1
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Belousov A, Maslov I, Orekhov P, Khorn P, Kuzmichev P, Baleeva N, Motov V, Bogorodskiy A, Krasnova S, Mineev K, Zinchenko D, Zernii E, Ivanovich V, Permyakov S, Hofkens J, Hendrix J, Cherezov V, Gensch T, Mishin A, Baranov M, Mishin A, Borshchevskiy V. Monitoring GPCR conformation with GFP-inspired dyes. iScience 2024; 27:110466. [PMID: 39156645 PMCID: PMC11326922 DOI: 10.1016/j.isci.2024.110466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 05/15/2024] [Accepted: 07/02/2024] [Indexed: 08/20/2024] Open
Abstract
Solvatochromic compounds have emerged as valuable environment-sensitive probes for biological research. Here we used thiol-reactive solvatochromic analogs of the green fluorescent protein (GFP) chromophore to track conformational changes in two proteins, recoverin and the A2A adenosine receptor (A2AAR). Two dyes showed Ca2+-induced fluorescence changes when attached to recoverin. Our best-performing dye, DyeC, exhibited agonist-induced changes in both intensity and shape of its fluorescence spectrum when attached to A2AAR; none of these effects were observed with other common environment-sensitive dyes. Molecular dynamics simulations showed that activation of the A2AAR led to a more confined and hydrophilic environment for DyeC. Additionally, an allosteric modulator of A2AAR induced distinct fluorescence changes in the DyeC spectrum, indicating a unique receptor conformation. Our study demonstrated that GFP-inspired dyes are effective for detecting structural changes in G protein-coupled receptors (GPCRs), offering advantages such as intensity-based and ratiometric tracking, redshifted fluorescence spectra, and sensitivity to allosteric modulation.
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Affiliation(s)
- Anatoliy Belousov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Ivan Maslov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, 3590 Diepenbeek, Belgium
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, 3001 Leuven, Belgium
| | - Philipp Orekhov
- Faculty of Biology, Shenzhen MSU-BIT University, Shenzhen 518172, China
- Sechenov University, Moscow 119146, Russia
| | - Polina Khorn
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Pavel Kuzmichev
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Nadezhda Baleeva
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Vladislav Motov
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | | | - Svetlana Krasnova
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
- National Research University Higher School of Economics, Moscow 101000, Russia
| | - Konstantin Mineev
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Dmitry Zinchenko
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino 142290, Russia
| | - Evgeni Zernii
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia
| | | | - Sergei Permyakov
- Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino 142292, Russia
| | - Johan Hofkens
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, 3001 Leuven, Belgium
- Max Plank Institute for Polymer Research, Mainz, Germany
| | - Jelle Hendrix
- Dynamic Bioimaging Lab, Advanced Optical Microscopy Centre, Biomedical Research Institute, Agoralaan C (BIOMED), Hasselt University, 3590 Diepenbeek, Belgium
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, 3001 Leuven, Belgium
| | - Vadim Cherezov
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
| | - Thomas Gensch
- Laboratory for Photochemistry and Spectroscopy, Division for Molecular Imaging and Photonics, Department of Chemistry, KU Leuven, 3001 Leuven, Belgium
| | - Alexander Mishin
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
| | - Mikhail Baranov
- Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia
- Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Alexey Mishin
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
| | - Valentin Borshchevskiy
- Moscow Institute of Physics and Technology, Dolgoprudny 141701, Russia
- Joint Institute for Nuclear Research, Dubna 141980, Russian Federation
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2
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Jensen D, Ruiz Manzano A, Rector M, Tomko E, Record M, Galburt E. High-throughput, fluorescent-aptamer-based measurements of steady-state transcription rates for the Mycobacterium tuberculosis RNA polymerase. Nucleic Acids Res 2023; 51:e99. [PMID: 37739412 PMCID: PMC10602862 DOI: 10.1093/nar/gkad761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 08/04/2023] [Accepted: 09/11/2023] [Indexed: 09/24/2023] Open
Abstract
The first step in gene expression is the transcription of DNA sequences into RNA. Regulation at the level of transcription leads to changes in steady-state concentrations of RNA transcripts, affecting the flux of downstream functions and ultimately cellular phenotypes. Changes in transcript levels are routinely followed in cellular contexts via genome-wide sequencing techniques. However, in vitro mechanistic studies of transcription have lagged with respect to throughput. Here, we describe the use of a real-time, fluorescent-aptamer-based method to quantitate steady-state transcription rates of the Mycobacterium tuberculosis RNA polymerase. We present clear controls to show that the assay specifically reports on promoter-dependent, full-length RNA transcription rates that are in good agreement with the kinetics determined by gel-resolved, α-32P NTP incorporation experiments. We illustrate how the time-dependent changes in fluorescence can be used to measure regulatory effects of nucleotide concentrations and identity, RNAP and DNA concentrations, transcription factors, and antibiotics. Our data showcase the ability to easily perform hundreds of parallel steady-state measurements across varying conditions with high precision and reproducibility to facilitate the study of the molecular mechanisms of bacterial transcription.
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Affiliation(s)
- Drake Jensen
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63108, USA
| | - Ana Ruiz Manzano
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63108, USA
| | - Maxwell Rector
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Eric J Tomko
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63108, USA
| | - M Thomas Record
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Eric A Galburt
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63108, USA
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3
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Jiang S, Shi H, Zhang Q, Wang ZY, Zhang Y, Zhang CY. Rolling circle transcription amplification-directed construction of tandem spinach-based fluorescent light-up biosensor for label-free sensing of β-glucosyltransferase activity. Biosens Bioelectron 2023; 237:115513. [PMID: 37419074 DOI: 10.1016/j.bios.2023.115513] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/17/2023] [Accepted: 07/03/2023] [Indexed: 07/09/2023]
Abstract
β-glucosyltransferase (β-GT) can specifically catalyze the conversion of 5-hydroxymethylcytosine (5-hmC) to 5-glucosylhydroxy methylcytosine (5-ghmC), and it is associated with the control of phage-specific gene expression by affecting transcription process in vivo and in vitro. The current strategies for β-GT assay usually involve expensive equipment, laborious treatment, radioactive hazard, and poor sensitivity. Here, we report a Spinach-based fluorescent light-up biosensor for label-free measurement of β-GT activity by utilizing 5-hmC glucosylation-initiated rolling circle transcription amplification (RCTA). We design a 5-hmC-modified multifunctional circular detection probe (5-hmC-MCDP) that integrates the functions of target-recognition, signal transduction, and transcription amplification in one probe. The introduction of β-GT catalyzes 5-hmC glucosylation of 5-hmC-MCDP probe, protecting the glucosylated 5-mC-MCDP probe from the cleavage by MspI. The remaining 5-hmC-MCDP probe can initiate RCTA reaction with the aid of T7 RNA polymerase, generating tandem Spinach RNA aptamers. The tandem Spinach RNA aptamers can be lightened up by fluorophore 3,5-difluoro-4-hydroxybenzylidene imidazolinone, facilitating label-free measurement of β-GT activity. Notably, the high specificity of MspI-catalyzed cleavage of nonglucosylated probe can efficiently inhibit nonspecific amplification, endowing this assay with a low background. Due to the higher efficiency of RCTA than the canonical promoter-initiated RNA synthesis, the signal-to-noise ratio of RCTA is 4.6-fold higher than that of linear template-based transcription amplification. This method is capable of sensitively detecting β-GT activity with a limit of detection of 2.03 × 10-5 U/mL, and it can be used for the screening of inhibitors and determination of kinetic parameters, with great potential in epigenetic research and drug discovery.
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Affiliation(s)
- Su Jiang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Huanhuan Shi
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Qian Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China
| | - Zi-Yue Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China.
| | - Yan Zhang
- College of Chemistry and Chemical Engineering, Qilu Normal University, Jinan, 250200, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan, 250014, China; School of Chemistry and Chemical Engineering, Southeast University, Nanjing, 211189, China.
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4
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Peng Y, Shu L, Deng X, Huang X, Mo X, Du F, Tang Z. Live-Cell Imaging of Endogenous RNA with a Genetically Encoded Fluorogenic Allosteric Aptamer. Anal Chem 2023; 95:13762-13768. [PMID: 37661353 DOI: 10.1021/acs.analchem.2c05724] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Imaging and tracking tools for natural cellular RNA with improved biocompatibility, specificity, and sensitivity are critical to understanding RNA function and providing insights into disease therapeutics. We developed a new genetically encoded sensor using fluorogenic allosteric aptamer (FaApt) for the sensitive imaging of the localization and dynamics of RNA targets in live cells. Target RNAs can be specifically recognized with our sensor by forming perfectly complementary duplexes, which in turn can induce allosteric structural changes of the sensor to refold the native conformation of fluorogenic RNA aptamers. We demonstrated the ability of the sensor to monitor the effect of tumor necrosis factor and small-molecule inhibitor on the expression abundance of CXCL1 and survivin mRNA in human cancer cells, respectively. The asymmetrical distribution of endogenous Squint mRNA was confirmed in developing zebrafish embryos through microinjection of FaApt probes. This study provides an effective molecular tool for sensitive imaging and tracking endogenous RNA in living cells. Due to the high specificity and small size of our sensor system, it is expected to be applied to early diagnosis of RNA marker-related diseases and real-time evaluation of the treatment process.
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Affiliation(s)
- Yan Peng
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Linjuan Shu
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 6100141, P. R. China
| | - Xiongfei Deng
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xin Huang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Xianming Mo
- State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu 6100141, P. R. China
| | - Feng Du
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
| | - Zhuo Tang
- Natural Products Research Center, Chengdu Institute of Biology, Chinese Academy of Science, Chengdu 610041, P. R. China
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5
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Lee KH, Song J, Kim S, Han SR, Lee SW. Real-time monitoring strategies for optimization of in vitro transcription and quality control of RNA. Front Mol Biosci 2023; 10:1229246. [PMID: 37771458 PMCID: PMC10523567 DOI: 10.3389/fmolb.2023.1229246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/16/2023] [Indexed: 09/30/2023] Open
Abstract
RNA-based therapeutics and vaccines are opening up new avenues for modern medicine. To produce these useful RNA-based reagents, in vitro transcription (IVT) is an important reaction that primarily determines the yield and quality of the product. Therefore, IVT condition should be well optimized to achieve high yield and purity of transcribed RNAs. To this end, real-time monitoring of RNA production during IVT, which allows for fine tuning of the condition, would be required. Currently, light-up RNA aptamer and fluorescent dye pairs are considered as useful strategies to monitor IVT in real time. Fluorophore-labeled antisense probe-based methods can also be used for real-time IVT monitoring. In addition, a high-performance liquid chromatography (HPLC)-based method that can monitor IVT reagent consumption has been developed as a powerful tool to monitor IVT reaction in near real-time. This mini-review briefly introduces some strategies and examples for real-time IVT monitoring and discusses pros and cons of IVT monitoring methods.
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Affiliation(s)
| | - Jaehwi Song
- R&D Center, Rznomics Inc., Seongnam, Republic of Korea
| | | | | | - Seong-Wook Lee
- R&D Center, Rznomics Inc., Seongnam, Republic of Korea
- Department of Bioconvergence Engineering, Research Institute of Advanced Omics, Dankook University, Yongin, Republic of Korea
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6
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Bains J, Qureshi N, Ceylan B, Wacker A, Schwalbe H. Cell-free transcription-translation system: a dual read-out assay to characterize riboswitch function. Nucleic Acids Res 2023; 51:e82. [PMID: 37409574 PMCID: PMC10450168 DOI: 10.1093/nar/gkad574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 05/27/2023] [Accepted: 07/04/2023] [Indexed: 07/07/2023] Open
Abstract
Cell-free protein synthesis assays have become a valuable tool to understand transcriptional and translational processes. Here, we established a fluorescence-based coupled in vitro transcription-translation assay as a read-out system to simultaneously quantify mRNA and protein levels. We utilized the well-established quantification of the expression of shifted green fluorescent protein (sGFP) as a read-out of protein levels. In addition, we determined mRNA quantities using a fluorogenic Mango-(IV) RNA aptamer that becomes fluorescent upon binding to the fluorophore thiazole orange (TO). We utilized a Mango-(IV) RNA aptamer system comprising four subsequent Mango-(IV) RNA aptamer elements with improved sensitivity by building Mango arrays. The design of this reporter assay resulted in a sensitive read-out with a high signal-to-noise ratio, allowing us to monitor transcription and translation time courses in cell-free assays with continuous monitoring of fluorescence changes as well as snapshots of the reaction. Furthermore, we applied this dual read-out assay to investigate the function of thiamine-sensing riboswitches thiM and thiC from Escherichia coli and the adenine-sensing riboswitch ASW from Vibrio vulnificus and pbuE from Bacillus subtilis, which represent transcriptional and translational on- and off-riboswitches, respectively. This approach enabled a microplate-based application, a valuable addition to the toolbox for high-throughput screening of riboswitch function.
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Affiliation(s)
- Jasleen Kaur Bains
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Nusrat Shahin Qureshi
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Betül Ceylan
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Anna Wacker
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University, Frankfurt am Main, Hesse 60438, Germany
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7
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Allchin ER, Rosch JC, Stoneman AD, Kim H, Lippmann ES. Generalized Strategy for Engineering Mammalian Cell-Compatible RNA-Based Biosensors from Random Sequence Libraries. ACS Sens 2023; 8:2079-2086. [PMID: 37155734 DOI: 10.1021/acssensors.3c00388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Fluorescent RNA-based biosensors are useful tools for real-time detection of molecules in living cells. These biosensors typically consist of a chromophore-binding aptamer and a target-binding aptamer, whereby the chromophore-binding aptamer is destabilized until a target is captured, which causes a conformational change to permit chromophore binding and an increase in fluorescence. The target-binding region is typically fabricated using known riboswitch motifs, which are already known to have target specificity and undergo structural changes upon binding. However, known riboswitches only exist for a limited number of molecules, significantly constraining biosensor design. To overcome this challenge, we designed a framework for producing mammalian cell-compatible biosensors using aptamers selected from a large random library by Capture-SELEX. As a proof-of-concept, we generated and characterized a fluorescent RNA biosensor against L-dopa, the precursor of several neurotransmitters. Overall, we suggest that this approach will have utility for generating RNA biosensors that can reliably detect custom targets in mammalian cells.
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Affiliation(s)
- Everett R Allchin
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Jonah C Rosch
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Alexander D Stoneman
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Hyosung Kim
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
| | - Ethan S Lippmann
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37212, United States
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8
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Advances in
G
‐quadruplexes‐based fluorescent imaging. Biopolymers 2022; 113:e23528. [DOI: 10.1002/bip.23528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 11/16/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022]
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9
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Qin W, Li L, Yang F, Wang S, Yang GY. High-throughput iSpinach fluorescent aptamer-based real-time monitoring of in vitro transcription. BIORESOUR BIOPROCESS 2022; 9:112. [PMID: 38647769 PMCID: PMC10991154 DOI: 10.1186/s40643-022-00598-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/30/2022] [Indexed: 11/10/2022] Open
Abstract
In vitro transcription (IVT) is an essential technique for RNA synthesis. Methods for the accurate and rapid screening of IVT conditions will facilitate RNA polymerase engineering, promoter optimization, and screening for new transcription inhibitor drugs. However, traditional polyacrylamide gel electrophoresis (PAGE) and high-performance liquid chromatography methods are labor intensive, time consuming and not compatible with real-time analysis. Here, we developed an inexpensive, high-throughput, and real-time detection method for the monitoring of in vitro RNA synthesis called iSpinach aptamer-based monitoring of Transcription Activity in Real-time (STAR). STAR has a detection speed at least 100 times faster than conventional PAGE method and provides comparable results in the analysis of in vitro RNA synthesis reactions. It also can be used as an easy and quantitative method to detect the catalytic activity of T7 RNA polymerase. To further demonstrate the utility of STAR, it was applied to optimize the initially transcribed region of the green fluorescent protein gene and the 3T4T variants demonstrated significantly enhanced transcription output, with at least 1.7-fold and 2.8-fold greater output than the wild-type DNA template and common transcription template, respectively. STAR may provide a valuable tool for many biotechnical applications related to the transcription process, which may pave the way for the development of better RNA-related enzymes and new drugs.
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Affiliation(s)
- Weitong Qin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Liang Li
- Hzymes Biotechnology Co. Ltd, Hubei, 430010, China
| | - Fan Yang
- Hzymes Biotechnology Co. Ltd, Hubei, 430010, China
| | - Siyuan Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Guang-Yu Yang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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10
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Fluorogenic RNA aptamers to probe transcription initiation and co-transcriptional RNA folding by multi-subunit RNA polymerases. Methods Enzymol 2022; 675:207-233. [DOI: 10.1016/bs.mie.2022.07.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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11
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Krissanaprasit A, Key CM, Pontula S, LaBean TH. Self-Assembling Nucleic Acid Nanostructures Functionalized with Aptamers. Chem Rev 2021; 121:13797-13868. [PMID: 34157230 DOI: 10.1021/acs.chemrev.0c01332] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Researchers have worked for many decades to master the rules of biomolecular design that would allow artificial biopolymer complexes to self-assemble and function similarly to the diverse biochemical constructs displayed in natural biological systems. The rules of nucleic acid assembly (dominated by Watson-Crick base-pairing) have been less difficult to understand and manipulate than the more complicated rules of protein folding. Therefore, nucleic acid nanotechnology has advanced more quickly than de novo protein design, and recent years have seen amazing progress in DNA and RNA design. By combining structural motifs with aptamers that act as affinity handles and add powerful molecular recognition capabilities, nucleic acid-based self-assemblies represent a diverse toolbox for use by bioengineers to create molecules with potentially revolutionary biological activities. In this review, we focus on the development of self-assembling nucleic acid nanostructures that are functionalized with nucleic acid aptamers and their great potential in wide ranging application areas.
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Affiliation(s)
- Abhichart Krissanaprasit
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Carson M Key
- Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, United States
| | - Sahil Pontula
- Department of Physics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States.,Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Thomas H LaBean
- Department of Materials Science and Engineering, College of Engineering, North Carolina State University, Raleigh, North Carolina 27695, United States
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12
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Kolmar T, Büllmann SM, Sarter C, Höfer K, Jäschke A. Development of High-Performance Pyrimidine Nucleoside and Oligonucleotide Diarylethene Photoswitches. Angew Chem Int Ed Engl 2021; 60:8164-8173. [PMID: 33476096 PMCID: PMC8049081 DOI: 10.1002/anie.202014878] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 01/05/2021] [Indexed: 01/17/2023]
Abstract
Nucleosidic and oligonucleotidic diarylethenes (DAEs) are an emerging class of photochromes with high application potential. However, their further development is hampered by the poor understanding of how the chemical structure modulates the photochromic properties. Here we synthesized 26 systematically varied deoxyuridine- and deoxycytidine-derived DAEs and analyzed reaction quantum yields, composition of the photostationary states, thermal and photochemical stability, and reversibility. This analysis identified two high-performance photoswitches with near-quantitative, fully reversible back-and-forth switching and no detectable thermal or photochemical deterioration. When incorporated into an oligonucleotide with the sequence of a promotor, the nucleotides maintained their photochromism and allowed the modulation of the transcription activity of T7 RNA polymerase with an up to 2.4-fold turn-off factor, demonstrating the potential for optochemical control of biological processes.
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Affiliation(s)
- Theresa Kolmar
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
| | - Simon M. Büllmann
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
| | - Christopher Sarter
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
| | - Katharina Höfer
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular BiotechnologyHeidelberg UniversityIm Neuenheimer Feld 36469120HeidelbergGermany
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13
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Kolmar T, Büllmann SM, Sarter C, Höfer K, Jäschke A. Development of High‐Performance Pyrimidine Nucleoside and Oligonucleotide Diarylethene Photoswitches. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014878] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Theresa Kolmar
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Simon M. Büllmann
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Christopher Sarter
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Katharina Höfer
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
| | - Andres Jäschke
- Institute of Pharmacy and Molecular Biotechnology Heidelberg University Im Neuenheimer Feld 364 69120 Heidelberg Germany
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14
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Ryckelynck M. Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More. Methods Mol Biol 2021; 2166:73-102. [PMID: 32710404 DOI: 10.1007/978-1-0716-0712-1_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The central role of RNA in living systems made it highly desirable to have noninvasive and sensitive technologies allowing for imaging the synthesis and the location of these molecules in living cells. This need motivated the development of small pro-fluorescent molecules called "fluorogens" that become fluorescent upon binding to genetically encodable RNAs called "light-up aptamers." Yet, the development of these fluorogen/light-up RNA pairs is a long and thorough process starting with the careful design of the fluorogen and pursued by the selection of a specific and efficient synthetic aptamer. This chapter summarizes the main design and the selection strategies used up to now prior to introducing the main pairs. Then, the vast application potential of these molecules for live-cell RNA imaging and other applications is presented and discussed.
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Affiliation(s)
- Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France.
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15
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Swetha P, Fan Z, Wang F, Jiang JH. Genetically encoded light-up RNA aptamers and their applications for imaging and biosensing. J Mater Chem B 2021; 8:3382-3392. [PMID: 31984401 DOI: 10.1039/c9tb02668a] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Intracellular small ligands and biomacromolecules are playing crucial roles not only as executors but also as regulators. It is essential to develop tools to investigate their dynamics to interrogate their functions and reflect the cellular status. Light-up RNA aptamers are RNA sequences that can bind with their cognate nonfluorescent fluorogens and greatly activate their fluorescence. The emergence of genetically encoded light-up RNA aptamers has provided fascinating tools for studying intracellular small ligands and biomacromolecules owing to their high fluorescence activation degree and facile programmability. Here we review the burgeoning field of light-up RNA aptamers. We first briefly introduce light-up RNA aptamers with a focus on the photophysical properties of the fluorogens. Then design strategies of genetically encoded light-up RNA aptamer based sensors including turn-on, signal amplification and ratiometric rationales are emphasized.
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Affiliation(s)
- Puchakayala Swetha
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hu-nan University, Changsha, 410082, P. R. China.
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16
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Kartje ZJ, Janis HI, Mukhopadhyay S, Gagnon KT. Revisiting T7 RNA polymerase transcription in vitro with the Broccoli RNA aptamer as a simplified real-time fluorescent reporter. J Biol Chem 2020; 296:100175. [PMID: 33303627 PMCID: PMC7948468 DOI: 10.1074/jbc.ra120.014553] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 12/03/2020] [Accepted: 12/10/2020] [Indexed: 11/06/2022] Open
Abstract
Methods for rapid and high-throughput screening of transcription in vitro to examine reaction conditions, enzyme mutants, promoter variants, and small molecule modulators can be extremely valuable tools. However, these techniques may be difficult to establish or inaccessible to many researchers. To develop a straightforward and cost-effective platform for assessing transcription in vitro, we used the "Broccoli" RNA aptamer as a direct, real-time fluorescent transcript readout. To demonstrate the utility of our approach, we screened the effect of common reaction conditions and components on bacteriophage T7 RNA polymerase (RNAP) activity using a common quantitative PCR instrument for fluorescence detection. Several essential conditions for in vitro transcription by T7 RNAP were confirmed with this assay, including the importance of enzyme and substrate concentrations, covariation of magnesium and nucleoside triphosphates, and the effects of several typical additives. When we used this method to assess all possible point mutants of a canonical T7 RNAP promoter, our results coincided well with previous reports. This approach should translate well to a broad variety of bacteriophage in vitro transcription systems and provides a platform for developing fluorescence-based readouts of more complex transcription systems in vitro.
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Affiliation(s)
- Zachary J Kartje
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Helen I Janis
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA
| | - Shaoni Mukhopadhyay
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois, USA
| | - Keith T Gagnon
- Department of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois, USA; Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, Illinois, USA.
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17
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Kariper IA, Üstündağ Z, Caglayan MO. A sensitive spectrophotometric ellipsometry based Aptasensor for the vascular endothelial growth factor detection. Talanta 2020; 225:121982. [PMID: 33592730 DOI: 10.1016/j.talanta.2020.121982] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 12/02/2020] [Accepted: 12/05/2020] [Indexed: 01/02/2023]
Abstract
A sensitive and selective, aptamer and spectroscopic ellipsometry based sensor is reported here for the early diagnosis of breast cancer, which is a common type of cancer following lung cancer. It was aimed to develop a single-step and label-free assay for the sensitive and selective detection of VEGF165. To this end, two different aptamers and spectroscopic ellipsometry were used. In the presented study, by determining the appropriate aptamer immobilization conditions, the spectroscopic ellipsometry technique was successfully applied for the detection of VEGF165 at the range of 1 pM-1000 pM in the buffer. Aptasensors have a detection limit of 5.81 pM and 4.29 pM, respectively.
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Affiliation(s)
| | - Zafer Üstündağ
- Dumlupinar University, Chemistry Department, 43100, Kütahya, Turkey
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18
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Abdolahzadeh A, Dolgosheina EV, Unrau PJ. RNA detection with high specificity and sensitivity using nested fluorogenic Mango NASBA. RNA (NEW YORK, N.Y.) 2019; 25:1806-1813. [PMID: 31551299 PMCID: PMC6859864 DOI: 10.1261/rna.072629.119] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 09/16/2019] [Indexed: 05/30/2023]
Abstract
There is a pressing need for nucleic acid-based assays that are capable of rapidly and reliably detecting pathogenic organisms. Many of the techniques available for the detection of pathogenic RNA possess one or more limiting factors that make the detection of low-copy RNA challenging. Although RT-PCR is the most commonly used method for detecting pathogen-related RNA, it requires expensive thermocycling equipment and is comparatively slow. Isothermal methods promise procedural simplicity but have traditionally suffered from amplification artifacts that tend to preclude easy identification of target nucleic acids. Recently, the isothermal SHERLOCK system overcame this problem by using CRISPR to distinguish amplified target sequences from artifactual background signal. However, this system comes at the cost of introducing considerable enzymatic complexity and a corresponding increase in total assay time. Therefore, simpler and less expensive strategies are highly desirable. Here, we demonstrate that by nesting NASBA primers and modifying the NASBA inner primers to encode an RNA Mango aptamer sequence we can dramatically increase the sensitivity of NASBA to 1.5 RNA molecules per microliter. As this isothermal nucleic acid detection scheme directly produces a fluorescent reporter, real-time detection is intrinsic to the assay. Nested Mango NASBA is highly specific and, in contrast to existing RNA detection systems, offers a cheap, simple, and specific way to rapidly detect single-molecule amounts of pathogenic RNA.
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Affiliation(s)
- Amir Abdolahzadeh
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Elena V Dolgosheina
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Peter J Unrau
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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19
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Aufdembrink LM, Hoog TG, Pawlak MR, Bachan BF, Heili JM, Engelhart AE. Methods for thermal denaturation studies of nucleic acids in complex with fluorogenic dyes. Methods Enzymol 2019; 623:23-43. [PMID: 31239049 DOI: 10.1016/bs.mie.2019.05.029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Thermal denaturation is a common technique in the biophysical study of nucleic acids. These experiments are typically performed by monitoring the increase in absorbance (hyperchromism) of a sample at 260nm with temperature (Mergny & Lacroix, 2003; Puglisi & Tinoco, 1989). This wavelength is chosen as nucleic acids of mixed sequence typically exhibit their maximum absorbance here. Exceptions exist, however, some noncanonical nucleic acid structures exhibit differing spectral changes with temperature, resulting in other wavelengths being convenient reporters of secondary structure. In the case of nucleic acids that bind visible light-absorbing ligands, such as fluorogenic aptamers, another wavelength can be a convenient reporter of secondary structure stability and RNA-ligand recognition. As it can be difficult, if not impossible, to know which wavelength to employ a priori, we have developed a system for obtaining the full UV-visible spectrum of a sample at each wavelength, allowing for the subsequent extraction of the absorbance-temperature profile at the desired wavelength. Here, we describe the apparatus and software used to do so. We also describe another technique for the use of a qPCR instrument for measuring secondary structure stability of fluorescent nucleic acid-ligand complexes.
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Affiliation(s)
- Lauren M Aufdembrink
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, United States
| | - Tanner G Hoog
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, United States
| | - Matthew R Pawlak
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, United States
| | - Benjamin F Bachan
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, United States
| | - Joseph M Heili
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, United States; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States
| | - Aaron E Engelhart
- Department of Genetics, Cell Biology, and Development, University of Minnesota, Minneapolis, MN, United States; Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, United States.
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20
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Sensitive monitoring of RNA transcription by optical amplification of cationic conjugated polymers. Talanta 2019; 203:314-321. [PMID: 31202345 DOI: 10.1016/j.talanta.2019.05.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 04/12/2019] [Accepted: 05/10/2019] [Indexed: 01/08/2023]
Abstract
We reported a new strategy for sensitive monitoring in vitro RNA synthesis in real time based on fluorescence resonance energy transfer (FRET) from water-soluble conjugated polymer poly (9, 9-bis (6'-N, N, N,-trimethylammonium) hexyl) fluorene-co-alt-1,4-phenylene) bromide (PFP) to fluorogenic RNA aptamer/fluorophore (Spanich2/DFHBI and Broccoli/DFHBI) system. In this strategy, RNA of interest was transcribed accompanied by the Spanich2 or Broccoli. Then the 3, 5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) bound to the RNA aptamer sequence and thereby induced a fluorescence signal. PFP was used as the fluorescence energy donor, and Spanich2/DFHBI was the fluorescence energy acceptor. The fluorescence signal of Spanich2/DFHBI was amplified by light-harvesting and fluorescence amplification ability of PFP via FRET. And the limit of detection (LOD) (0.29 nM) was near 10-fold lower than that of RNA aptamer/DFHBI (LOD is 2.8 nM) alone by measuring the FRET ratio, which greatly reduced the variation of background signals. Most importantly, the addition of PFP did not interfere with RNA transcription in vitro, so this method was successfully applied to sensitively monitor RNA transcription and effect of T7 RNA polymerase inhibitor in real time, supplying a sensitive and simple method to study the modulation and inhibitor of RNA polymerase in vitro.
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21
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Truong L, Ferré-D'Amaré AR. From fluorescent proteins to fluorogenic RNAs: Tools for imaging cellular macromolecules. Protein Sci 2019; 28:1374-1386. [PMID: 31017335 DOI: 10.1002/pro.3632] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 04/23/2019] [Indexed: 01/01/2023]
Abstract
The explosion in genome-wide sequencing has revealed that noncoding RNAs are ubiquitous and highly conserved in biology. New molecular tools are needed for their study in live cells. Fluorescent RNA-small molecule complexes have emerged as powerful counterparts to fluorescent proteins, which are well established, universal tools in the study of proteins in cell biology. No naturally fluorescent RNAs are known; all current fluorescent RNA tags are in vitro evolved or engineered molecules that bind a conditionally fluorescent small molecule and turn on its fluorescence by up to 5000-fold. Structural analyses of several such fluorescence turn-on aptamers show that these compact (30-100 nucleotides) RNAs have diverse molecular architectures that can restrain their photoexcited fluorophores in their maximally fluorescent states, typically by stacking between planar nucleotide arrangements, such as G-quadruplexes, base triples, or base pairs. The diversity of fluorogenic RNAs as well as fluorophores that are cell permeable and bind weakly to endogenous cellular macromolecules has already produced RNA-fluorophore complexes that span the visual spectrum and are useful for tagging and visualizing RNAs in cells. Because the ligand binding sites of fluorogenic RNAs are not constrained by the need to autocatalytically generate fluorophores as are fluorescent proteins, they may offer more flexibility in molecular engineering to generate photophysical properties that are tailored to experimental needs.
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Affiliation(s)
- Lynda Truong
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland, 20892-8012
| | - Adrian R Ferré-D'Amaré
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, Bethesda, Maryland, 20892-8012
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22
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Zhou M, Teng X, Li Y, Deng R, Li J. Cascade Transcription Amplification of RNA Aptamer for Ultrasensitive MicroRNA Detection. Anal Chem 2019; 91:5295-5302. [PMID: 30912425 DOI: 10.1021/acs.analchem.9b00124] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
MicroRNAs (miRNAs) play a critical role in multifarious biological processes and being deemed to be important biomarkers for clinical cancer diagnosis, prognosis, and therapy. Thus, assays for sensitive and accurate quantification of miRNAs are highly demanded. Herein, we have constructed a RNA aptamer involved cascade transcription amplification method (termed RACTA), enabling label-free, ultrasensitive, and specific detection of miRNA. Target miRNA-initiated strand-displacement amplification would allow for the production of plenty of ssDNA that triggers the subsequent transcriptional amplification of spinach RNA aptamers. Consequently, transcribed tremendous spinach aptamers activated fluorophore DFHBI (( Z)-4-(3,5-difluoro-4-hydroxybenzylidene)-1,2-dimethyl-1 H-imidazol-5(4 H)-one) for miRNA quantitative analysis. RACTA outperforms conventional strand displacement amplification (SDA) at both background and amplification rate due to the light-up mechanism of DFHBI dye-Spinach aptamer and cascade signal amplification of RACTA. Thus, the signal-to-noise ratio of RACTA was increased by about 20-fold compared to that of SDA. This RACTA assay could confer a highly sensitive detection of miRNA with a detection limit of 5.12 × 10-18 M and excellent specificity enabling differentiation between miRNAs and homologous families. Besides, this assay has been successfully demonstrated for quantification of miRNAs in different cell lines. Therefore, the proposed method holds great potential for miRNA biomarker based early diagnosis and prognosis monitoring.
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Affiliation(s)
- Mengxi Zhou
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Tsinghua University , Beijing 100084 , China
| | - Xucong Teng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Tsinghua University , Beijing 100084 , China
| | - Yue Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Tsinghua University , Beijing 100084 , China
| | - Ruijie Deng
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Tsinghua University , Beijing 100084 , China
| | - Jinghong Li
- Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology , Tsinghua University , Beijing 100084 , China
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23
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Wang F, Wang L, Zou X, Duan S, Li Z, Deng Z, Luo J, Lee SY, Chen S. Advances in CRISPR-Cas systems for RNA targeting, tracking and editing. Biotechnol Adv 2019; 37:708-729. [PMID: 30926472 DOI: 10.1016/j.biotechadv.2019.03.016] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Revised: 03/26/2019] [Accepted: 03/26/2019] [Indexed: 12/21/2022]
Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) systems, especially type II (Cas9) systems, have been widely used in gene/genome targeting. Modifications of Cas9 enable these systems to become platforms for precise DNA manipulations. However, the utilization of CRISPR-Cas systems in RNA targeting remains preliminary. The discovery of type VI CRISPR-Cas systems (Cas13) shed light on RNA-guided RNA targeting. Cas13d, the smallest Cas13 protein, with a length of only ~930 amino acids, is a promising platform for RNA targeting compatible with viral delivery systems. Much effort has also been made to develop Cas9, Cas13a and Cas13b applications for RNA-guided RNA targeting. The discovery of new RNA-targeting CRISPR-Cas systems as well as the development of RNA-targeting platforms with Cas9 and Cas13 will promote RNA-targeting technology substantially. Here, we review new advances in RNA-targeting CRISPR-Cas systems as well as advances in applications of these systems in RNA targeting, tracking and editing. We also compare these Cas protein-based technologies with traditional technologies for RNA targeting, tracking and editing. Finally, we discuss remaining questions and prospects for the future.
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Affiliation(s)
- Fei Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Lianrong Wang
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Xuan Zou
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology, Yuseong-gu, 34141 Daejeon, Republic of Korea
| | - Suling Duan
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China
| | - Zhiqiang Li
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China
| | - Jie Luo
- Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China
| | - Sang Yup Lee
- Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Korea Advanced Institute of Science and Technology, Yuseong-gu, 34141 Daejeon, Republic of Korea.
| | - Shi Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery, Ministry of Education, Brain Center, School of Pharmaceutical Sciences, Zhongnan Hospital, Wuhan University, Wuhan 430071, Hubei, China; Taihe Hospital, Hubei University of Medicine, Shiyan 442000, Hubei, China.
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Luo X, Xue B, Feng G, Zhang J, Lin B, Zeng P, Li H, Yi H, Zhang XL, Zhu H, Nie Z. Lighting up the Native Viral RNA Genome with a Fluorogenic Probe for the Live-Cell Visualization of Virus Infection. J Am Chem Soc 2019; 141:5182-5191. [PMID: 30860368 DOI: 10.1021/jacs.8b10265] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
RNA viruses represent a major global health threat, and the visualization of their RNA genome in infected cells is essential for virological research and clinical diagnosis. Due to the lack of chemical toolkits for the live-cell imaging of viral RNA genomes, especially native viral genomes without labeling and genetic modification, studies on native virus infection at the single-live-cell level are challenging. Herein, taking hepatitis C virus (HCV) as a representative RNA virus, we propose that the innate noncanonical G-quadruplex (G4) structure of viral RNA can serve as a specific imaging target and report a new benzothiazole-based G4-targeted fluorescence light-up probe, ThT-NE, for the direct visualization of the native RNA genome of HCV in living host cells. We demonstrate the use of the ThT-NE probe for several previously intractable applications, including the sensitive detection of individual virus-infected cells by small-molecule staining, real-time monitoring of the subcellular distribution of the viral RNA genome in live cells, and continuous live-cell tracking of the infection and propagation of clinically isolated native HCV. The fluorogenic-probe-based viral RNA light-up system opens up a promising chemical strategy for cutting-edge live-cell viral analysis, providing a potentially powerful tool for viral biology, medical diagnosis, and drug development.
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Affiliation(s)
- Xingyu Luo
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology , Hunan University , Changsha 410082 , People's Republic of China
| | - Binbin Xue
- Institute of Pathogen Biology and Immunology of College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics , Hunan University , Changsha 410082 , People's Republic of China
| | - Guangfu Feng
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology , Hunan University , Changsha 410082 , People's Republic of China
| | - Jiaheng Zhang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology , Hunan University , Changsha 410082 , People's Republic of China
| | - Bin Lin
- Pharmaceutical Engineering & Key Laboratory of Structure-Based Drug Design & Discovery, Ministry of Education , Shenyang Pharmaceutical University , Shenyang 110016 , People's Republic of China
| | - Pan Zeng
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology , Hunan University , Changsha 410082 , People's Republic of China
| | - Huiyi Li
- Institute of Pathogen Biology and Immunology of College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics , Hunan University , Changsha 410082 , People's Republic of China
| | - Haibo Yi
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology , Hunan University , Changsha 410082 , People's Republic of China
| | - Xiao-Lian Zhang
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology and Department of Immunology, School of Medicine , Wuhan University , Wuhan 430071 , Hubei , People's Republic of China
| | - Haizhen Zhu
- Institute of Pathogen Biology and Immunology of College of Biology, State Key Laboratory of Chemo/Biosensing and Chemometrics , Hunan University , Changsha 410082 , People's Republic of China
| | - Zhou Nie
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan Provincial Key Laboratory of Biomacromolecular Chemical Biology , Hunan University , Changsha 410082 , People's Republic of China
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25
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Cox KJ, Subramanian HKK, Samaniego CC, Franco E, Choudhary A. A universal method for sensitive and cell-free detection of CRISPR-associated nucleases. Chem Sci 2019; 10:2653-2662. [PMID: 30996981 PMCID: PMC6419926 DOI: 10.1039/c8sc03426e] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 12/28/2018] [Indexed: 12/18/2022] Open
Abstract
A multitude of biological applications for CRISPR-associated (Cas) nucleases have propelled the development of robust cell-based methods for quantitation of on- and off-target activities of these nucleases. However, emerging applications of these nucleases require cell-free methods that are simple, sensitive, cost effective, high throughput, multiplexable, and generalizable to all classes of Cas nucleases. Current methods for cell-free detection are cumbersome, expensive, or require sophisticated sequencing technologies, hindering their widespread application beyond the field of life sciences. Developing such cell-free assays is challenging for multiple reasons, including that Cas nucleases are single-turnover enzymes that must be present in large excess over their substrate and that different classes of Cas nucleases exhibit wildly different operating mechanisms. Here, we report the development of a cell-free method wherein Cas nuclease activity is amplified via an in vitro transcription reaction that produces a fluorescent RNA:small-molecule adduct. We demonstrate that our method is sensitive, detecting activity from low nanomolar concentrations of several families of Cas nucleases, and can be conducted in a high-throughput microplate fashion with a simple fluorescent-based readout. We provide a mathematical framework for quantifying the activities of these nucleases and demonstrate two applications of our method, namely the development of a logic circuit and the characterization of an anti-CRISPR protein. We anticipate our method will be valuable to those studying Cas nucleases and will allow the application of Cas nuclease beyond the field of life sciences.
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Affiliation(s)
- Kurt J Cox
- Chemical Biology and Therapeutics Science , Broad Institute of MIT and Harvard , 415 Main Street, Rm 3012 , Cambridge , MA 02142 , USA . ; ; Tel: +1 617 714 7445
- Department of Medicine , Harvard Medical School , Boston , MA 02115 , USA
- Divisions of Renal Medicine and Engineering , Brigham and Women's Hospital , Boston , MA 02115 , USA
| | - Hari K K Subramanian
- Department of Mechanical Engineering , University of California - Riverside , Riverside , CA - 92521 , USA . ; Tel: +1 951 827 2442
| | - Christian Cuba Samaniego
- Department of Mechanical Engineering , University of California - Riverside , Riverside , CA - 92521 , USA . ; Tel: +1 951 827 2442
| | - Elisa Franco
- Department of Mechanical Engineering , University of California - Riverside , Riverside , CA - 92521 , USA . ; Tel: +1 951 827 2442
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science , Broad Institute of MIT and Harvard , 415 Main Street, Rm 3012 , Cambridge , MA 02142 , USA . ; ; Tel: +1 617 714 7445
- Department of Medicine , Harvard Medical School , Boston , MA 02115 , USA
- Divisions of Renal Medicine and Engineering , Brigham and Women's Hospital , Boston , MA 02115 , USA
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26
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Modular cell-internalizing aptamer nanostructure enables targeted delivery of large functional RNAs in cancer cell lines. Nat Commun 2018; 9:2283. [PMID: 29891903 PMCID: PMC5995956 DOI: 10.1038/s41467-018-04691-x] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 05/09/2018] [Indexed: 02/07/2023] Open
Abstract
Large RNAs and ribonucleoprotein complexes have powerful therapeutic potential, but effective cell-targeted delivery tools are limited. Aptamers that internalize into target cells can deliver siRNAs (<15 kDa, 19–21 nt/strand). We demonstrate a modular nanostructure for cellular delivery of large, functional RNA payloads (50–80 kDa, 175–250 nt) by aptamers that recognize multiple human B cell cancer lines and transferrin receptor-expressing cells. Fluorogenic RNA reporter payloads enable accelerated testing of platform designs and rapid evaluation of assembly and internalization. Modularity is demonstrated by swapping in different targeting and payload aptamers. Both modules internalize into leukemic B cell lines and remained colocalized within endosomes. Fluorescence from internalized RNA persists for ≥2 h, suggesting a sizable window for aptamer payloads to exert influence upon targeted cells. This demonstration of aptamer-mediated, cell-internalizing delivery of large RNAs with retention of functional structure raises the possibility of manipulating endosomes and cells by delivering large aptamers and regulatory RNAs. Large RNAs and ribonucleoprotein complexes have shown potential as novel therapeutic agents, but their targeted delivery to cells is still challenging. Here the authors present a modular aptamer nanostructure for intracellular delivery of RNAs up to 250 nucleotides to cancer cells.
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27
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Torelli E, Kozyra JW, Gu JY, Stimming U, Piantanida L, Voïtchovsky K, Krasnogor N. Isothermal folding of a light-up bio-orthogonal RNA origami nanoribbon. Sci Rep 2018; 8:6989. [PMID: 29725066 PMCID: PMC5934368 DOI: 10.1038/s41598-018-25270-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 04/12/2018] [Indexed: 12/27/2022] Open
Abstract
RNA presents intringuing roles in many cellular processes and its versatility underpins many different applications in synthetic biology. Nonetheless, RNA origami as a method for nanofabrication is not yet fully explored and the majority of RNA nanostructures are based on natural pre-folded RNA. Here we describe a biologically inert and uniquely addressable RNA origami scaffold that self-assembles into a nanoribbon by seven staple strands. An algorithm is applied to generate a synthetic De Bruijn scaffold sequence that is characterized by the lack of biologically active sites and repetitions larger than a predetermined design parameter. This RNA scaffold and the complementary staples fold in a physiologically compatible isothermal condition. In order to monitor the folding, we designed a new split Broccoli aptamer system. The aptamer is divided into two nonfunctional sequences each of which is integrated into the 5' or 3' end of two staple strands complementary to the RNA scaffold. Using fluorescence measurements and in-gel imaging, we demonstrate that once RNA origami assembly occurs, the split aptamer sequences are brought into close proximity forming the aptamer and turning on the fluorescence. This light-up 'bio-orthogonal' RNA origami provides a prototype that can have potential for in vivo origami applications.
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Affiliation(s)
- Emanuela Torelli
- Interdisciplinary Computing and Complex BioSystems (ICOS), School of Computing Science, Centre for Synthetic Biology and Bioeconomy (CSBB), Centre for Bacterial Cell Biology (CBCB), Newcastle University, Newcastle upon Tyne, NE4 5TG, United Kingdom.
| | - Jerzy Wieslaw Kozyra
- Interdisciplinary Computing and Complex BioSystems (ICOS), School of Computing Science, Centre for Synthetic Biology and Bioeconomy (CSBB), Centre for Bacterial Cell Biology (CBCB), Newcastle University, Newcastle upon Tyne, NE4 5TG, United Kingdom
| | - Jing-Ying Gu
- School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Ulrich Stimming
- School of Chemistry, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Luca Piantanida
- Department of Physics, Durham University, Durham, DH1 3LE, United Kingdom
| | - Kislon Voïtchovsky
- Department of Physics, Durham University, Durham, DH1 3LE, United Kingdom
| | - Natalio Krasnogor
- Interdisciplinary Computing and Complex BioSystems (ICOS), School of Computing Science, Centre for Synthetic Biology and Bioeconomy (CSBB), Centre for Bacterial Cell Biology (CBCB), Newcastle University, Newcastle upon Tyne, NE4 5TG, United Kingdom.
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28
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Rumlová M, Ruml T. In vitro methods for testing antiviral drugs. Biotechnol Adv 2018; 36:557-576. [PMID: 29292156 PMCID: PMC7127693 DOI: 10.1016/j.biotechadv.2017.12.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/22/2017] [Accepted: 12/27/2017] [Indexed: 12/24/2022]
Abstract
Despite successful vaccination programs and effective treatments for some viral infections, humans are still losing the battle with viruses. Persisting human pandemics, emerging and re-emerging viruses, and evolution of drug-resistant strains impose continuous search for new antiviral drugs. A combination of detailed information about the molecular organization of viruses and progress in molecular biology and computer technologies has enabled rational antivirals design. Initial step in establishing efficacy of new antivirals is based on simple methods assessing inhibition of the intended target. We provide here an overview of biochemical and cell-based assays evaluating the activity of inhibitors of clinically important viruses.
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Affiliation(s)
- Michaela Rumlová
- Department of Biotechnology, University of Chemistry and Technology, Prague 166 28, Czech Republic.
| | - Tomáš Ruml
- Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague 166 28, Czech Republic.
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29
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Bouhedda F, Autour A, Ryckelynck M. Light-Up RNA Aptamers and Their Cognate Fluorogens: From Their Development to Their Applications. Int J Mol Sci 2017; 19:ijms19010044. [PMID: 29295531 PMCID: PMC5795994 DOI: 10.3390/ijms19010044] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 12/14/2017] [Accepted: 12/15/2017] [Indexed: 12/31/2022] Open
Abstract
An RNA-based fluorogenic module consists of a light-up RNA aptamer able to specifically interact with a fluorogen to form a fluorescent complex. Over the past decade, significant efforts have been devoted to the development of such modules, which now cover the whole visible spectrum, as well as to their engineering to serve in a wide range of applications. In this review, we summarize the different strategies used to develop each partner (the fluorogen and the light-up RNA aptamer) prior to giving an overview of their applications that range from live-cell RNA imaging to the set-up of high-throughput drug screening pipelines. We then conclude with a critical discussion on the current limitations of these modules and how combining in vitro selection with screening approaches may help develop even better molecules.
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Affiliation(s)
- Farah Bouhedda
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, UPR 9002, F-67000 Strasbourg, France.
| | - Alexis Autour
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, UPR 9002, F-67000 Strasbourg, France.
| | - Michael Ryckelynck
- Architecture et Réactivité de l'ARN, CNRS, Université de Strasbourg, UPR 9002, F-67000 Strasbourg, France.
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30
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Chen J, Liu Z, Peng H, Zheng Y, Lin Z, Liu A, Chen W, Lin X. Electrochemical DNA biosensor based on grafting-to mode of terminal deoxynucleoside transferase-mediated extension. Biosens Bioelectron 2017; 98:345-349. [DOI: 10.1016/j.bios.2017.07.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/01/2017] [Accepted: 07/05/2017] [Indexed: 01/27/2023]
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31
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Synthetic biological approaches for RNA labelling and imaging: design principles and future opportunities. Curr Opin Biotechnol 2017; 48:153-158. [DOI: 10.1016/j.copbio.2017.04.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 04/07/2017] [Accepted: 04/17/2017] [Indexed: 12/15/2022]
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32
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Bertucci A, Porchetta A, Ricci F. Antibody-Templated Assembly of an RNA Mimic of Green Fluorescent Protein. Anal Chem 2017; 90:1049-1053. [PMID: 29131585 DOI: 10.1021/acs.analchem.7b02102] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
One of the most intriguing ways through which nature achieves regulation of biological pathways encompasses the coordination of noncovalent interactions that bring biomolecules to be colocalized in a designated restricted space. Inspired by this mechanism, we have explored the possibility of using antibodies as bivalent biomolecular substrates for the templated assembly of a functional RNA structure. We have developed a biosupramolecular complementation assay by assembling a fluorescent Spinach aptamer, which is a synthetic RNA mimic of the Green Fluorescent Protein, from its split segments. We have employed two antigen-tagged RNA strands that, upon binding to the target antibody, are colocalized in a confined space and can reassemble into the native Spinach conformation, yielding a measurable fluorescence emission as a function of the templating antibody concentration. We have demonstrated the generality of our approach using two different antigen/antibody systems and found that both platforms show high binding affinity, specificity for the target antibody, and enough selectivity to work in crude cellular extracts. This study highlights the potential of biosupramolecular RNA engineering for the development of innovative biomimetic tools for nanobiotechnology and bioanalytical assays.
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Affiliation(s)
- Alessandro Bertucci
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata , Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Alessandro Porchetta
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata , Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Francesco Ricci
- Department of Chemical Sciences and Technologies, University of Rome Tor Vergata , Via della Ricerca Scientifica 1, 00133, Rome, Italy
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33
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Kajita K, Nakano H, Sato H. A theoretical study on the optical absorption of green fluorescent protein chromophore in solutions. MOLECULAR SIMULATION 2017. [DOI: 10.1080/08927022.2017.1315769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ken Kajita
- Department of Molecular Engineering, Kyoto University, Kyoto, Japan
| | - Hiroshi Nakano
- Department of Molecular Engineering, Kyoto University, Kyoto, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Kyoto University, Kyoto, Japan
- Elements Strategy Initiative for Catalysts and Batteries (ESICB), Kyoto University, Kyoto, Japan
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34
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Zhang C, Wu R, Li Y, Zhang Q, Yang J. Programmable Regulation of DNA Conjugation to Gold Nanoparticles via Strand Displacement. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:12285-12290. [PMID: 28976767 DOI: 10.1021/acs.langmuir.7b02620] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Methods for conjugating DNA to gold nanoparticles (AuNPs) have recently attracted considerable attention. The ability to control such conjugation in a programmable way is of great interest. Here, we have developed a logic-based method for manipulating the conjugation of thiolated DNA species to AuNPs via cascading DNA strand displacement. Using this method, several logic-based operation systems are established and up to three kinds of DNA signals are introduced at the same time. In addition, a more sensitive catalytic logic-based operation is also achieved based on an entropy-driven process. In the experiment, all of the DNA/AuNPs conjugation results are verified by agrose gel. This strategy promises great potential for automatically conjugating DNA stands onto label-free gold nanoparticles and can be extended to constructing DNA/nanoparticle devices for applications in diagnostics, biosensing, and molecular robotics.
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Affiliation(s)
- Cheng Zhang
- Institute of Software, School of Electronics Engineering and Computer Science, Peking University, Key laboratory of High Confidence Software Technologies, Ministry of Education, Beijing 100871, China
| | - Ranfeng Wu
- School of Control and Computer Engineering, North China Electric Power University , Beijing 102206, China
| | - Yifan Li
- School of Control and Computer Engineering, North China Electric Power University , Beijing 102206, China
| | - Qiang Zhang
- College of Computer Science and Technology, Dalian University of Technology , Dalian, 116624, China
| | - Jing Yang
- School of Control and Computer Engineering, North China Electric Power University , Beijing 102206, China
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35
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Alam KK, Tawiah KD, Lichte MF, Porciani D, Burke DH. A Fluorescent Split Aptamer for Visualizing RNA-RNA Assembly In Vivo. ACS Synth Biol 2017; 6:1710-1721. [PMID: 28548488 PMCID: PMC5603824 DOI: 10.1021/acssynbio.7b00059] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
![]()
RNA–RNA
assembly governs key biological processes and is
a powerful tool for engineering synthetic genetic circuits. Characterizing
RNA assembly in living cells often involves monitoring fluorescent
reporter proteins, which are at best indirect measures of underlying
RNA–RNA hybridization events and are subject to additional
temporal and load constraints associated with translation and activation
of reporter proteins. In contrast, RNA aptamers that sequester small
molecule dyes and activate their fluorescence are increasingly utilized
in genetically encoded strategies to report on RNA-level events. Split-aptamer
systems have been rationally designed to generate signal upon hybridization
of two or more discrete RNA transcripts, but none directly function
when expressed in vivo. We reasoned that the improved
physiological properties of the Broccoli aptamer enable construction
of a split-aptamer system that could function in living cells. Here
we present the Split-Broccoli system, in which self-assembly is nucleated
by a thermostable, three-way junction RNA architecture and fluorescence
activation requires both strands. Functional assembly of the system
approximately follows second-order kinetics in vitro and improves when cotranscribed, rather than when assembled from
purified components. Split-Broccoli fluorescence
is digital in vivo and retains functional modularity
when fused to RNAs that regulate circuit function through RNA–RNA
hybridization, as demonstrated with an RNA Toehold switch. Split-Broccoli represents the first functional split-aptamer
system to operate in vivo. It offers a genetically
encoded and nondestructive platform to monitor and exploit RNA–RNA
hybridization, whether as an all-RNA, stand-alone AND gate or as a
tool for monitoring assembly of RNA–RNA hybrids.
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Affiliation(s)
- Khalid K. Alam
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Bond
Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Kwaku D. Tawiah
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Bond
Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
| | - Matthew F. Lichte
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Bond
Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
| | - David Porciani
- Bond
Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
- Department
of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri 65212, United States
| | - Donald H. Burke
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
- Bond
Life Sciences Center, University of Missouri, Columbia, Missouri 65211, United States
- Department
of Molecular Microbiology and Immunology, University of Missouri, Columbia, Missouri 65212, United States
- Department
of Bioengineering, University of Missouri, Columbia, Missouri 65211, United States
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36
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Ying ZM, Wu Z, Tu B, Tan W, Jiang JH. Genetically Encoded Fluorescent RNA Sensor for Ratiometric Imaging of MicroRNA in Living Tumor Cells. J Am Chem Soc 2017; 139:9779-9782. [PMID: 28714696 DOI: 10.1021/jacs.7b04527] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Light-up RNA aptamers are valuable tools for fluorescence imaging of RNA in living cells and thus for elucidating RNA functions and dynamics. However, no light-up RNA sensor has been reported for imaging of microRNAs (miRs) in mammalian cells. We report a novel genetically encoded RNA sensor for fluorescent imaging of miRs in living tumor cells using a light-up RNA aptamer that binds to sulforhodamine and separates it from a conjugated contact quencher. On the basis of the structural switching mechanism for molecular beacon, we show that the RNA sensor activates high-contrast fluorescence from the sulforhodamine-quencher conjugate when its stem-loop responsive motif hybridizes with target miR. The RNA sensor can be stably expressed within a designed tRNA scaffold in tumor cells and deliver light-up response to miR target. We also realize the RNA sensor for dual-emission, ratiometric imaging by coexpression of RNA sensor with GFP, enabling quantitative studies of target miR in living cells. Our design may provide a new paradigm for developing robust, sensitive light-up RNA sensors for RNA imaging applications.
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Affiliation(s)
- Zhan-Ming Ying
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University , Changsha 410082, People's Republic of China
| | - Zhan Wu
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University , Changsha 410082, People's Republic of China
| | - Bin Tu
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University , Changsha 410082, People's Republic of China
| | - Weihong Tan
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University , Changsha 410082, People's Republic of China
| | - Jian-Hui Jiang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University , Changsha 410082, People's Republic of China
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37
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van Gijtenbeek LA, Kok J. Illuminating Messengers: An Update and Outlook on RNA Visualization in Bacteria. Front Microbiol 2017; 8:1161. [PMID: 28690601 PMCID: PMC5479882 DOI: 10.3389/fmicb.2017.01161] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/07/2017] [Indexed: 01/04/2023] Open
Abstract
To be able to visualize the abundance and spatiotemporal features of RNAs in bacterial cells would permit obtaining a pivotal understanding of many mechanisms underlying bacterial cell biology. The first methods that allowed observing single mRNA molecules in individual cells were introduced by Bertrand et al. (1998) and Femino et al. (1998). Since then, a plethora of techniques to image RNA molecules with the aid of fluorescence microscopy has emerged. Many of these approaches are useful for the large eukaryotic cells but their adaptation to study RNA, specifically mRNA molecules, in bacterial cells progressed relatively slow. Here, an overview will be given of fluorescent techniques that can be used to reveal specific RNA molecules inside fixed and living single bacterial cells. It includes a critical evaluation of their caveats as well as potential solutions.
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Affiliation(s)
- Lieke A van Gijtenbeek
- Department of Molecular Genetics, Faculty of Science and Engineering, University of GroningenGroningen, Netherlands
| | - Jan Kok
- Department of Molecular Genetics, Faculty of Science and Engineering, University of GroningenGroningen, Netherlands
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38
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Ma DL, Wu C, Dong ZZ, Tam WS, Wong SW, Yang C, Li G, Leung CH. The Development of G-Quadruplex-Based Assays for the Detection of Small Molecules and Toxic Substances. Chem Asian J 2017; 12:1851-1860. [PMID: 28470784 DOI: 10.1002/asia.201700533] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Indexed: 11/12/2022]
Abstract
G-Quadruplexes can be induced to form guanine-rich DNA sequences by certain small molecules or metal ions. In concert with an appropriate signal transducer, such as a fluorescent dye or a phosphorescent metal complex, the ligand-recognition event can be transduced into a luminescent response. This focus review aims to highlight recent examples of aptamer-based and metal-mediated G-quadruplex assays for the detection of small molecules and toxic substances in the last three years. We discuss the mechanisms and features of the different assays and present an outlook and a perspective for the future of this field.
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Affiliation(s)
- Dik-Lung Ma
- Department of Chemistry, Faculty of Science, Hong Kong Baptist University
| | - Chun Wu
- Department of Chemistry, Faculty of Science, Hong Kong Baptist University
| | - Zhen-Zhen Dong
- Department of Chemistry, Faculty of Science, Hong Kong Baptist University
| | - Wing-Sze Tam
- Department of Chemistry, Faculty of Science, Hong Kong Baptist University
| | - Sze-Wan Wong
- Department of Chemistry, Faculty of Science, Hong Kong Baptist University
| | - Chao Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau
| | - Guodong Li
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau
| | - Chung-Hang Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau
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39
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Ong WQ, Citron YR, Sekine S, Huang B. Live Cell Imaging of Endogenous mRNA Using RNA-Based Fluorescence "Turn-On" Probe. ACS Chem Biol 2017; 12:200-205. [PMID: 28103687 DOI: 10.1021/acschembio.6b00586] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Messenger RNA (mRNA) plays a critical role in cellular growth and development. However, there have been limited methods available to visualize endogenous mRNA in living cells with ease. We have designed RNA-based fluorescence "turn-on" probes that target mRNA by fusing an unstable form of Spinach with target-complementary sequences. These probes have been demonstrated to be selective, stable, and capable of targeting various mRNAs for live E. coli imaging.
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Affiliation(s)
- Wei Qiang Ong
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, San
Francisco, California 94143, United States
| | - Y. Rose Citron
- Graduate
Program of Biophysics, University of California, San Francisco, San Francisco, California 94143, United States
| | - Sayaka Sekine
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, San
Francisco, California 94143, United States
| | - Bo Huang
- Department
of Pharmaceutical Chemistry, University of California, San Francisco, San
Francisco, California 94143, United States
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40
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Detection of human immunodeficiency virus RNAs in living cells using Spinach RNA aptamers. Virus Res 2016; 228:141-146. [PMID: 27914932 DOI: 10.1016/j.virusres.2016.11.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Revised: 10/28/2016] [Accepted: 11/23/2016] [Indexed: 12/22/2022]
Abstract
Many techniques currently used to measure HIV RNA production in cells suffer from limitations that include high background signal or the potential to destroy cellular context. Fluorophore-binding RNA aptamers offer the potential for visualizing RNAs directly in living cells with minimal cellular perturbation. We inserted a sequence encoding a fluorophore-binding RNA aptamer, known as Spinach, into the HIV genome such that predicted RNA secondary structures in both Spinach and HIV were preserved. Chimeric HIV-Spinach RNAs were functionally validated in vitro by testing their ability to enhance the fluorescence of a conditional fluorophore (DFHBI), which specifically binds Spinach. Fluorescence microscopy and PCR were used to verify expression of HIV-Spinach RNAs in human cells. HIV-1 gag RNA production and fluorescence were measured by qPCR and fluorometry, respectively. HIV-Spinach RNAs were fluorometrically detectable in vitro and were transcribed in human cell lines and primary cells, with both spliced and unspliced species detected by PCR. HIV-Spinach RNAs were visible by fluorescence microscopy in living cells, although signal was reproducibly weak. Cells expressing HIV-Spinach RNAs were capable of producing fluorometrically detectable virions, although detection of single viral particles was not possible. In summary, we have investigated a novel method for detecting HIV RNAs in living cells using the Spinach RNA aptamer. Despite the limitations of the present aptamer/fluorophore combination, this is the first application of this technology to an infectious disease and provides a foundation for future research into improved methods for studying HIV expression.
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41
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Ageely EA, Kartje ZJ, Rohilla KJ, Barkau CL, Gagnon KT. Quadruplex-Flanking Stem Structures Modulate the Stability and Metal Ion Preferences of RNA Mimics of GFP. ACS Chem Biol 2016; 11:2398-406. [PMID: 27467146 DOI: 10.1021/acschembio.6b00047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The spinach family of RNA aptamers are RNA mimics of green fluorescent protein (GFP) that have previously been designed to address the challenges of imaging RNA inside living cells. However, relatively low levels of free intracellular magnesium limited the practical use of these aptamers. Recent cell-based selections identified the broccoli RNA aptamer, which requires less magnesium for fluorescence, but the basis for magnesium preference remained unclear. Here, we find that the broccoli RNA structure is very similar to that of baby spinach, a truncated version of the spinach aptamer. Differences in stability and metal ion preferences between these two aptamers, and among broccoli mutants, are primarily associated with the sequence and structure of predicted quadruplex-flanking stem structures. Mutation of purine-purine pairs in broccoli at the terminal stem-quadruplex transition caused reversion of broccoli to a higher magnesium dependence. Unique duplex-to-quadruplex transitions in GFP-mimic RNAs likely explain their sensitivity to magnesium for stability and fluorescence. Thus, optimizations designed to improve aptamers should take into consideration the role of metal ions in stabilizing the transitions and interactions between independently folding RNA structural motifs.
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Affiliation(s)
- Eman A. Ageely
- Department
of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Zachary J. Kartje
- Department
of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
| | - Kushal J. Rohilla
- Department
of Biochemistry and Molecular Biology, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901, United States
| | - Christopher L. Barkau
- Department
of Biochemistry and Molecular Biology, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901, United States
| | - Keith T. Gagnon
- Department
of Chemistry and Biochemistry, Southern Illinois University, Carbondale, Illinois 62901, United States
- Department
of Biochemistry and Molecular Biology, Southern Illinois University, School of Medicine, Carbondale, Illinois 62901, United States
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42
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Abstract
Seeing is not only believing; it also includes understanding. Cellular imaging with GFP in live cells has been transformative in many research fields. Modulation of cellular regulation is tightly regulated and innovative imaging technologies contribute to further understand cellular signaling and physiology. New types of genetically encoded biosensors have been developed over the last decade. They are RNA aptamers that bind with their cognate fluorogen ligands and activate their fluorescence. The emergence and the evolution of these RNA aptamers as well as their conversion into a wide spectrum of applications are examined in a global way.
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Affiliation(s)
- Jonathan Ouellet
- Department of Chemistry and Physics, Monmouth UniversityWest Long Branch, NJ, USA
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43
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Pfeiffer F, Mayer G. Selection and Biosensor Application of Aptamers for Small Molecules. Front Chem 2016; 4:25. [PMID: 27379229 PMCID: PMC4908669 DOI: 10.3389/fchem.2016.00025] [Citation(s) in RCA: 143] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Accepted: 05/30/2016] [Indexed: 12/12/2022] Open
Abstract
Small molecules play a major role in the human body and as drugs, toxins, and chemicals. Tools to detect and quantify them are therefore in high demand. This review will give an overview about aptamers interacting with small molecules and their selection. We discuss the current state of the field, including advantages as well as problems associated with their use and possible solutions to tackle these. We then discuss different kinds of small molecule aptamer-based sensors described in literature and their applications, ranging from detecting drinking water contaminations to RNA imaging.
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Affiliation(s)
- Franziska Pfeiffer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
| | - Günter Mayer
- Department of Chemical Biology, Life and Medical Sciences Institute, University of Bonn Bonn, Germany
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44
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Bose S, Chakrabarty S, Ghosh D. Effect of Solvation on Electron Detachment and Excitation Energies of a Green Fluorescent Protein Chromophore Variant. J Phys Chem B 2016; 120:4410-20. [DOI: 10.1021/acs.jpcb.6b03723] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Samik Bose
- Physical
and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Suman Chakrabarty
- Physical
and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Debashree Ghosh
- Physical
and Materials Chemistry
Division, CSIR-National Chemical Laboratory, Pune 411008, India
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45
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Autour A, Westhof E, Ryckelynck M. iSpinach: a fluorogenic RNA aptamer optimized for in vitro applications. Nucleic Acids Res 2016; 44:2491-500. [PMID: 26932363 PMCID: PMC4824111 DOI: 10.1093/nar/gkw083] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 02/01/2016] [Indexed: 01/03/2023] Open
Abstract
Using random mutagenesis and high throughput screening by microfluidic-assisted In Vitro Compartmentalization, we report the isolation of an order of magnitude times brighter mutants of the light-up RNA aptamers Spinach that are far less salt-sensitive and with a much higher thermal stability than the parent molecule. Further engineering gave iSpinach, a molecule with folding and fluorescence properties surpassing those of all currently known aptamer based on the fluorogenic co-factor 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI). We illustrate the potential of iSpinach in a new sensitive and high throughput-compatible fluorogenic assay that measures co-transcriptionally the catalytic constant (kcat) of a model ribozyme.
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Affiliation(s)
- Alexis Autour
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 rue René Descartes, 67084, Strasbourg, France
| | - Eric Westhof
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 rue René Descartes, 67084, Strasbourg, France
| | - Michael Ryckelynck
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de biologie moléculaire et cellulaire du CNRS, 15 rue René Descartes, 67084, Strasbourg, France
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DasGupta S, Shelke SA, Li NS, Piccirilli JA. Spinach RNA aptamer detects lead(II) with high selectivity. Chem Commun (Camb) 2016; 51:9034-7. [PMID: 25940073 DOI: 10.1039/c5cc01526j] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Spinach RNA aptamer contains a G-quadruplex motif that serves as a platform for binding and fluorescence activation of a GFP-like fluorophore. Here we show that Pb(2+) induces formation of Spinach's G-quadruplex and activates fluorescence with high selectivity and sensitivity. This device establishes the first example of an RNA-based sensor that provides a simple and inexpensive tool for Pb(2+) detection.
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Affiliation(s)
- Saurja DasGupta
- Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA.
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Zhang H, Pi F, Shu D, Vieweger M, Guo P. Using RNA nanoparticles with thermostable motifs and fluorogenic modules for real-time detection of RNA folding and turnover in prokaryotic and eukaryotic cells. Methods Mol Biol 2016; 1297:95-111. [PMID: 25895998 DOI: 10.1007/978-1-4939-2562-9_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
RNA nanotechnology is an emerging field at the interface of biochemistry and nanomaterials that shows immense promise for applications in nanomedicines, therapeutics and nanotechnology. Noncoding RNAs, such as siRNA, miRNA, ribozymes, and riboswitches, play important roles in the regulation of cellular processes. They carry out highly specific functions on a compact and efficient footprint. The properties of specificity and small size make them excellent modules in the construction of multifaceted RNA nanoparticles for targeted delivery and therapy. Biological activity of RNA molecules, however, relies on their proper folding. Therefore their thermodynamic and biochemical stability in the cellular environment is critical. Consequently, it is essential to assess global fold and intracellular lifetime of multifaceted RNA nanoparticles to optimize their therapeutic effectiveness. Here, we describe a method to express and assemble stable RNA nanoparticles in cells, and to assess the folding and turnover rate of RNA nanoparticles in vitro as well as in vivo in real time using a thermostable core motif derived from pRNA of bacteriophage Phi29 DNA packaging motor and fluorogenic RNA modules.
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Affiliation(s)
- Hui Zhang
- Nanobiotechnology Center, Markey Cancer Center, Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, USA,
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48
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Zhang J, Fei J, Leslie BJ, Han KY, Kuhlman TE, Ha T. Tandem Spinach Array for mRNA Imaging in Living Bacterial Cells. Sci Rep 2015; 5:17295. [PMID: 26612428 PMCID: PMC4661537 DOI: 10.1038/srep17295] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 10/15/2015] [Indexed: 12/24/2022] Open
Abstract
Live cell RNA imaging using genetically encoded fluorescent labels is an important tool for monitoring RNA activities. A recently reported RNA aptamer-fluorogen system, the Spinach, in which an RNA aptamer binds and induces the fluorescence of a GFP-like 3,5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) ligand, can be readily tagged to the RNA of interest. Although the aptamer-fluorogen system is sufficient for imaging highly abundant non-coding RNAs (tRNAs, rRNAs, etc.), it performs poorly for mRNA imaging due to low brightness. In addition, whether the aptamer-fluorogen system may perturb the native RNA characteristics has not been systematically characterized at the levels of RNA transcription, translation and degradation. To increase the brightness of these aptamer-fluorogen systems, we constructed and tested tandem arrays containing multiple Spinach aptamers (8-64 aptamer repeats). Such arrays enhanced the brightness of the tagged mRNA molecules by up to ~17 fold in living cells. Strong laser excitation with pulsed illumination further increased the imaging sensitivity of Spinach array-tagged RNAs. Moreover, transcriptional fusion to the Spinach array did not affect mRNA transcription, translation or degradation, indicating that aptamer arrays might be a generalizable labeling method for high-performance and low-perturbation live cell RNA imaging.
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Affiliation(s)
- Jichuan Zhang
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jingyi Fei
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Benjamin J. Leslie
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Howard Hughes Medical Institute, Baltimore, MD 21205 USA
| | - Kyu Young Han
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Howard Hughes Medical Institute, Baltimore, MD 21205 USA
| | - Thomas E. Kuhlman
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Taekjip Ha
- Department of Physics and Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218 USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD 21205 USA
- Howard Hughes Medical Institute, Baltimore, MD 21205 USA
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Abstract
Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.
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Affiliation(s)
- Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Qian Li
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.,School of Life Science & Technology, ShanghaiTech University , Shanghai 200031, China
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Walker CL, Lukyanov KA, Yampolsky IV, Mishin AS, Bommarius AS, Duraj-Thatte AM, Azizi B, Tolbert LM, Solntsev KM. Fluorescence imaging using synthetic GFP chromophores. Curr Opin Chem Biol 2015; 27:64-74. [DOI: 10.1016/j.cbpa.2015.06.002] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Revised: 05/21/2015] [Accepted: 06/05/2015] [Indexed: 01/22/2023]
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