1
|
Mukherjee P, Dutta J, Roy M, Thakur TK, Mitra A. Plant growth-promoting rhizobacterial secondary metabolites in augmenting heavy metal(loid) phytoremediation: An integrated green in situ ecorestorative technology. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2024; 31:55851-55894. [PMID: 39251536 DOI: 10.1007/s11356-024-34706-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 11/17/2022] [Indexed: 09/11/2024]
Abstract
In recent times, increased geogenic and human-centric activities have caused significant heavy metal(loid) (HM) contamination of soil, adversely impacting environmental, plant, and human health. Phytoremediation is an evolving, cost-effective, environment-friendly, in situ technology that employs indigenous/exotic plant species as natural purifiers to remove toxic HM(s) from deteriorated ambient soil. Interestingly, the plant's rhizomicrobiome is pivotal in promoting overall plant nutrition, health, and phytoremediation. Certain secondary metabolites produced by plant growth-promoting rhizobacteria (PGPR) directly participate in HM bioremediation through chelation/mobilization/sequestration/bioadsorption/bioaccumulation, thus altering metal(loid) bioavailability for their uptake, accumulation, and translocation by plants. Moreover, the metallotolerance of the PGPR and the host plant is another critical factor for the successful phytoremediation of metal(loid)-polluted soil. Among the phytotechniques available for HM remediation, phytoextraction/phytoaccumulation (HM mobilization, uptake, and accumulation within the different plant tissues) and phytosequestration/phytostabilization (HM immobilization within the soil) have gained momentum in recent years. Natural metal(loid)-hyperaccumulating plants have the potential to assimilate increased levels of metal(loid)s, and several such species have already been identified as potential candidates for HM phytoremediation. Furthermore, the development of transgenic rhizobacterial and/or plant strains with enhanced environmental adaptability and metal(loid) uptake ability using genetic engineering might open new avenues in PGPR-assisted phytoremediation technologies. With the use of the Geographic Information System (GIS) for identifying metal(loid)-impacted lands and an appropriate combination of normal/transgenic (hyper)accumulator plant(s) and rhizobacterial inoculant(s), it is possible to develop efficient integrated phytobial remediation strategies in boosting the clean-up process over vast regions of HM-contaminated sites and eventually restore ecosystem health.
Collapse
Affiliation(s)
- Pritam Mukherjee
- Department of Oceanography, Techno India University, West Bengal, EM 4/1 Sector V, Salt Lake, Kolkata, 700091, West Bengal, India.
| | - Joystu Dutta
- Department of Environmental Science, University Teaching Department, Sant Gahira Guru University, Ambikapur, 497001, Chhattisgarh, India
| | - Madhumita Roy
- Department of Microbiology, Bose Institute, P-1/12, CIT Road, Scheme VIIM, Kankurgachi, Kolkata, 700054, West Bengal, India
| | - Tarun Kumar Thakur
- Department of Environmental Science, Indira Gandhi National Tribal University, Amarkantak, 484886, Madhya Pradesh, India
| | - Abhijit Mitra
- Department of Marine Science, University of Calcutta, 35 B. C. Road, Kolkata, 700019, West Bengal, India
| |
Collapse
|
2
|
Zhang H, Vandesompele J, Braeckmans K, De Smedt SC, Remaut K. Nucleic acid degradation as barrier to gene delivery: a guide to understand and overcome nuclease activity. Chem Soc Rev 2024; 53:317-360. [PMID: 38073448 DOI: 10.1039/d3cs00194f] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Gene therapy is on its way to revolutionize the treatment of both inherited and acquired diseases, by transferring nucleic acids to correct a disease-causing gene in the target cells of patients. In the fight against infectious diseases, mRNA-based therapeutics have proven to be a viable strategy in the recent Covid-19 pandemic. Although a growing number of gene therapies have been approved, the success rate is limited when compared to the large number of preclinical and clinical trials that have been/are being performed. In this review, we highlight some of the hurdles which gene therapies encounter after administration into the human body, with a focus on nucleic acid degradation by nucleases that are extremely abundant in mammalian organs, biological fluids as well as in subcellular compartments. We overview the available strategies to reduce the biodegradation of gene therapeutics after administration, including chemical modifications of the nucleic acids, encapsulation into vectors and co-administration with nuclease inhibitors and discuss which strategies are applied for clinically approved nucleic acid therapeutics. In the final part, we discuss the currently available methods and techniques to qualify and quantify the integrity of nucleic acids, with their own strengths and limitations.
Collapse
Affiliation(s)
- Heyang Zhang
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Jo Vandesompele
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| | - Kevin Braeckmans
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Stefaan C De Smedt
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
- Centre for Nano- and Biophotonics, Ghent University, 9000 Ghent, Belgium
| | - Katrien Remaut
- Laboratory for General Biochemistry and Physical Pharmacy, Department of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium.
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium
| |
Collapse
|
3
|
Montiel L, Spada F, Crisp A, Serdjukow S, Carell T, Frischmuth T. Divergent Synthesis of Ultrabright and Dendritic Xanthenes for Enhanced Click-Chemistry-Based Bioimaging. Chemistry 2023; 29:e202202633. [PMID: 36317813 PMCID: PMC10107433 DOI: 10.1002/chem.202202633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Indexed: 12/13/2022]
Abstract
Biorthogonal labelling with fluorescent small molecules is an indispensable tool for diagnostic and biomedical applications. In dye-based 5-ethynyl-2'-deoxyuridine (EdU) cell proliferation assays, augmentation of the fluorescent signal entails an overall enhancement in the sensitivity and quality of the method. To this end, a rapid, divergent synthetic procedure that provides ready-to-click pH-insensitive rhodamine dyes exhibiting outstanding brightness was established. Compared to the shortest available synthesis of related high quantum-yielding rhodamines, two fewer synthetic steps are required. In a head-to-head imaging comparison involving copper(I)-catalyzed azide alkyne cycloaddition reactions with in vitro administered EdU, our new 3,3-difluoroazetidine rhodamine azide outperformed the popular 5-TAMRA-azide, making it among the best available choices when it comes to fluorescent imaging of DNA. In a further exploration of the fluorescence properties of these dyes, a set of bis-MPA dendrons carrying multiple fluorescein or rhodamine units was prepared by branching click chemistry. Fluorescence self-quenching of fluorescein- and rhodamine-functionalized dendrons limited the suitability of the dyes as labels in EdU-based experiments but provided new insights into these effects.
Collapse
Affiliation(s)
- Luis Montiel
- Baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (Munich), Germany.,Department of Chemistry, Institut für Chemische Epigenetik München (ICEM), Ludwig-Maximilians-Universität München (LMU), Butenandtstr. 5-13, 81377, Munich, Germany
| | - Fabio Spada
- Baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (Munich), Germany
| | - Antony Crisp
- Baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (Munich), Germany
| | - Sascha Serdjukow
- Baseclick GmbH, Floriansbogen 2-4, 82061, Neuried (Munich), Germany
| | - Thomas Carell
- Department of Chemistry, Institut für Chemische Epigenetik München (ICEM), Ludwig-Maximilians-Universität München (LMU), Butenandtstr. 5-13, 81377, Munich, Germany
| | | |
Collapse
|
4
|
Sequence-dependence of Cy3 and Cy5 dyes in 3' terminally-labeled single-stranded DNA. Sci Rep 2022; 12:14803. [PMID: 36045146 PMCID: PMC9428881 DOI: 10.1038/s41598-022-19069-9] [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: 06/20/2022] [Accepted: 08/24/2022] [Indexed: 11/16/2022] Open
Abstract
Fluorescence is an ideal tool to see and manipulate nucleic acids, and engage in their rich and complex biophysical properties. Labeling is the preferred approach to track and quantify fluorescence with nucleic acids and cyanine dyes are emblematic in this context. The fluorescent properties of cyanine dyes are known to be sequence-dependent, with purines in the immediate vicinity increasing the fluorescence intensity of Cy3 and Cy5 dyes, and the ability of nucleobases to modulate the photophysical properties of common fluorophores may influence fluorescence measurements in critical assays such as FISH, qPCR or high-throughput sequencing. In this paper, we comprehensively map the sequence-dependence of Cy3 and Cy5 dyes in 3ʹ-fluorescently labeled single-stranded DNA by preparing the complete permutation library of the 5 consecutive nucleotides immediately adjacent to the dye, or 1024 sequences. G-rich motifs dominate the high fluorescence range, while C-rich motifs lead to significant quenching, an observation consistent with 5ʹ-labeled systems. We also uncover GCGC patterns in the extreme top range of fluorescence, a feature specific to 3ʹ-Cy3 and Cy5 oligonucleotides. This study represents the final piece in linking nucleotide identity to fluorescence changes for Cy3, Cy5 and fluorescein in all 3ʹ, 5ʹ, single-stranded and double-stranded DNA formats.
Collapse
|
5
|
Eustáquio R, Prates Ramalho JP, Caldeira AT, Pereira A. Development of new 2-piperidinium-4-styrylcoumarin derivatives with large Stokes shifts as potential fluorescent labels for biomolecules. RSC Adv 2022; 12:8477-8484. [PMID: 35424831 PMCID: PMC8984815 DOI: 10.1039/d2ra00716a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 03/03/2022] [Indexed: 11/21/2022] Open
Abstract
A series of novel 2-piperidinium-4-styrylcoumarin derivatives, with large Stokes shifts and high fluorescence quantum yields, were synthesized using an efficient and low-cost synthetic strategy as potential fluorescent labels for biomolecules. Density functional theory and time-dependent density functional theory calculations were performed in order to rationalize the observed photophysical properties.
Collapse
Affiliation(s)
- Raquel Eustáquio
- HERCULES Laboratory, City University of Macau Chair in Sustainable Heritage, University of Évora Largo Marquês de Marialva 8 7000-809 Évora Portugal
| | - João P Prates Ramalho
- Chemistry Department, School of Sciences and Technology, University of Évora Rua Romão Ramalho 59 7000-671 Évora Portugal
- LAQV-REQUIMTE, University of Évora Rua Romão Ramalho 59 7000-671 Évora Portugal
| | - Ana T Caldeira
- HERCULES Laboratory, City University of Macau Chair in Sustainable Heritage, University of Évora Largo Marquês de Marialva 8 7000-809 Évora Portugal
- Chemistry Department, School of Sciences and Technology, University of Évora Rua Romão Ramalho 59 7000-671 Évora Portugal
| | - António Pereira
- HERCULES Laboratory, City University of Macau Chair in Sustainable Heritage, University of Évora Largo Marquês de Marialva 8 7000-809 Évora Portugal
- Chemistry Department, School of Sciences and Technology, University of Évora Rua Romão Ramalho 59 7000-671 Évora Portugal
| |
Collapse
|
6
|
Eustáquio R, Ramalho JPP, Caldeira AT, Pereira A. New Red-Shifted 4-Styrylcoumarin Derivatives as Potential Fluorescent Labels for Biomolecules. Molecules 2022; 27:1461. [PMID: 35268562 PMCID: PMC8912076 DOI: 10.3390/molecules27051461] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 11/30/2022] Open
Abstract
Important scientific areas, such as cellular biology, medicine, pharmacy, and environmental sciences, are dependent on very sensitive analytical techniques to track and detect biomolecules. In this work, we develop a simple, low-cost and effective synthetic strategy to produce new red-shifted 4-styrylcoumarin derivatives as promising inexpensive fluorescent labels for biomolecules. The extension of the delocalized π-electron system results in bathochromic shifts in these new coumarin derivatives, which also present large Stokes shifts. In addition, density functional theory and time-dependent density functional theory calculations helped to rationalize the photophysical properties observed by the experimental results.
Collapse
Affiliation(s)
- Raquel Eustáquio
- Hercules Laboratory, University of Évora, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal; (R.E.); (A.T.C.)
| | - João P. Prates Ramalho
- Chemistry Department, School of Sciences and Technology, University of Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal;
- Laqv-Requimte, University of Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal
| | - Ana T. Caldeira
- Hercules Laboratory, University of Évora, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal; (R.E.); (A.T.C.)
- Chemistry Department, School of Sciences and Technology, University of Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal;
| | - António Pereira
- Hercules Laboratory, University of Évora, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal; (R.E.); (A.T.C.)
- Chemistry Department, School of Sciences and Technology, University of Évora, Rua Romão Ramalho 59, 7000-671 Évora, Portugal;
| |
Collapse
|
7
|
Mantovanelli L, Gaastra BF, Poolman B. Fluorescence-based sensing of the bioenergetic and physicochemical status of the cell. CURRENT TOPICS IN MEMBRANES 2021; 88:1-54. [PMID: 34862023 DOI: 10.1016/bs.ctm.2021.10.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Fluorescence-based sensors play a fundamental role in biological research. These sensors can be based on fluorescent proteins, fluorescent probes or they can be hybrid systems. The availability of a very large dataset of fluorescent molecules, both genetically encoded and synthetically produced, together with the structural insights on many sensing domains, allowed to rationally design a high variety of sensors, capable of monitoring both molecular and global changes in living cells or in in vitro systems. The advancements in the fluorescence-imaging field helped researchers to obtain a deeper understanding of how and where specific changes occur in a cell or in vitro by combining the readout of the fluorescent sensors with the spatial information provided by fluorescent microscopy techniques. In this review we give an overview of the state of the art in the field of fluorescent biosensors and fluorescence imaging techniques, and eventually guide the reader through the choice of the best combination of fluorescent tools and techniques to answer specific biological questions. We particularly focus on sensors for probing the bioenergetics and physicochemical status of the cell.
Collapse
Affiliation(s)
- Luca Mantovanelli
- Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Bauke F Gaastra
- Department of Biochemistry, University of Groningen, Groningen, the Netherlands
| | - Bert Poolman
- Department of Biochemistry, University of Groningen, Groningen, the Netherlands.
| |
Collapse
|
8
|
Sunami T, Hirano Y, Tamada T, Kono H. Structural basis for designing an array of engrailed homeodomains. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2020; 76:824-833. [PMID: 32876058 DOI: 10.1107/s2059798320009237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 07/07/2020] [Indexed: 11/10/2022]
Abstract
Small DNA-binding proteins that target desired sequences have the potential to act as a scaffold for molecular tools such as genome editing. In this study, an engrailed homeodomain (EHD) was chosen and it was evaluated whether it could be used as a molecular module that can connect to itself to recognize a longer target sequence. It was previously shown that two EHDs connected by a linker (EHD2) recognize a target sequence twice as long as that recognized by a single EHD in cells only when Arg53 in each EHD in the tandem protein is mutated to alanine {(EHD[R53A])2}. To investigate the recognition mechanism of (EHD[R53A])2, the crystal structure of the (EHD[R53A])2-DNA complex was determined at 1.6 Å resolution. The individual EHDs were found to adopt the typical homeodomain fold. Most importantly, the base-specific interactions in the major groove necessary for the affinity/specificity of wild-type EHD were preserved in (EHD[R53A])2. Bacterial assays confirmed that the base-specific interactions are retained under cellular conditions. These observations indicate that the R53A mutation only causes a loss of the arginine-phosphate interaction at the protein-DNA interface, which reduces the DNA-binding affinity compared with the wild type. It is therefore concluded that (EHD[R53A])2 precisely recognizes tandem target sites within cells, enabling the individual EHDs to concurrently bind to the target sites with modest binding affinity. This suggests that modulation of the binding activity of each EHD is vital to construct a protein array that can precisely recognize a sequence with multiple target sites.
Collapse
Affiliation(s)
- Tomoko Sunami
- Molecular Modeling and Simulation Group, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa 619-0215, Japans
| | - Yu Hirano
- Structural Biology Group, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Taro Tamada
- Structural Biology Group, National Institutes for Quantum and Radiological Science and Technology, 2-4 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Hidetoshi Kono
- Molecular Modeling and Simulation Group, National Institutes for Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa 619-0215, Japans
| |
Collapse
|
9
|
Shen T, Zhang Y, Zhou S, Lin S, Zhang XB, Zhu G. Nucleic Acid Immunotherapeutics for Cancer. ACS APPLIED BIO MATERIALS 2020; 3:2838-2849. [PMID: 33681722 DOI: 10.1021/acsabm.0c00101] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The past decade has witnessed the blossom of two fields: nucleic acid therapeutics and cancer immunotherapy. Unlike traditional small molecule medicines or protein biologics, nucleic acid therapeutics have characteristic features such as storing genetic information, immunomodulation, and easy conformational recovery. Immunotherapy uses the patients' own immune system to treat cancer. A variety of strategies have been developed for cancer immunotherapy including immune checkpoint blockade, adoptive cell transfer therapy, therapeutic vaccines, and oncolytic virotherapy. Interestingly, nucleic acid therapeutics have emerged as a pivotal class of regimen for cancer immunotherapy. Examples of such nucleic acid immunotherapeutics include immunostimulatory DNA/RNA, mRNA/plasmids that can be translated into immunotherapeutic proteins/peptides, and genome-editing nucleic acids. Like many other therapeutic nucleic acids, nucleic acid immunotherapeutics often require chemical modifications to protect them from enzymatic degradation and need drug delivery systems for optimal delivery to target tissues and cells and subcellular locations. In this review, we attempted to summarize recent advancement in the interfacial field of nucleic acid immunotherapeutics for cancer treatment.
Collapse
Affiliation(s)
- Tingting Shen
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China; Department of Pharmaceutics, Center for Pharmaceutical Engineering and Sciences-School of Pharmacy; Massey Cancer Center; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Yu Zhang
- Department of Pharmaceutics, Center for Pharmaceutical Engineering and Sciences-School of Pharmacy; Massey Cancer Center; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298, United States; Department of Rehabilitation Medicine, Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Shurong Zhou
- Department of Pharmaceutics, Center for Pharmaceutical Engineering and Sciences-School of Pharmacy; Massey Cancer Center; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Shuibin Lin
- Department of Rehabilitation Medicine, Center for Translational Medicine, Precision Medicine Institute, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiao-Bing Zhang
- Molecular Sciences and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering and College of Biology, Collaborative Innovation Center for Molecular Engineering and Theranostics, Hunan University, Changsha 410082, China
| | - Guizhi Zhu
- Department of Pharmaceutics, Center for Pharmaceutical Engineering and Sciences-School of Pharmacy; Massey Cancer Center; Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| |
Collapse
|
10
|
Okamoto A. Next-generation fluorescent nucleic acids probes for microscopic analysis of intracellular nucleic acids. Appl Microsc 2019; 49:14. [PMID: 33580316 PMCID: PMC7818349 DOI: 10.1186/s42649-019-0017-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 10/30/2019] [Indexed: 01/09/2023] Open
Abstract
Fluorescence imaging of nucleic acids is a very important technique necessary to understand gene expression and the resulting changes in cell function. This mini-review focuses on sequence-specific fluorescence imaging of intracellular RNA and methylated DNA using fluorescent nucleic acid probes. A couple of functional fluorescent nucleic acid probes developed by our laboratory are introduced and the examples of their application to fluorescence imaging of intracellular nucleic acids are described.
Collapse
Affiliation(s)
- Akimitsu Okamoto
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan.
| |
Collapse
|
11
|
|
12
|
Schwechheimer C, Doll L, Wagenknecht HA. Synthesis of Dye-Modified Oligonucleotides via Copper(I)-Catalyzed Alkyne Azide Cycloaddition Using On- and Off-Bead Approaches. ACTA ACUST UNITED AC 2019; 72:4.80.1-4.80.13. [PMID: 29927126 DOI: 10.1002/cpnc.47] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Fluorescence molecular imaging is widely used to visualize and observe different biomolecules, in particular DNA and RNA, in vivo and in real time. Typically, DNA strands are tagged with only one fluorophore, and, in the case of molecular beacons, an additional quencher is conjugated, which bears the risk of false-positive or false-negative results because only fluorescence intensities at one fluorescence wavelength (color) are compared. To address this drawback, the concept of "DNA/RNA traffic lights," which is characterized by a fluorescence color change due to energy transfer between two dyes, was developed by our working group. For these DNA and RNA systems, the oligonucleotides are post-synthetically labeled, specifically after solid-phase synthesis by chemical means, with a fluorescent dye using copper(I)-catalyzed cycloaddition at the 2' position of single uridines. In order to functionalize oligonucleotides with several different labels, an on-resin method is required to ensure the necessary selectivity. This unit describes two different CuAAC ("click") approaches-in solution (post-synthetic) and on solid phase (during synthesis)-for the attachment of fluorophores to the 2' position of DNA. © 2018 by John Wiley & Sons, Inc.
Collapse
Affiliation(s)
| | - Larissa Doll
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | | |
Collapse
|
13
|
Sabale PM, Ambi UB, Srivatsan SG. A Lucifer-Based Environment-Sensitive Fluorescent PNA Probe for Imaging Poly(A) RNAs. Chembiochem 2018; 19:826-835. [PMID: 29396904 PMCID: PMC5972818 DOI: 10.1002/cbic.201700661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 12/14/2022]
Abstract
Fluorescence‐based oligonucleotide (ON) hybridization probes greatly aid the detection and profiling of RNA sequences in cells. However, certain limitations such as target accessibility and hybridization efficiency in cellular environments hamper their broad application because RNAs can form complex and stable structures. In this context, we have developed a robust hybridization probe suitable for imaging RNA in cells by combining the properties of 1) a new microenvironment‐sensitive fluorescent nucleobase analogue, obtained by attaching the Lucifer chromophore (1,8‐naphthalimide) at the 5‐position of uracil, and 2) a peptide nucleic acid (PNA) capable of forming stable hybrids with RNA. The fluorescence of the PNA base analogue labeled with the Lucifer chromophore, when incorporated into PNA oligomers and hybridized to complementary and mismatched ONs, is highly responsive to its neighboring base environment. Notably, the PNA base reports the presence of an adenine repeat in an RNA ON with reasonable enhancement in fluorescence. This feature of the emissive analogue enabled the construction of a poly(T) PNA probe for the efficient visualization of polyadenylated [poly(A)] RNAs in cells—poly(A) being an important motif that plays vital roles in the lifecycle of many types of RNA. Our results demonstrate that such responsive fluorescent nucleobase analogues, when judiciously placed in PNA oligomers, could generate useful hybridization probes to detect nucleic acid sequences in cells and also to image them.
Collapse
Affiliation(s)
- Pramod M Sabale
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
| | - Uddhav B Ambi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
| |
Collapse
|
14
|
Santos AP, Ferreira LJ, Oliveira MM. Concerted Flexibility of Chromatin Structure, Methylome, and Histone Modifications along with Plant Stress Responses. BIOLOGY 2017; 6:biology6010003. [PMID: 28275209 PMCID: PMC5371996 DOI: 10.3390/biology6010003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 01/05/2017] [Accepted: 01/10/2017] [Indexed: 12/12/2022]
Abstract
The spatial organization of chromosome structure within the interphase nucleus, as well as the patterns of methylome and histone modifications, represent intersecting layers that influence genome accessibility and function. This review is focused on the plastic nature of chromatin structure and epigenetic marks in association to stress situations. The use of chemical compounds (epigenetic drugs) or T-DNA-mediated mutagenesis affecting epigenetic regulators (epi-mutants) are discussed as being important tools for studying the impact of deregulated epigenetic backgrounds on gene function and phenotype. The inheritability of epigenetic marks and chromatin configurations along successive generations are interpreted as a way for plants to “communicate” past experiences of stress sensing. A mechanistic understanding of chromatin and epigenetics plasticity in plant response to stress, including tissue- and genotype-specific epigenetic patterns, may help to reveal the epigenetics contributions for genome and phenotype regulation.
Collapse
Affiliation(s)
- Ana Paula Santos
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit. Av. da República, 2780-157 Oeiras, Portugal.
| | - Liliana J Ferreira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit. Av. da República, 2780-157 Oeiras, Portugal.
| | - M Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Genomics of Plant Stress Unit. Av. da República, 2780-157 Oeiras, Portugal.
| |
Collapse
|
15
|
Rowland CE, Brown CW, Medintz IL, Delehanty JB. Intracellular FRET-based probes: a review. Methods Appl Fluoresc 2015; 3:042006. [PMID: 29148511 DOI: 10.1088/2050-6120/3/4/042006] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Probes that exploit Förster resonance energy transfer (FRET) in their feedback mechanism are touted for their sensitivity, robustness, and low background, and thanks to the exceptional distance dependence of the energy transfer process, they provide a means of probing lengthscales well below the resolution of light. These attributes make FRET-based probes superbly suited to an intracellular environment, and recent developments in biofunctionalization and expansion of imaging capabilities have put them at the forefront of intracellular studies. Here, we present an overview of the engineering and execution of a variety of recent intracellular FRET probes, highlighting the diversity of this class of materials and the breadth of application they have found in the intracellular environment.
Collapse
Affiliation(s)
- Clare E Rowland
- Center for Bio/Molecular Science and Engineering, Code 6900, US Naval Research Laboratory, Washington, DC 20375, USA. National Research Council, Washington, DC 20036, USA
| | | | | | | |
Collapse
|
16
|
Zhu Z, Leung CWT, Zhao X, Wang Y, Qian J, Tang BZ, He S. Using AIE Luminogen for Long-term and Low-background Three-Photon Microscopic Functional Bioimaging. Sci Rep 2015; 5:15189. [PMID: 26470006 PMCID: PMC4606727 DOI: 10.1038/srep15189] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Accepted: 09/21/2015] [Indexed: 12/12/2022] Open
Abstract
Fluorescent probes are one of the most popularly used bioimaging markers to monitor metabolic processes of living cells. However, long-term light excitation always leads to photobleaching of fluorescent probes, unavoidable autofluorescence as well as photodamage of cells. To overcome these limitations, we synthesized a type of photostable luminogen named TPE-TPP with an aggregation induced emission (AIE) characteristic, and achieved its three-photon imaging with femtosecond laser excitation of 1020 nm. By using TPE-TPP as fluorescent probes, three-photon microscopy under 1020 nm excitation showed little photo-damage, as well as low autofluorescence to HeLa cells. Due to the AIE effect, the TPE-TPP nanoaggregates uptaken by cells were resistant to photobleaching under three-photon excitation for an extended period of time. Furthermore, we demonstrated that for the present TPE-TPP AIE the three-photon microscopy (with 1020 nm excitation) had a better signal to noise ratio than the two-photon microscopy (with 810 nm excitation) in tissue imaging.
Collapse
Affiliation(s)
- Zhenfeng Zhu
- State Key Laboratory of Modern Optical Instrumentation (Zhejiang University), Centre for Optical and Electromagnetic Research, Zhejiang Provincial Key Laboratory for Sensing Technologies, JORCEP (Sino-Swedish Joint Research Center of Photonics), Zhejiang University, Hangzhou, 310058, China
| | - Chris W T Leung
- Department of Chemistry, The Hong Kong University of Science &Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Xinyuan Zhao
- Bioelectromagnetics Laboratory, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Yalun Wang
- State Key Laboratory of Modern Optical Instrumentation (Zhejiang University), Centre for Optical and Electromagnetic Research, Zhejiang Provincial Key Laboratory for Sensing Technologies, JORCEP (Sino-Swedish Joint Research Center of Photonics), Zhejiang University, Hangzhou, 310058, China
| | - Jun Qian
- State Key Laboratory of Modern Optical Instrumentation (Zhejiang University), Centre for Optical and Electromagnetic Research, Zhejiang Provincial Key Laboratory for Sensing Technologies, JORCEP (Sino-Swedish Joint Research Center of Photonics), Zhejiang University, Hangzhou, 310058, China
| | - Ben Zhong Tang
- Department of Chemistry, The Hong Kong University of Science &Technology, Clear Water Bay, Kowloon, Hong Kong, China
| | - Sailing He
- Bioelectromagnetics Laboratory, Zhejiang University School of Medicine, Hangzhou 310058, China
| |
Collapse
|
17
|
Abstract
The spectrum of RNA functions in the cell continues to widen and new types of RNA molecules continue to be discovered. However, methods to access and manipulate endogenous RNAs in live cells are limited. Here we describe a universal technique for labeling natural RNAs in live cells with the probes synthesized by the cell. The method is based on fluorescent protein complementation in combination with a split aptamer approach. Two RNA probes containing split aptamer sequences flanked with the antisense RNA target sequences are assembled on the target RNA to form a fluorescent ribonucleoprotein (RNP) complex. The mechanism of complex formation ensures highly sensitive RNA detection allowing visualization of endogenous bacterial mRNAs. We demonstrate the great potential of this method by detecting chromosomally low-level expressed unmodified bacterial mRNA in living bacterial cells. This method holds promise to become a broadly used tool in basic research, and eventually in diagnostics and therapeutics.
Collapse
Affiliation(s)
- Irina Smolina
- Department of Biomedical Engineering, Boston University, Boston, MA, 01225, USA,
| | | |
Collapse
|
18
|
Sharma AK, Plant JJ, Rangel AE, Meek KN, Anamisis AJ, Hollien J, Heemstra JM. Fluorescent RNA labeling using self-alkylating ribozymes. ACS Chem Biol 2014; 9:1680-4. [PMID: 24896502 DOI: 10.1021/cb5002119] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The ability to fluorescently label specific RNA sequences is of significant utility for both in vitro and live cell applications. Currently, most RNA labeling methods utilize RNA-nucleic acid or RNA-protein molecular recognition. However, in the search for improved RNA labeling methods, harnessing the small-molecule recognition capabilities of RNA is rapidly emerging as a promising alternative. Along these lines, we propose a novel strategy in which a ribozyme acts to promote self-alkylation with a fluorophore, providing a robust, covalent linkage between the RNA and the fluorophore. Here we describe the selection and characterization of ribozymes that promote self-labeling with fluorescein iodoacetamide (FIA). Kinetic studies reveal a second-order rate constant that is on par with those of other reactions used for biomolecular labeling. Additionally, we demonstrate that labeling is specific to the ribozyme sequences, as FIA does not react nonspecifically with RNA.
Collapse
Affiliation(s)
- Ashwani K. Sharma
- Department of Chemistry and the Center
for Cell and Genome Science and ‡Department of Biology
and the Center for Cell and Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Joshua J. Plant
- Department of Chemistry and the Center
for Cell and Genome Science and ‡Department of Biology
and the Center for Cell and Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Alexandra E. Rangel
- Department of Chemistry and the Center
for Cell and Genome Science and ‡Department of Biology
and the Center for Cell and Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Kirsten N. Meek
- Department of Chemistry and the Center
for Cell and Genome Science and ‡Department of Biology
and the Center for Cell and Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - April J. Anamisis
- Department of Chemistry and the Center
for Cell and Genome Science and ‡Department of Biology
and the Center for Cell and Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Julie Hollien
- Department of Chemistry and the Center
for Cell and Genome Science and ‡Department of Biology
and the Center for Cell and Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| | - Jennifer M. Heemstra
- Department of Chemistry and the Center
for Cell and Genome Science and ‡Department of Biology
and the Center for Cell and Genome Science, University of Utah, Salt Lake
City, Utah 84112, United States
| |
Collapse
|
19
|
Kadam U, Moeller CA, Irudayaraj J, Schulz B. Effect of T-DNA insertions on mRNA transcript copy numbers upstream and downstream of the insertion site in Arabidopsis thaliana explored by surface enhanced Raman spectroscopy. PLANT BIOTECHNOLOGY JOURNAL 2014; 12:568-77. [PMID: 24460907 DOI: 10.1111/pbi.12161] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 12/12/2013] [Accepted: 12/15/2013] [Indexed: 05/23/2023]
Abstract
We report the effect of a T-DNA insertion on the expression level of mRNA transcripts of the TWISTED DWARF 1 (TWD1) gene upstream and downstream of the T-DNA insertion site in Arabidopsis. A novel approach based on surface-enhanced Raman spectroscopy (SERS) was developed to detect and quantify the effect of a T-DNA insertion on mRNA transcript accumulation at 5'- and 3'-ends of the TWD1 gene. A T-DNA insertion mutant in the TWD1 gene (twd1-2) was chosen to test the sensitivity and the feasibility of the approach. The null mutant of the FK506-like immunophilin protein TWD1 in Arabidopsis shows severe dwarfism and strong disoriented growth of plant organs. A spontaneous arising suppressor allele of twd1-2 called twd-sup displayed an intermediate phenotype between wild type and the knockout phenotype of twd1-2. Both twd1 mutant alleles have identical DNA sequences at the TWD1 locus including the T-DNA insertion in the fourth intron of the TWD1 gene but they show clear variability in the mutant phenotype. We present here the development and application of SERS-based mRNA detection and quantification using the expression of the TWD1 gene in wild type and both mutant alleles. The hallmarks of our SERS approach are a robust and fast assay to detect up to 0.10 fm of target molecules including the ability to omit in vitro transcription and amplification steps after RNA isolation. Instead we perform direct quantification of RNA molecules. This enables us to detect and quantify rare RNA molecules at high levels of precision and sensitivity.
Collapse
Affiliation(s)
- Ulhas Kadam
- Department of Agricultural & Biological Engineering, Purdue University, West Lafayette, IN, USA; Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, IN, USA; Bindley Bioscience Center, Purdue University, West Lafayette, IN, USA; Birck Nanotechnology Center, Purdue University, West Lafayette, IN, USA
| | | | | | | |
Collapse
|
20
|
Boutorine AS, Novopashina DS, Krasheninina OA, Nozeret K, Venyaminova AG. Fluorescent probes for nucleic Acid visualization in fixed and live cells. Molecules 2013; 18:15357-97. [PMID: 24335616 PMCID: PMC6270009 DOI: 10.3390/molecules181215357] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Revised: 11/20/2013] [Accepted: 12/05/2013] [Indexed: 12/13/2022] Open
Abstract
This review analyses the literature concerning non-fluorescent and fluorescent probes for nucleic acid imaging in fixed and living cells from the point of view of their suitability for imaging intracellular native RNA and DNA. Attention is mainly paid to fluorescent probes for fluorescence microscopy imaging. Requirements for the target-binding part and the fluorophore making up the probe are formulated. In the case of native double-stranded DNA, structure-specific and sequence-specific probes are discussed. Among the latest, three classes of dsDNA-targeting molecules are described: (i) sequence-specific peptides and proteins; (ii) triplex-forming oligonucleotides and (iii) polyamide oligo(N-methylpyrrole/N-methylimidazole) minor groove binders. Polyamides seem to be the most promising targeting agents for fluorescent probe design, however, some technical problems remain to be solved, such as the relatively low sequence specificity and the high background fluorescence inside the cells. Several examples of fluorescent probe applications for DNA imaging in fixed and living cells are cited. In the case of intracellular RNA, only modified oligonucleotides can provide such sequence-specific imaging. Several approaches for designing fluorescent probes are considered: linear fluorescent probes based on modified oligonucleotide analogs, molecular beacons, binary fluorescent probes and template-directed reactions with fluorescence probe formation, FRET donor-acceptor pairs, pyrene excimers, aptamers and others. The suitability of all these methods for living cell applications is discussed.
Collapse
Affiliation(s)
- Alexandre S. Boutorine
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Darya S. Novopashina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
| | - Olga A. Krasheninina
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
- Department of Natural Sciences, Novosibirsk State University, Pirogova Str., 2, Novosibirsk 630090, Russia
| | - Karine Nozeret
- Muséum National d’Histoire Naturelle, CNRS, UMR 7196, INSERM, U565, 57 rue Cuvier, B.P. 26, Paris Cedex 05, F-75231, France; E-Mail:
| | - Alya G. Venyaminova
- Institute of Chemical Biology and Fundamental Medicine, Siberian Division of Russian Academy of Sciences, Lavrentyev Ave., 8, Novosibirsk 630090, Russia; E-Mails: (D.S.N.); (O.A.K.); (A.G.V.)
| |
Collapse
|
21
|
Tokmakov AA, Hashimoto T, Hasegawa Y, Iguchi S, Iwasaki T, Fukami Y. Monitoring gene expression in a single Xenopus oocyte using multiple cytoplasmic collections and quantitative RT-PCR. FEBS J 2013; 281:104-14. [PMID: 24165194 DOI: 10.1111/febs.12576] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 10/10/2013] [Accepted: 10/21/2013] [Indexed: 11/27/2022]
Abstract
Oocytes and eggs of the African clawed frog, Xenopus laevis, are commonly used in gene expression studies. However, monitoring transcript levels in the individual living oocytes remains challenging. To address this challenge, we used a technique based on multiple repeated collections of nanoliter volumes of cytoplasmic material from a single oocyte. Transcript quantification was performed by quantitative RT-PCR. The technique allowed monitoring of heterologous gene expression in a single oocyte without affecting its viability. We also used this approach to profile the expression of endogenous genes in living Xenopus oocytes. Although frog oocytes are traditionally viewed as a homogenous cell population, a significant degree of gene expression variation was observed among the individual oocytes. A lognormal distribution of transcript levels was revealed in the oocyte population. Finally, using this technique, we observed a dramatic decrease in the content of various cytoplasmic mRNAs in aging unfertilized eggs but not in oocytes, suggesting a link between mRNA degradation and egg apoptosis.
Collapse
|
22
|
Genetic encoding of fluorescent RNA ensures a bright future for visualizing nucleic acid dynamics. Trends Biotechnol 2012; 30:621-6. [PMID: 23127753 DOI: 10.1016/j.tibtech.2012.09.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 09/19/2012] [Indexed: 11/22/2022]
Abstract
Recently RNA localization has been appreciated as an essential post-transcriptional mechanism to program local proteome composition and function. Although RNA has been visualized using diverse techniques, the use of the bacteriophage MS2 method to encode genetically fluorescent RNA has revolutionized the study of RNA dynamics in living cells. Here, I highlight the strength of MS2 compared to other techniques, and how further evolution of this system will enable the visualization of RNA in the context of complex live-cell dynamics. Although the generation of MS2-fluorescence resonance energy transfer (FRET) and MS2-bifluorescence complementation (BiFC) will require further development, it has the potential to increase significantly the signal-to-noise ratio, which is the major obstacle to rapid live-cell imaging of RNA.
Collapse
|
23
|
Abstract
Imaging technologies developed in the early 20th century achieved contrast solely by relying on macroscopic and morphological differences between the tissues of interest and the surrounding tissues. Since then, there has been a movement toward imaging at the cellular and molecular level in order to visualize biological processes. This rapidly growing field is known as molecular imaging. In the last decade, many methodologies for imaging proteins have emerged. However, most of these approaches cannot be extended to imaging beyond the proteome. Here, we highlight some of the recently developed technologies that enable imaging of non-proteinaceous molecules in the cell: lipids, signalling molecules, inorganic ions, glycans, nucleic acids, small-molecule metabolites, and protein post-translational modifications such as phosphorylation and methylation.
Collapse
Affiliation(s)
- Pamela V. Chang
- Department of Chemistry, University of California, Berkeley, 94720, USA
| | - Carolyn R. Bertozzi
- Department of Chemistry, University of California, Berkeley, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, U.S.A
- Howard Hughes Medical Institute, University of California, Berkeley, U.S.A
| |
Collapse
|
24
|
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.
Collapse
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
| | | | | | | | | |
Collapse
|
25
|
Ikeda S, Kubota T, Wang DO, Yanagisawa H, Umemoto T, Okamoto A. Design and synthesis of caged fluorescent nucleotides and application to live-cell RNA imaging. Chembiochem 2011; 12:2871-80. [PMID: 22215304 DOI: 10.1002/cbic.201100523] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Indexed: 12/23/2022]
Abstract
A binary photocontrolled nucleic acid probe that contains a nucleotide modified with one photolabile nitrobenzyl unit and two hybridization-sensitive thiazole orange units has been designed for area-specific fluorescence imaging of RNA in a cell. The synthesized probe emitted very weak fluorescence regardless of the presence of the complementary RNA, whereas it showed hybridization-sensitive fluorescence emission at 532 nm after photoirradiation at 360 or 405 nm for uncaging. Fluorescence suppression of the caged probe was attributed to a decrease in the duplex-formation ability. Caged fluorescent nucleotides with other emission wavelengths (622 and 724 nm) were also synthesized in this study; they were uncaged by 360 nm irradiation, and emitted fluorescence in the presence of the complementary RNA. Such probes were applied to area-specific RNA imaging in a cell. Only probes in the defined irradiation area were activated by uncaging irradiation, and subnuclear mRNA diffusion in a living cell was monitored.
Collapse
Affiliation(s)
- Shuji Ikeda
- Advanced Science Institute, RIKEN, Wako, Saitama 351-0198, Japan
| | | | | | | | | | | |
Collapse
|
26
|
How to screen non-viral gene delivery systems in vitro? J Control Release 2011; 154:218-32. [PMID: 21600249 DOI: 10.1016/j.jconrel.2011.05.001] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2010] [Revised: 03/31/2011] [Accepted: 05/01/2011] [Indexed: 11/21/2022]
Abstract
Screening of new gene delivery candidates regarding transfection efficiency and toxicity is usually performed by reading out transgene expression levels relative to a reference formulation after in vitro transfection. However, over the years and among different laboratories, this screening has been performed in a variety of cell lines, using a variety of conditions and read-out systems, and by comparison to a variety of reference formulations. This makes a direct comparison of results difficult, if not impossible. Reaching a consensus would enable placing new results into context of previous findings and estimate the overall contribution to the improvement of non-viral gene delivery. In this paper we illustrate the sensitivity of transfection outcomes on testing conditions chosen, and propose a screening protocol with the aim of standardization within the field.
Collapse
|
27
|
Tilsner J, Flors C. FIT for purpose: PNA-based probes enable mRNA imaging in living cells. Chembiochem 2011; 12:1007-9. [PMID: 21465629 DOI: 10.1002/cbic.201100139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2011] [Indexed: 01/06/2023]
Affiliation(s)
- Jens Tilsner
- Institute of Molecular Plant Sciences, University of Edinburgh, UK.
| | | |
Collapse
|
28
|
Okabe K, Harada Y, Zhang J, Tadakuma H, Tani T, Funatsu T. Real time monitoring of endogenous cytoplasmic mRNA using linear antisense 2'-O-methyl RNA probes in living cells. Nucleic Acids Res 2011; 39:e20. [PMID: 21106497 PMCID: PMC3045578 DOI: 10.1093/nar/gkq1196] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2010] [Revised: 10/27/2010] [Accepted: 11/05/2010] [Indexed: 12/21/2022] Open
Abstract
Visualization and monitoring of endogenous mRNA in the cytoplasm of living cells promises a significant comprehension of refined post-transcriptional regulation. Fluorescently labeled linear antisense oligonucleotides can bind to natural mRNA in a sequence-specific way and, therefore, provide a powerful tool in probing endogenous mRNA. Here, we investigated the feasibility of using linear antisense probes to monitor the variable and dynamic expression of endogenous cytoplasmic mRNAs. Two linear antisense 2'-O-methyl RNA probes, which have different interactive fluorophores at the 5'-end of one probe and at the 3'-end of the other, were used to allow fluorescence resonance energy transfer (FRET) upon hybridization to the target mRNA. By characterizing the formation of the probe-mRNA hybrids in living cells, we found that the probe composition and concentration are crucial parameters in the visualization of endogenous mRNA with high specificity. Furthermore, rapid hybridization (within 1 min) of the linear antisense probe enabled us to visualize dynamic processes of endogenous c-fos mRNA, such as fast elevation of levels after gene induction and the localization of c-fos mRNA in stress granules in response to cellular stress. Thus, our approach provides a basis for real time monitoring of endogenous cytoplasmic mRNA in living cells.
Collapse
Affiliation(s)
- Kohki Okabe
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, The Tokyo Metropolitan Institute of Medical Science, 1-6-2 Kamikitazawa Setagaya-ku, Tokyo 156-8506, The Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Honmachi Sakyo-ku, Kyoto 606-8501, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Kumamoto, Kumamoto 860-8555 and Center for NanoBio Integration, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-8656, Japan
| | - Yoshie Harada
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, The Tokyo Metropolitan Institute of Medical Science, 1-6-2 Kamikitazawa Setagaya-ku, Tokyo 156-8506, The Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Honmachi Sakyo-ku, Kyoto 606-8501, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Kumamoto, Kumamoto 860-8555 and Center for NanoBio Integration, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-8656, Japan
| | - Junwei Zhang
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, The Tokyo Metropolitan Institute of Medical Science, 1-6-2 Kamikitazawa Setagaya-ku, Tokyo 156-8506, The Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Honmachi Sakyo-ku, Kyoto 606-8501, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Kumamoto, Kumamoto 860-8555 and Center for NanoBio Integration, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-8656, Japan
| | - Hisashi Tadakuma
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, The Tokyo Metropolitan Institute of Medical Science, 1-6-2 Kamikitazawa Setagaya-ku, Tokyo 156-8506, The Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Honmachi Sakyo-ku, Kyoto 606-8501, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Kumamoto, Kumamoto 860-8555 and Center for NanoBio Integration, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-8656, Japan
| | - Tokio Tani
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, The Tokyo Metropolitan Institute of Medical Science, 1-6-2 Kamikitazawa Setagaya-ku, Tokyo 156-8506, The Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Honmachi Sakyo-ku, Kyoto 606-8501, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Kumamoto, Kumamoto 860-8555 and Center for NanoBio Integration, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-8656, Japan
| | - Takashi Funatsu
- Graduate School of Pharmaceutical Sciences, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-0033, The Tokyo Metropolitan Institute of Medical Science, 1-6-2 Kamikitazawa Setagaya-ku, Tokyo 156-8506, The Institute for Integrated Cell-Material Sciences, Kyoto University, Yoshida-Honmachi Sakyo-ku, Kyoto 606-8501, Graduate School of Frontier Sciences, the University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa-shi, Chiba 277-8562, Department of Biological Sciences, Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami Kumamoto, Kumamoto 860-8555 and Center for NanoBio Integration, the University of Tokyo, 7-3-1 Hongo Bunkyo-ku, Tokyo 113-8656, Japan
| |
Collapse
|
29
|
Abstract
The analysis of the spatial-dynamic properties of DNA and RNA molecules in living cells will greatly extend our knowledge of genome organization and gene expression regulation in the cell nucleus. The development of hybridization methods allowing detection of specific endogenous DNA and RNA sequences in living cells has therefore been a challenge for many years. However, there are many technical issues that have proven so far to be difficult, or even impossible, to overcome. As a result, in most situations, the application of in vivo hybridization methods is currently limited to the visualization of highly repetitive DNA sequences or abundant RNA species. We describe a protocol that enables the visualization and tracking of telomeres in living cells by hybridization with a fluorescent peptide nucleic acid (PNA) probe. Furthermore, we describe a method that allows the detection of abundant endogenous RNAs in living cells by microinjecting fluorescently labeled complementary 2'-O-methyl RNA probes.
Collapse
|
30
|
Lee J, Lee KH, Jeon J, Dragulescu-Andrasi A, Xiao F, Rao J. Combining SELEX screening and rational design to develop light-up fluorophore-RNA aptamer pairs for RNA tagging. ACS Chem Biol 2010; 5:1065-74. [PMID: 20809562 DOI: 10.1021/cb1001894] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We report here a new small molecule fluorogen and RNA aptamer pair for RNA labeling. The small-molecule fluorogen is designed on the basis of fluorescently quenched sulforhodamine dye. The SELEX (Systematic Evolution of Ligands by EXponential enrichment) procedure and fluorescence screening in E. coli have been applied to discover the aptamer that can specifically activate the fluorogen with micromolar binding affinity. The systematic mutation and truncation study on the aptamer structure determined the minimum binding domain of the aptamer. A series of rationally modified fluorogen analogues have been made to probe the interacting groups of fluorogen with the aptamer. These results led to the design of a much improved fluorogen ASR 7 that displayed a 33-fold increase in the binding affinity for the selected aptamer in comparison to the original ASR 1 and an 88-fold increase in the fluorescence emission after the aptamer binding. This study demonstrates the value of combining in vitro SELEX and E. coli fluorescence screening with rational modifications in discovering and optimizing new fluorogen-RNA aptamer labeling pairs.
Collapse
Affiliation(s)
| | - Kyung Hyun Lee
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology
| | - Jongho Jeon
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology
| | | | - Fei Xiao
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology
| | - Jianghong Rao
- Department of Chemistry
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology
| |
Collapse
|
31
|
Rouquette J, Cremer C, Cremer T, Fakan S. Functional nuclear architecture studied by microscopy: present and future. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2010; 282:1-90. [PMID: 20630466 DOI: 10.1016/s1937-6448(10)82001-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In this review we describe major contributions of light and electron microscopic approaches to the present understanding of functional nuclear architecture. The large gap of knowledge, which must still be bridged from the molecular level to the level of higher order structure, is emphasized by differences of currently discussed models of nuclear architecture. Molecular biological tools represent new means for the multicolor visualization of various nuclear components in living cells. New achievements offer the possibility to surpass the resolution limit of conventional light microscopy down to the nanometer scale and require improved bioinformatics tools able to handle the analysis of large amounts of data. In combination with the much higher resolution of electron microscopic methods, including ultrastructural cytochemistry, correlative microscopy of the same cells in their living and fixed state is the approach of choice to combine the advantages of different techniques. This will make possible future analyses of cell type- and species-specific differences of nuclear architecture in more detail and to put different models to critical tests.
Collapse
Affiliation(s)
- Jacques Rouquette
- Biocenter, Ludwig Maximilians University (LMU), Martinsried, Germany
| | | | | | | |
Collapse
|
32
|
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.
Collapse
|
33
|
Zhang Z, Dharmakumar R, Mascheri N, Fan Z, Wu S, Li D. Comparison of Superparamagnetic and Ultrasmall Superparamagnetic Iron Oxide Cell Labeling for Tracking Green Fluorescent Protein Gene Marker with Negative and Positive Contrast Magnetic Resonance Imaging. Mol Imaging 2009. [DOI: 10.2310/7290.2009.00008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The objectives of this study were to investigate the feasibility of imaging green fluorescent protein (GFP)-expressing cells labeled with iron oxide nanoparticles with the fast low-angle positive contrast steady-state free precession (FLAPS) method and to compare them with the traditional negative contrast technique. The GFP-R3230Ac cell line (GFP cell) was incubated for 24 hours using 20 μg Fe/mL concentration of superparamagnetic iron oxide (SPIO) and ultrasmall superparamagnetic iron oxide (USPIO) nanoparticles. Cell samples were prepared for iron content analysis and cell function evaluation. The labeled cells were imaged using positive contrast with FLAPS imaging, and FLAPS images were compared with negative contrast T2*-weighted images. The results demonstrated that SPIO and USPIO labeling of GFP cells had no effect on cell function or GFP expression. Labeled cells were successfully imaged with both positive and negative contrast magnetic resonance imaging (MRI). The labeled cells were observed as a narrow band of signal enhancement surrounding signal voids in FLAPS images and were visible as signal voids in T2*-weighted images. Positive contrast and negative contrast imaging were both valuable for visualizing labeled GFP cells. MRI of labeled cells with GFP expression holds potential promise for monitoring the temporal and spatial migration of gene markers and cells, thereby enhancing the understanding of cell- and gene-based therapeutic strategies.
Collapse
Affiliation(s)
- Zhuoli Zhang
- From the Departments of Radiology and Biomedical Engineering, Northwestern University, Chicago, IL; VirtualScopics, Inc. Rochester, NY; and Medical Imaging Institute of Tianjin, Tianjin, China
| | - Rohan Dharmakumar
- From the Departments of Radiology and Biomedical Engineering, Northwestern University, Chicago, IL; VirtualScopics, Inc. Rochester, NY; and Medical Imaging Institute of Tianjin, Tianjin, China
| | - Nicole Mascheri
- From the Departments of Radiology and Biomedical Engineering, Northwestern University, Chicago, IL; VirtualScopics, Inc. Rochester, NY; and Medical Imaging Institute of Tianjin, Tianjin, China
| | - Zhaoyang Fan
- From the Departments of Radiology and Biomedical Engineering, Northwestern University, Chicago, IL; VirtualScopics, Inc. Rochester, NY; and Medical Imaging Institute of Tianjin, Tianjin, China
| | - Shengyong Wu
- From the Departments of Radiology and Biomedical Engineering, Northwestern University, Chicago, IL; VirtualScopics, Inc. Rochester, NY; and Medical Imaging Institute of Tianjin, Tianjin, China
| | - Debiao Li
- From the Departments of Radiology and Biomedical Engineering, Northwestern University, Chicago, IL; VirtualScopics, Inc. Rochester, NY; and Medical Imaging Institute of Tianjin, Tianjin, China
| |
Collapse
|
34
|
Furukawa K, Abe H, Hibino K, Sako Y, Tsuneda S, Ito Y. Reduction-Triggered Fluorescent Amplification Probe for the Detection of Endogenous RNAs in Living Human Cells. Bioconjug Chem 2009; 20:1026-36. [DOI: 10.1021/bc900040t] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kazuhiro Furukawa
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Hiroshi Abe
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Kayo Hibino
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yasushi Sako
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Satoshi Tsuneda
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Cellar Informatics Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| |
Collapse
|
35
|
Abstract
Commonly used techniques for analyzing gene expression, such as polymerase chain reaction (PCR), microarrays, and in situ hybridization, have proven invaluable in understanding RNA processing and regulation. However, these techniques rely on the use of lysed and/or fixed cells and are therefore limited in their ability to provide important spatial-temporal information. This has led to the development of numerous techniques for imaging RNA in living cells, some of which have already provided important insight into the dynamic role RNA plays in dictating cell behavior. Here we review the fluorescent probes that have allowed for RNA imaging in living cells and discuss their utility and limitations. Common challenges faced by fluorescent probes, such as probe design, delivery, and target accessibility, are also discussed. It is expected that continued advancements in live cell imaging of RNA will open new and exciting opportunities in a wide range of biological and medical applications.
Collapse
Affiliation(s)
- Gang Bao
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332;
| | - Won Jong Rhee
- Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332;
| | - Andrew Tsourkas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| |
Collapse
|
36
|
Valencia-Burton M, Broude NE. Visualization of RNA using fluorescence complementation triggered by aptamer-protein interactions (RFAP) in live bacterial cells. ACTA ACUST UNITED AC 2008; Chapter 17:Unit 17.11. [PMID: 18228500 DOI: 10.1002/0471143030.cb1711s37] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This unit describes a method allowing RNA visualization in live cells. The method is based on fluorescent protein complementation regulated by RNA-aptamer/RNA-binding protein interactions. Based on these two principles, a fluorescent ribonucleoprotein complex is assembled inside the cell only in response to the presence of the aptamer sequence on the target RNA.
Collapse
Affiliation(s)
- Maria Valencia-Burton
- Center for Advanced Biotechnology, College of Engineering, Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | | |
Collapse
|
37
|
Kim IH, Nagel J, Otten S, Knerr B, Eils R, Rohr K, Dietzel S. Quantitative comparison of DNA detection by GFP-lac repressor tagging, fluorescence in situ hybridization and immunostaining. BMC Biotechnol 2007; 7:92. [PMID: 18096031 PMCID: PMC2254608 DOI: 10.1186/1472-6750-7-92] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2007] [Accepted: 12/20/2007] [Indexed: 11/26/2022] Open
Abstract
Background GFP-fusion proteins and immunostaining are methods broadly applied to investigate the three-dimensional organization of cells and cell nuclei, the latter often studied in addition by fluorescence in situ hybridization (FISH). Direct comparisons of these detection methods are scarce, however. Results We provide a quantitative comparison of all three approaches. We make use of a cell line that contains a transgene array of lac operator repeats which are detected by GFP-lac repressor fusion proteins. Thus we can detect the same structure in individual cells by GFP fluorescence, by antibodies against GFP and by FISH with a probe against the transgene array. Anti-GFP antibody detection was repeated after FISH. Our results show that while all four signals obtained from a transgene array generally showed qualitative and quantitative similarity, they also differed in details. Conclusion Each of the tested methods revealed particular strengths and weaknesses, which should be considered when interpreting respective experimental results. Despite the required denaturation step, FISH signals in structurally preserved cells show a surprising similarity to signals generated before denaturation.
Collapse
Affiliation(s)
- Il-Han Kim
- University of Heidelberg, BIOQUANT, IPMB, and German Cancer Research Center (DKFZ), Dept. Bioinformatics and FunctionalGenomics, Biomedical Computer Vision Group, Im Neuenheimer Feld 267, 69120 Heidelberg, Germany.
| | | | | | | | | | | | | |
Collapse
|
38
|
Wiesmeijer K, Krouwels IM, Tanke HJ, Dirks RW. Chromatin movement visualized with photoactivable GFP-labeled histone H4. Differentiation 2007; 76:83-90. [PMID: 18021258 DOI: 10.1111/j.1432-0436.2007.00234.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cell nucleus is highly organized with chromosomes occupying discrete, partially overlapping territories, and proteins that localize to specific nuclear compartments. This spatial organization of the nucleus is considered to be dynamic in response to environmental and cellular conditions to support changes in transcriptional programs. Chromatin, however, is relatively immobile when analyzed in living cells and shows a constrained Brownian type of movement. A possible explanation for this relative immobility is that chromatin interacts with a nuclear matrix structure and/or with nuclear compartments. Here, we explore the use of photoactivatable GFP fused to histone H4 as a potential tool to analyze the mobility of chromatin at various nuclear compartments. Selective photoactivation of photoactivatable-GFP at defined nuclear regions was achieved by two-photon excitation with 820 nm light. Nuclear speckles, which are considered storage sites of splicing factors, were visualized by coexpression of a fluorescent protein fused to splicing factor SF2/ASF. The results reveal a constrained chromatin motion, which is not affected by transcriptional inhibition, and suggests an intimate interaction of chromatin with speckles.
Collapse
Affiliation(s)
- Karien Wiesmeijer
- Department of Molecular Cell Biology, Leiden University Medical Center, Postal zone S1-P, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | | | | | | |
Collapse
|
39
|
Reddy GV, Gordon SP, Meyerowitz EM. Unravelling developmental dynamics: transient intervention and live imaging in plants. Nat Rev Mol Cell Biol 2007; 8:491-501. [PMID: 17522592 DOI: 10.1038/nrm2188] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Plant development is dynamic in nature. This is exemplified in developmental patterning, in which roots and shoots rapidly elongate while simultaneously giving rise to precisely positioned new organs over a time course of minutes to hours. In this Review, we emphasize the insights gained from simultaneous use of live imaging and transient perturbation technologies to capture the dynamic properties of plant processes.
Collapse
Affiliation(s)
- G Venugopala Reddy
- Department of Botany and Plant Sciences, 2150 Batchelor Hall, University of California, Riverside, California 92521, USA.
| | | | | |
Collapse
|
40
|
Mo ZH, Yang XC, Guo KP, Wen ZY. A nanogold-quenched fluorescence duplex probe for homogeneous DNA detection based on strand displacement. Anal Bioanal Chem 2007; 389:493-7. [PMID: 17641878 DOI: 10.1007/s00216-007-1477-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2007] [Revised: 06/24/2007] [Accepted: 06/26/2007] [Indexed: 01/12/2023]
Abstract
A nanogold-quenched fluorescence duplex probe has been developed for lighting up homogenous hybridization assays. This novel probe is constructed from two strands of different lengths, and labeled by nanogold and a fluorophore at the long-strand 5'-end and the short-strand 3'-end, respectively. The two tags are in close contact, resulting in complete quenching of the probe fluorescence. If perfectly complemented to the nanogold-labeled strand, a long target oligonucleotide would displace the short fluorophore-labeled strand, and as a result, restore the fluorescence. By using nanogold in the probe, an extremely high quenching efficiency (99.1%) and removal of free fluorophore-labeled strand is achieved. The signal-to-noise ratio and the detection limit (50 pmol L(-1)) of homogenous assays are therefore improved significantly, in comparison with similar probes using organic acceptors. Moreover, the probe has a great inhibition effect on hybridization to a mismatched oligonucleotide. This effect provides the assay with a high specificity, and particularly the assay has great potential in applications for discriminating variations in sequences. The assay sensitivity could be markedly enhanced by using fluorescent materials in the signal strand that are brighter and not quenched by nucleobases.
Collapse
Affiliation(s)
- Z-H Mo
- Micro-System Research Center, College of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China.
| | | | | | | |
Collapse
|
41
|
An inexpensive fluorescent labeling protocol for bioactive natural products utilizing Cu(I)-catalyzed Huisgen reaction. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.04.069] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
42
|
|
43
|
Valencia-Burton M, McCullough RM, Cantor CR, Broude NE. RNA visualization in live bacterial cells using fluorescent protein complementation. Nat Methods 2007; 4:421-7. [PMID: 17401371 DOI: 10.1038/nmeth1023] [Citation(s) in RCA: 147] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2006] [Accepted: 02/01/2007] [Indexed: 01/12/2023]
Abstract
We describe a technique for the detection and localization of RNA transcripts in living cells. The method is based on fluorescent-protein complementation regulated by the interaction of a split RNA-binding protein with its corresponding RNA aptamer. In our design, the RNA-binding protein is the eukaryotic initiation factor 4A (eIF4A). eIF4A is dissected into two fragments, and each fragment is fused to split fragments of the enhanced green fluorescent protein (EGFP). Coexpression of the two protein fusions in the presence of a transcript containing eIF4A-interacting RNA aptamer resulted in the restoration of EGFP fluorescence in Escherichia coli cells. We also applied this technique to the visualization of an aptamer-tagged mRNA and 5S ribosomal RNA (rRNA). We observed distinct spatial and temporal changes in fluorescence within single cells, reflecting the nature of the transcript.
Collapse
Affiliation(s)
- Maria Valencia-Burton
- Center for Advanced Biotechnology and Department of Biomedical Engineering, Boston University, 36 Cummington St., Boston, Massachusetts 02215, USA
| | | | | | | |
Collapse
|
44
|
Buszczak M, Paterno S, Lighthouse D, Bachman J, Planck J, Owen S, Skora AD, Nystul TG, Ohlstein B, Allen A, Wilhelm JE, Murphy TD, Levis RW, Matunis E, Srivali N, Hoskins RA, Spradling AC. The carnegie protein trap library: a versatile tool for Drosophila developmental studies. Genetics 2006; 175:1505-31. [PMID: 17194782 PMCID: PMC1840051 DOI: 10.1534/genetics.106.065961] [Citation(s) in RCA: 438] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Metazoan physiology depends on intricate patterns of gene expression that remain poorly known. Using transposon mutagenesis in Drosophila, we constructed a library of 7404 protein trap and enhancer trap lines, the Carnegie collection, to facilitate gene expression mapping at single-cell resolution. By sequencing the genomic insertion sites, determining splicing patterns downstream of the enhanced green fluorescent protein (EGFP) exon, and analyzing expression patterns in the ovary and salivary gland, we found that 600-900 different genes are trapped in our collection. A core set of 244 lines trapped different identifiable protein isoforms, while insertions likely to act as GFP-enhancer traps were found in 256 additional genes. At least 8 novel genes were also identified. Our results demonstrate that the Carnegie collection will be useful as a discovery tool in diverse areas of cell and developmental biology and suggest new strategies for greatly increasing the coverage of the Drosophila proteome with protein trap insertions.
Collapse
Affiliation(s)
- Michael Buszczak
- Howard Hughes Medical Institute Research Laboratories, Department of Embryology, Carnegie Institution of Washington, Baltimore, Maryland 21218, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Abstract
By taking advantage of combinations of the many rich properties of photons, new forms of optical microscopy can now be used to visualize features of samples beyond thickness and density variations. We are now within reach of viewing the motions, orientations, binding kinetics and specific transient associations of previously 'submicroscopic' cellular structures and single molecules.
Collapse
Affiliation(s)
- Daniel Axelrod
- Department of Physics & Biophysics Research Division, University of Michigan, Ann Arbor, Michigan 48109, USA.
| | | |
Collapse
|
46
|
Abstract
A combinatorial library of 1336 fluorescent styryl molecules was synthesized aiming to select dyes that are photostable, non-toxic, and specific for RNA molecules in living cells . These dyes are potentially important to the study of gene expression in live cells.
Collapse
Affiliation(s)
- Roeland W Dirks
- Department of Molecular Cell Biology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | | |
Collapse
|