest problems in drug delivery and targeted therapy. In this review, we focus on the use of CPPs and related peptides for delivery of imaging contrast agents and radionuclides to cells and tissues with the ultimate goal of in vivo molecular imaging and molecular radiotherapy of intracellular and even intranuclear targets.
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Affiliation(s)
- Veerle Kersemans
- Gray Institute for Radiation Oncology and Biology, University of Oxford/Old Road Campus Research Building, Off Roosevelt Drive, Churchill Hospital, Oxford OX3 7DQ, UK.
| | - Bart Cornelissen
- Gray Institute for Radiation Oncology and Biology, University of Oxford/Old Road Campus Research Building, Off Roosevelt Drive, Churchill Hospital, Oxford OX3 7DQ, UK.
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Chen AK, Behlke MA, Tsourkas A. Sub-cellular trafficking and functionality of 2'-O-methyl and 2'-O-methyl-phosphorothioate molecular beacons. Nucleic Acids Res 2010; 37:e149. [PMID: 19820111 PMCID: PMC2794186 DOI: 10.1093/nar/gkp837] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Molecular beacons (MBs) have shown great potential for the imaging of RNAs within single living cells; however, the ability to perform accurate measurements of RNA expression can be hampered by false-positives resulting from nonspecific interactions and/or nuclease degradation. These false-positives could potentially be avoided by introducing chemically modified oligonucleotides into the MB design. In this study, fluorescence microscopy experiments were performed to elucidate the subcellular trafficking, false-positive signal generation, and functionality of 2′-O-methyl (2Me) and 2′-O-methyl-phosphorothioate (2MePS) MBs. The 2Me MBs exhibited rapid nuclear sequestration and a gradual increase in fluorescence over time, with nearly 50% of the MBs being opened nonspecifically within 24 h. In contrast, the 2MePS MBs elicited an instantaneous increase in false-positives, corresponding to ∼5–10% of the MBs being open, but little increase was observed over the next 24 h. Moreover, trafficking to the nucleus was slower. After 24 h, both MBs were localized in the nucleus and lysosomal compartments, but only the 2MePS MBs were still functional. When the MBs were retained in the cytoplasm, via conjugation to NeutrAvidin, a significant reduction in false-positives and improvement in functionality was observed. Overall, these results have significant implications for the design and applications of MBs for intracellular RNA measurement.
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Affiliation(s)
- Antony K Chen
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104 and Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
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44
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Zon G. Automated synthesis of phosphorus–sulfur analogs of nucleic acids—25 years on: potential therapeutic agents and proven utility in biotechnology. NEW J CHEM 2010. [DOI: 10.1039/b9nj00577c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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45
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Lowe AB. Thiol-ene “click” reactions and recent applications in polymer and materials synthesis. Polym Chem 2010. [DOI: 10.1039/b9py00216b] [Citation(s) in RCA: 1194] [Impact Index Per Article: 85.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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46
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Cliver DO. Capsid and Infectivity in Virus Detection. FOOD AND ENVIRONMENTAL VIROLOGY 2009; 1:123-128. [PMID: 20234879 PMCID: PMC2837222 DOI: 10.1007/s12560-009-9020-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2009] [Accepted: 10/30/2009] [Indexed: 05/02/2023]
Abstract
The spectacular achievements and elegance of viral RNA analyses have somewhat obscured the importance of the capsid in transmission of viruses via food and water. The capsid's essential roles are protection of the RNA when the virion is outside the host cell and initiation of infection when the virion contacts a receptor on an appropriate host cell. Capsids of environmentally transmitted viruses are phenomenally durable. Fortuitous properties of the capsid include antigenicity, isoelectric point(s), sometimes hemagglutination, and perhaps others. These can potentially be used to characterize capsid changes that cause or accompany loss of viral infectivity and may be valuable in distinguishing native from inactivated virus when molecular detection methods are used.
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Affiliation(s)
- Dean O. Cliver
- Food Safety, University of California, VM:PHR, One Shields Avenue, Davis, CA 95616 USA
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47
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Abstract
Powerful methods now allow the imaging of specific mRNAs in living cells. These methods enlist fluorescent proteins to illuminate mRNAs, use labeled oligonucleotide probes and exploit aptamers that render organic dyes fluorescent. The intracellular dynamics of mRNA synthesis, transport and localization can be analyzed at higher temporal resolution with these methods than has been possible with traditional fixed-cell or biochemical approaches. These methods have also been adopted to visualize and track single mRNA molecules in real time. This review explores the promises and limitations of these methods.
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48
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Shedding light on virus replication. Proc Natl Acad Sci U S A 2008; 105:17213-4. [PMID: 18997007 DOI: 10.1073/pnas.0809841105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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