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Liu X, Shi Q, Qi P, Wang Z, Zhang T, Zhang S, Wu J, Guo Z, Chen J, Zhang Q. Recent advances in living cell nucleic acid probes based on nanomaterials for early cancer diagnosis. Asian J Pharm Sci 2024; 19:100910. [PMID: 38948397 PMCID: PMC11214190 DOI: 10.1016/j.ajps.2024.100910] [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: 06/30/2023] [Revised: 11/16/2023] [Accepted: 02/05/2024] [Indexed: 07/02/2024] Open
Abstract
The early diagnosis of cancer is vital for effective treatment and improved prognosis. Tumor biomarkers, which can be used for the early diagnosis, treatment, and prognostic evaluation of cancer, have emerged as a topic of intense research interest in recent years. Nucleic acid, as a type of tumor biomarker, contains vital genetic information, which is of great significance for the occurrence and development of cancer. Currently, living cell nucleic acid probes, which enable the in situ imaging and dynamic monitoring of nucleic acids, have become a rapidly developing field. This review focuses on living cell nucleic acid probes that can be used for the early diagnosis of tumors. We describe the fundamental design of the probe in terms of three units and focus on the roles of different nanomaterials in probe delivery.
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Affiliation(s)
- Xuyao Liu
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Qi Shi
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Peng Qi
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Ziming Wang
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Tongyue Zhang
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
| | - Sijia Zhang
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Jiayan Wu
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Zhaopei Guo
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Jie Chen
- Key Laboratory of Polymer Ecomaterials, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun 130022, China
| | - Qiang Zhang
- Department of Thyroid Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun 130021, China
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2
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Tepper O, Appella DH, Zheng H, Dzikowski R, Yavin E. A Biotinylated cpFIT-PNA Platform for the Facile Detection of Drug Resistance to Artemisinin in Plasmodium falciparum. ACS Sens 2024; 9:1458-1464. [PMID: 38446423 PMCID: PMC10964236 DOI: 10.1021/acssensors.3c02553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 02/05/2024] [Accepted: 02/23/2024] [Indexed: 03/07/2024]
Abstract
The evolution of drug resistance to many antimalarial drugs in the lethal strain of malaria (Plasmodium falciparum) has been a great concern over the past 50 years. Among these drugs, artemisinin has become less effective for treating malaria. Indeed, several P. falciparum variants have become resistant to this drug, as elucidated by specific mutations in the pfK13 gene. This study presents the development of a diagnostic kit for the detection of a common point mutation in the pfK13 gene of P. falciparum, namely, the C580Y point mutation. FIT-PNAs (forced-intercalation peptide nucleic acid) are DNA mimics that serve as RNA sensors that fluoresce upon hybridization to their complementary RNA. Herein, FIT-PNAs were designed to sense the C580Y single nucleotide polymorphism (SNP) and were conjugated to biotin in order to bind these molecules to streptavidin-coated plates. Initial studies with synthetic RNA were conducted to optimize the sensing system. In addition, cyclopentane-modified PNA monomers (cpPNAs) were introduced to improve FIT-PNA sensing. Lastly, total RNA was isolated from red blood cells infected with P. falciparum (WT strain - NF54-WT or mutant strain - NF54-C580Y). Streptavidin plates loaded with either FIT-PNA or cpFIT-PNA were incubated with the total RNA. A significant difference in fluorescence for mutant vs WT total RNA was found only for the cpFIT-PNA probe. In summary, this study paves the way for a simple diagnostic kit for monitoring artemisinin drug resistance that may be easily adapted to malaria endemic regions.
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Affiliation(s)
- Odelia Tepper
- The
Institute for Drug Research, The School of Pharmacy, The Faculty of
Medicine, The Hebrew University of Jerusalem,
Hadassah Ein-Kerem, Jerusalem 9112102, Israel
| | - Daniel H. Appella
- Synthetic
Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC),
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, 8 Center Drive, Room 404, Bethesda, Maryland 20892, United States
| | - Hongchao Zheng
- Synthetic
Bioactive Molecules Section, Laboratory of Bioorganic Chemistry (LBC),
National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health, 8 Center Drive, Room 404, Bethesda, Maryland 20892, United States
| | - Ron Dzikowski
- Department
of Microbiology and Molecular Genetics, The institute for Medical
Research Israel - Canada, The Kuvin Center for the Study of Infectious
and Tropical Diseases, The Hebrew University-Hadassah
Medical School, Jerusalem 9112102, Israel
| | - Eylon Yavin
- The
Institute for Drug Research, The School of Pharmacy, The Faculty of
Medicine, The Hebrew University of Jerusalem,
Hadassah Ein-Kerem, Jerusalem 9112102, Israel
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3
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Schöllkopf S, Knoll A, Homer A, Seitz O. Double FIT hybridization probes – towards enhancing brightness, turn-on and specificity of RNA detection. Chem Sci 2023; 14:4166-4173. [PMID: 37063796 PMCID: PMC10094420 DOI: 10.1039/d3sc00363a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/22/2023] [Indexed: 03/31/2023] Open
Abstract
Efficient fluorogenic hybridization probes combine high brightness and specificity of fluorescence signaling with large turn-on of fluorescence.
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Affiliation(s)
- Sophie Schöllkopf
- Institut für Chemie, Humboldt-Universität zu Berlin 12489 Berlin Germany
| | - Andrea Knoll
- Institut für Chemie, Humboldt-Universität zu Berlin 12489 Berlin Germany
| | - Amal Homer
- Institut für Chemie, Humboldt-Universität zu Berlin 12489 Berlin Germany
| | - Oliver Seitz
- Institut für Chemie, Humboldt-Universität zu Berlin 12489 Berlin Germany
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4
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Sato Y, Miura H, Tanabe T, Okeke CU, Kikuchi A, Nishizawa S. Fluorescence Sensing of the Panhandle Structure of the Influenza A Virus RNA Promoter by Thiazole Orange Base Surrogate-Carrying Peptide Nucleic Acid Conjugated with Small Molecule. Anal Chem 2022; 94:7814-7822. [PMID: 35604144 DOI: 10.1021/acs.analchem.1c05488] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have developed a new class of triplex-forming peptide nucleic acid (PNA)-based fluorogenic probes for sensing of the panhandle structure of the influenza A virus (IAV) RNA promoter region. Here, a small molecule (DPQ) capable of selectively binding to the internal loop structure was conjugated with triplex-forming forced intercalation of the thiazole orange (tFIT) probe with natural PNA nucleobases. The resulting conjugate, tFIT-DPQ, showed a significant light-up response (83-fold) upon strong (Kd = 107 nM) and structure-selective binding to the IAV RNA promoter region under physiological conditions (pH 7.0, 100 mM NaCl). We demonstrated the conjugation of these two units through the suitable spacer was key to show useful binding and fluorogenic signaling functions. tFIT-DPQ facilitated the sensitive and selective detection of IAV RNA based on its binding to the promoter region. Furthermore, we found that tFIT-DPQ could work as a sensitive indicator for screening of test compounds targeting the IAV RNA promoter region in the fluorescence indicator displacement assay.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Hiromasa Miura
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Takaaki Tanabe
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Chioma Uche Okeke
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Akiko Kikuchi
- Department of Kampo and Integrative Medicine, Graduate School of Medicine, Tohoku University, Sendai 980-8575, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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5
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Wang Q, Xiao F, Su H, Liu H, Xu J, Tang H, Qin S, Fang Z, Lu Z, Wu J, Weng X, Zhou X. Inert Pepper aptamer-mediated endogenous mRNA recognition and imaging in living cells. Nucleic Acids Res 2022; 50:e84. [PMID: 35580055 PMCID: PMC9371900 DOI: 10.1093/nar/gkac368] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 04/01/2022] [Accepted: 05/12/2022] [Indexed: 02/06/2023] Open
Abstract
The development of RNA aptamers/fluorophores system is highly desirable for understanding the dynamic molecular biology of RNAs in vivo. Peppers-based imaging systems have been reported and applied for mRNA imaging in living cells. However, the need to insert corresponding RNA aptamer sequences into target RNAs and relatively low fluorescence signal limit its application in endogenous mRNA imaging. Herein, we remolded the original Pepper aptamer and developed a tandem array of inert Pepper (iPepper) fluorescence turn-on system. iPepper allows for efficient and selective imaging of diverse endogenous mRNA species in live cells with minimal agitation of the target mRNAs. We believe iPepper would significantly expand the applications of the aptamer/fluorophore system in endogenous mRNA imaging, and it has the potential to become a powerful tool for real-time studies in living cells and biological processing.
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Affiliation(s)
- Qi Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Feng Xiao
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Haomiao Su
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China.,Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA
| | - Hui Liu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Jinglei Xu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Heng Tang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Shanshan Qin
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Zhentian Fang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Ziang Lu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Jian Wu
- School of Medicine, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Xiaocheng Weng
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers-Ministry of Education, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China.,The Institute of Advanced Studies, Wuhan University, Luojiashan Street, Wuchang District, Wuhan, HuBei 430072, PR China
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6
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NISHIZAWA S, SATO T, LEE ETT, SAKAMOTO N, CHIBA T, TANABE T, YOSHINO Y, TAKAHASHI Y, SATO Y. Triplex-Forming Peptide Nucleic Acid Probes Having Cyanine Base Surrogates for Fluorogenic Sensing of Double-Stranded RNA. BUNSEKI KAGAKU 2022. [DOI: 10.2116/bunsekikagaku.71.133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Seiichi NISHIZAWA
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Takaya SATO
- Department of Chemistry, Graduate School of Science, Tohoku University
| | | | - Naonari SAKAMOTO
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Toshiki CHIBA
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Takaaki TANABE
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Yukina YOSHINO
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Yuki TAKAHASHI
- Department of Chemistry, Graduate School of Science, Tohoku University
| | - Yusuke SATO
- Department of Chemistry, Graduate School of Science, Tohoku University
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7
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Suss O, Motiei L, Margulies D. Broad Applications of Thiazole Orange in Fluorescent Sensing of Biomolecules and Ions. Molecules 2021; 26:2828. [PMID: 34068759 PMCID: PMC8126248 DOI: 10.3390/molecules26092828] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 04/26/2021] [Accepted: 04/27/2021] [Indexed: 12/13/2022] Open
Abstract
Fluorescent sensing of biomolecules has served as a revolutionary tool for studying and better understanding various biological systems. Therefore, it has become increasingly important to identify fluorescent building blocks that can be easily converted into sensing probes, which can detect specific targets with increasing sensitivity and accuracy. Over the past 30 years, thiazole orange (TO) has garnered great attention due to its low fluorescence background signal and remarkable 'turn-on' fluorescence response, being controlled only by its intramolecular torsional movement. These features have led to the development of numerous molecular probes that apply TO in order to sense a variety of biomolecules and metal ions. Here, we highlight the tremendous progress made in the field of TO-based sensors and demonstrate the different strategies that have enabled TO to evolve into a versatile dye for monitoring a collection of biomolecules.
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Affiliation(s)
| | | | - David Margulies
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel; (O.S.); (L.M.)
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8
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Wang J, Shang J, Xiang Y, Tong A. General Method for Post-Synthetic Modification of Oligonucleotides Based on Oxidative Amination of 4-Thio-2'-deoxyuridine. Bioconjug Chem 2021; 32:721-728. [PMID: 33730486 DOI: 10.1021/acs.bioconjchem.1c00016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Functionalized oligonucleotides (ONs) are widely applied as target binding molecules for biosensing and regulators for gene expression. Numerous efforts have been focused on developing facile methods for preparing these useful ONs carrying diverse modifications. Herein, we present a general method for postsynthetic modification of ONs via oxidative amination of 4-thio-2'-deoxyuridine (4SdU). 4SdU-containing ON can be derived by both alkyl and aromatic amines. Using this approach, ONs are successfully attached with alkyne/azide, biotin and dansylamide moieties, and these as-prepared ONs possess the expected biorthogonal reactivity, streptavidin affinity and fluorescent property, respectively. Furthermore, we also directly install fluorophores to the ON nucleobase based on oxidative amination of 4SdU, and these fluorophores exhibit distinct luminescence behaviors before and after conjugation. We believe our method will be a versatile strategy for constructing various functionalized ONs used in a wide range of nucleic acid applications.
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Affiliation(s)
- Jingyi Wang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Jiachen Shang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
| | - Aijun Tong
- Department of Chemistry, Beijing Key Laboratory for Microanalytical Methods and Instrumentation, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology (Ministry of Education), Tsinghua University, Beijing 100084, China
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9
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Abstract
Cyclopentane modified FIT-PNA (cpFIT-PNA) probes are reported as highly emissive RNA sensors with the highest reported brightness for FIT-PNAs. Compared to FIT-PNAs, cpFIT-PNAs have improved mismatch discrimination for several pyrimidine-pyrimidine single nucleotide variants (SNVs).
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Affiliation(s)
- Odelia Tepper
- The Institute for Drug Research, The School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem 91120, Israel.
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10
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Gao RR, Dong W. ATP and lanthanide ions derived coordination polymer nanoparticles as a novel family of versatile materials: Color-tunable emission, artificial tongues and logic devices. Microchem J 2021. [DOI: 10.1016/j.microc.2020.105753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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11
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Loibl N, Arenz C, Seitz O. Monitoring Dicer-Mediated miRNA-21 Maturation and Ago2 Loading by a Dual-Colour FIT PNA Probe Set. Chembiochem 2020; 21:2527-2532. [PMID: 32270536 PMCID: PMC7496889 DOI: 10.1002/cbic.202000173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/06/2020] [Indexed: 12/14/2022]
Abstract
The inhibition of micro RNA (miRNA) maturation by Dicer and loading matured miRNAs into the RNA-induced silencing complex (RISC) is envisioned as a modality for treatment of cancer. Existing methods for evaluating maturation either focus on the conversion of modified precursors or detect mature miRNA. Whereas the former is not applicable to native pre-miRNA, the latter approach underestimates maturation when both nonmatured and matured miRNA molecules are subject to cleavage. We present a set of two orthogonally labelled FIT PNA probes that distinguish between cleaved pre-miRNA and the mature miRNA duplex. The probes allow Dicer-mediated miR21 maturation to be monitored and Ago2-mediated unwinding of the miR21 duplex to be assayed. A two-channel fluorescence readout enables measurement in real-time without the need for specialized instrumentation or further enzyme mediated amplification.
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Affiliation(s)
- Natalia Loibl
- Department of ChemistryHumbolt-Universität zu BerlinBrook-Taylor-Strase 212489BerlinGermany
| | - Christoph Arenz
- Department of ChemistryHumbolt-Universität zu BerlinBrook-Taylor-Strase 212489BerlinGermany
| | - Oliver Seitz
- Department of ChemistryHumbolt-Universität zu BerlinBrook-Taylor-Strase 212489BerlinGermany
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12
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Ebrahimi SB, Samanta D, Mirkin CA. DNA-Based Nanostructures for Live-Cell Analysis. J Am Chem Soc 2020; 142:11343-11356. [DOI: 10.1021/jacs.0c04978] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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13
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Samanta D, Ebrahimi SB, Mirkin CA. Nucleic-Acid Structures as Intracellular Probes for Live Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1901743. [PMID: 31271253 PMCID: PMC6942251 DOI: 10.1002/adma.201901743] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/08/2019] [Indexed: 05/02/2023]
Abstract
The chemical composition of cells at the molecular level determines their growth, differentiation, structure, and function. Probing this composition is powerful because it provides invaluable insight into chemical processes inside cells and in certain cases allows disease diagnosis based on molecular profiles. However, many techniques analyze fixed cells or lysates of bulk populations, in which information about dynamics and cellular heterogeneity is lost. Recently, nucleic-acid-based probes have emerged as a promising platform for the detection of a wide variety of intracellular analytes in live cells with single-cell resolution. Recent advances in this field are described and common strategies for probe design, types of targets that can be identified, current limitations, and future directions are discussed.
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Affiliation(s)
- Devleena Samanta
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Sasha B Ebrahimi
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Chad A Mirkin
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
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14
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Knoll A, Kankowski S, Schöllkopf S, Meier JC, Seitz O. Chemo-biological mRNA imaging with single nucleotide specificity. Chem Commun (Camb) 2020; 55:14817-14820. [PMID: 31763632 DOI: 10.1039/c9cc06989e] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Unambiguous imaging of C → U edited mRNA calls for a method that distinguishes a locally high concentration of unbound probe or single nucleotide mismatched target from a locally low concentration of matched mRNA target. To address this issue, we combine FIT probes as a "chemical" detection system with the "biological" MS2 technique. Ratio measurements provide a convenient parameter to discriminate the edited from the unedited state of mRNA encoding for GlyR α2 in HEK cells.
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Affiliation(s)
- Andrea Knoll
- Humboldt University Berlin, Department of Chemistry, Brook-Taylor-Str. 2, D-12489 Berlin, Germany.
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15
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Cheng MSQ, Su MXX, Wang MXN, Sun MZY, Ou TM. Probes and drugs that interfere with protein translation via targeting to the RNAs or RNA-protein interactions. Methods 2019; 167:124-133. [PMID: 31185274 DOI: 10.1016/j.ymeth.2019.06.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 04/08/2019] [Accepted: 06/05/2019] [Indexed: 11/18/2022] Open
Abstract
Protein synthesis is critical to cell survival and translation regulation is essential to post-transcriptional gene expression regulation. Disorders of this process, particularly through RNA-binding proteins, is associated with the development and progression of a number of diseases, including cancers. However, the molecular mechanisms underlying the initiation of protein synthesis are intricate, making it difficult to find a drug that interferes with this process. Chemical probes are useful in elucidating the structures of RNA-protein complex and molecular mechanism of biological events. Moreover, some of these chemical probes show certain therapeutic benefits and can be further developed as leading compounds. Here, we will briefly review the general process and mechanism of protein synthesis, and emphasis on chemical probes in examples of probing the RNA structural changes and RNA-protein interactions. Moreover, the therapeutic potential of these probes is also discussed to give a comprehensive understanding.
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Affiliation(s)
- Miss Sui-Qi Cheng
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, Guangdong 510006, China
| | - Miss Xiao-Xuan Su
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, Guangdong 510006, China.
| | - Miss Xiao-Na Wang
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, Guangdong 510006, China
| | - Miss Zhi-Yin Sun
- Sun Yat-Sen University, School of Pharmaceutical Sciences, Guangzhou, Guangdong 510006, China
| | - Tian-Miao Ou
- Sun Yat-Sen University, School of Pharmaceutical Sciences, 132 Waihuan East Road, Guangzhou University City, Guangzhou, Guangdong, China.
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16
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Klimkowski P, De Ornellas S, Singleton D, El-Sagheer AH, Brown T. Design of thiazole orange oligonucleotide probes for detection of DNA and RNA by fluorescence and duplex melting. Org Biomol Chem 2019; 17:5943-5950. [PMID: 31157811 PMCID: PMC6686645 DOI: 10.1039/c9ob00885c] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
We have synthesised a range of thiazole orange (TO) functionalised oligonucleotides for nucleic acid detection in which TO is attached to the nucleobase or sugar of thymidine. The properties of duplexes between TO-probes and their DNA and RNA targets strongly depend on the length of the linker between TO and the oligonucleotide, the position of attachment of TO to the nucleotide (major or minor groove) and the mode of attachment of thiazole orange (via benzothiazole or quinoline moiety). This information can be used to design probes for detection of target nucleic acids by fluorescence or duplex melting. With cellular imaging in mind we show that 2'-OMe RNA probes with TO at the 5-position of uracil or the 2'-position of the ribose sugar are particularly effective, exhibiting up to 44-fold fluorescence enhancement against DNA and RNA, and high duplex stability. Excellent mismatch discrimination is achieved when the mispaired base is located adjacent to the TO-modified nucleotide rather than opposite to it. The simple design, ease of synthesis and favourable properties of these TO probes suggest applications in fluorescent imaging of DNA and RNA in a cellular context.
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Affiliation(s)
- Piotr Klimkowski
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
| | - Sara De Ornellas
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK. and Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Headley Way, Oxford, OX3 9DS, UK
| | - Daniel Singleton
- ATDBio, School of Chemistry University of Southampton, SO17 1BJ, UK
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK. and Chemistry Branch, Department of Science and Mathematics, Faculty of Petroleum and Mining Engineering, Suez University, Suez 43721, Egypt
| | - Tom Brown
- Department of Chemistry, University of Oxford, 12 Mansfield Road, Oxford, OX1 3TA, UK.
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17
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Šmidlehner T, Rožman A, Piantanida I. Advances in Cyanine - Amino Acid Conjugates and Peptides for Sensing of DNA, RNA and Protein Structures. Curr Protein Pept Sci 2019; 20:1040-1045. [PMID: 31092178 DOI: 10.2174/1389203720666190513084102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/23/2019] [Accepted: 04/06/2019] [Indexed: 12/27/2022]
Abstract
Small molecule spectrophotometric probes for DNA/RNA and proteins are of the utmost importance for diagnostics in biochemical and biomedical research. Both, naturally occurring and synthetic probes, often include peptide sequence responsible for the selectivity toward the particular target; however, commercially available dyes are restricted to single point attachment to the peptide (having one reactive group). Here presented are our recent advances in the development of novel amino acidfluorophore probes, with the unique characteristic of free N- and C-terminus available for incorporation at any peptide backbone position. Intriguingly, already monomeric amino acid-fluorophores showed recognition among various DNA/RNA, whereby steric impact and contribution of halogens is systematically studied. Moreover, some dyes revealed intracellular mitochondria specificity. Further, several hetero-dimeric chromophore systems were prepared, demonstrating that synergistic effect can lead to simultaneous DNA, RNA and protein fluorimetric recognition, combined with enzyme inhibition. Also, homodimeric cyanines equipped with chlorine revealed intriguing DNA/RNA selectivity in respect to well-known parent TOTO and YOYO dyes.
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Affiliation(s)
- Tamara Šmidlehner
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry. Ruder Boskovic Institute, Zagreb, Croatia
| | - Andrea Rožman
- Pliva Croatia Ltd, Research and Development, Zagreb, Croatia
| | - Ivo Piantanida
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry. Ruder Boskovic Institute, Zagreb, Croatia
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18
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Hashoul D, Shapira R, Falchenko M, Tepper O, Paviov V, Nissan A, Yavin E. Red-emitting FIT-PNAs: "On site" detection of RNA biomarkers in fresh human cancer tissues. Biosens Bioelectron 2019; 137:271-278. [PMID: 31121464 DOI: 10.1016/j.bios.2019.04.056] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 04/15/2019] [Accepted: 04/29/2019] [Indexed: 01/17/2023]
Abstract
To date, there are limited approaches for the direct and rapid visualization (on site) of tumor tissues for pathological assessment and for aiding cytoreductive surgery. Herein, we have designed FIT-PNAs (forced-intercalation-peptide nucleic acids) to detect two RNA cancer biomarkers. Firstly, a lncRNA (long noncoding RNA) termed CCAT1, has been shown as an oncogenic lncRNA over-expressed in a variety of cancers. The latter, an mRNA termed KRT20, has been shown to be over-expressed in metastases originating from colorectal cancer (CRC). To these FIT-PNAs, we have introduced the bis-quinoline (BisQ) cyanine dye that emits light in the red region (605-610 nm) of the visible spectrum. Most strikingly, spraying fresh human tissue taken from patients during cytoreductive surgery for peritoneal metastasis of colon cancer with an aqueous solution of CCAT1 FIT-PNA results in bright fluorescence in a matter of minutes. In fresh healthy tissue (from bariatric surgeries), no appreciable fluorescence is detected. In addition, a non-targeted FIT-PNA shows no fluorescent signal after spraying this FIT-PNA on fresh tumor tissue emphasizing the specificity of these molecular sensors. This study is the first to show on-site direct and immediate visualization of an RNA cancer biomarker on fresh human cancer tissues by topical application (spraying) of a molecular sensor.
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Affiliation(s)
- Dina Hashoul
- School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem, 91120, Israel
| | - Rachel Shapira
- Department of General and Oncological Surgery, The Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Maria Falchenko
- School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem, 91120, Israel
| | - Odelia Tepper
- School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem, 91120, Israel
| | - Vera Paviov
- Department of General and Oncological Surgery, The Chaim Sheba Medical Center, Tel Hashomer, Israel
| | - Aviram Nissan
- Department of General and Oncological Surgery, The Chaim Sheba Medical Center, Tel Hashomer, Israel.
| | - Eylon Yavin
- School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem, 91120, Israel.
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19
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Chamiolo J, Fang GM, Hövelmann F, Friedrich D, Knoll A, Loewer A, Seitz O. Comparing Agent-Based Delivery of DNA and PNA Forced Intercalation (FIT) Probes for Multicolor mRNA Imaging. Chembiochem 2018; 20:595-604. [PMID: 30326174 PMCID: PMC6470956 DOI: 10.1002/cbic.201800526] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Indexed: 12/19/2022]
Abstract
Fluorogenic oligonucleotide probes allow mRNA imaging in living cells. A key challenge is the cellular delivery of probes. Most delivery agents, such as cell‐penetrating peptides (CPPs) and pore‐forming proteins, require interactions with the membrane. Charges play an important role. To explore the influence of charge on fluorogenic properties and delivery efficiency, we compared peptide nucleic acid (PNA)‐ with DNA‐based forced intercalation (FIT) probes. Perhaps counterintuitively, fluorescence signaling by charged DNA FIT probes proved tolerant to CPP conjugation, whereas CPP–FIT PNA conjugates were affected. Live‐cell imaging was performed with a genetically engineered HEK293 cell line to allow the inducible expression of a specific mRNA target. Blob‐like features and high background were recurring nuisances of the tested CPP and lipid conjugates. By contrast, delivery by streptolysin‐O provided high enhancements of the fluorescence of the FIT probe upon target induction. Notably, DNA‐based FIT probes were brighter and more responsive than PNA‐based FIT probes. Optimized conditions enabled live‐cell multicolor imaging of three different mRNA target sequences.
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Affiliation(s)
- Jasmine Chamiolo
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany
| | - Ge-Min Fang
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany.,Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, P.R. China
| | - Felix Hövelmann
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany
| | - Dhana Friedrich
- Max Delbrück Centrum für Molekulare Medizin, Robert Rössle Strasse 10, 13125, Berlin, Germany.,Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 13, 64287, Darmstadt, Germany
| | - Andrea Knoll
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany
| | - Alexander Loewer
- Max Delbrück Centrum für Molekulare Medizin, Robert Rössle Strasse 10, 13125, Berlin, Germany.,Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 13, 64287, Darmstadt, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany
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20
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Affiliation(s)
- Teresa L. Mako
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Joan M. Racicot
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
| | - Mindy Levine
- Department of Chemistry, University of Rhode Island, 140 Flagg Road, Kingston, Rhode Island 02881, United States
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21
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Method for Imaging Live-Cell RNA Using an RNA Aptamer and a Fluorescent Probe. Methods Mol Biol 2018; 1649:305-318. [PMID: 29130206 DOI: 10.1007/978-1-4939-7213-5_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Live-cell imaging of mRNA dynamics is increasingly important to understanding spatially restricted gene expression. We recently developed a convenient and versatile method that uses a gene-specific RNA aptamer and a fluorescent probe to enable spatiotemporal imaging of endogenous mRNAs in living cells. The method was validated by live-cell imaging of the endogenous mRNA of β-actin. The new RNA-imaging technology might be useful for live-cell imaging of any RNA molecules.
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22
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Takada T, Ishino S, Takata A, Nakamura M, Fujitsuka M, Majima T, Yamana K. Rapid Electron Transfer of Stacked Heterodimers of Perylene Diimide Derivatives in a DNA Duplex. Chemistry 2018; 24:8228-8232. [DOI: 10.1002/chem.201800947] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Indexed: 01/11/2023]
Affiliation(s)
- Tadao Takada
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
| | - Syunya Ishino
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
| | - Ami Takata
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
| | - Mitsunobu Nakamura
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
| | - Mamoru Fujitsuka
- The Institute of Scientific and Industrial Research (SANKEN); Osaka University; Mihogaoka 8-1 Ibaraki, Osaka 567-0047 Japan
| | - Tetsuro Majima
- The Institute of Scientific and Industrial Research (SANKEN); Osaka University; Mihogaoka 8-1 Ibaraki, Osaka 567-0047 Japan
| | - Kazushige Yamana
- Department of Applied Chemistry; Graduate School of Engineering; University of Hyogo; 2167 Shosha Himeji Hyogo 671-2280 Japan
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23
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Peled I, Yavin E. Predictive Model for the Sequence-Dependent Fluorogenic Response of Forced-Intercalation Peptide Nucleic Acid. ACS OMEGA 2018; 3:3813-3818. [PMID: 30023882 PMCID: PMC6045369 DOI: 10.1021/acsomega.8b00184] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 03/23/2018] [Indexed: 06/08/2023]
Abstract
UNLABELLED The forced-intercalation peptide nucleic acid (FIT-PNA) concept, introduced by Seitz and co-workers, is based on replacing a nucleobase of the PNA sequence with a cyanine dye (such as thiazole orange). The cyanine dye is thus a surrogate base that is forced to intercalate in the duplex (e.g. , PNA DNA). This allows single-mismatch sensitivity as the introduction of a mismatch in the vicinity of the dye increases freedom of motion and leads to a significant depletion of its fluorescence because of the free rotation of the monomethine bond separating the two π-systems of the cyanine dye. Herein, we designed and synthesized six FIT-PNA probes, featuring bisquinoline (BisQ), a red-emitting cyanine dye recently developed in our laboratory for FIT-PNAs. By following PNA-DNA duplex fluorescence, we found new sequence-based factors governing the fluorescence response to the mismatched FIT-PNA:DNA duplex. Fluorogenic properties are correlated with the π-stacking energy of three distinctive base pair steps (BPSs) in the PNA:DNA duplex. The first two are the two BPSs opposite BisQ, whereas the third is the BPS of the mismatch position, which presumably becomes unstacked due to the mismatch. We suggest a predictive model for FIT-PNA single-mismatch detection mechanism, a model that can be used in future research to improve FIT-PNA design.
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Affiliation(s)
| | - Eylon Yavin
- E-mail: . Phone: +972-2-6758692. Fax: +972-2-6757574 (E.Y.)
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24
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Gaspar I, Hövelmann F, Chamiolo J, Ephrussi A, Seitz O. Quantitative mRNA Imaging with Dual Channel qFIT Probes to Monitor Distribution and Degree of Hybridization. ACS Chem Biol 2018; 13:742-749. [PMID: 29378392 DOI: 10.1021/acschembio.7b01007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Fluorogenic oligonucleotide probes facilitate the detection and localization of RNA targets within cells. However, quantitative measurements of mRNA abundance are difficult when fluorescence signaling is based on intensity changes because a high concentration of unbound probes cannot be distinguished from a low concentration of target-bound probes. Here, we introduce qFIT (quantitative forced intercalation) probes that allow the detection both of probe-target complexes and of unbound probes on separate, independent channels. A surrogate nucleobase based on thiazole orange (TO) probes the hybridization status. The second channel involves a nonresponsive near-IR dye, which serves as a reporter of concentration. We show that the undesirable perturbation of the hybridization reporter TO is avoided when the near-IR dye Cy7 is connected by means of short triazole linkages in an ≥18 nucleotides distance. We used the qFIT probes to localize and quantify oskar mRNA in fixed egg chambers of wild-type and mutant Drosophila melanogaster by wash-free fluorescence in situ hybridization. The measurements revealed a relative 400-fold enrichment of oskar within a 3000 μm3 large volume at the posterior pole of stage 8-9 oocytes, which peaked at a remarkably high 1.8 μM local concentration inside 0.075 μm3 volume units. We discuss detection limits and show that the number of oskar mRNA molecules per oocyte is independent of the oocyte size, which suggests that the final levels are attained already during the onset of oskar localization at stage 8.
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Affiliation(s)
- Imre Gaspar
- European Molecular Biology Laboratory (EMBL) Heidelberg, 69117 Heidelberg, Germany
| | - Felix Hövelmann
- Institut für Chemie der Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - Jasmine Chamiolo
- Institut für Chemie der Humboldt-Universität zu Berlin, 12489 Berlin, Germany
| | - Anne Ephrussi
- European Molecular Biology Laboratory (EMBL) Heidelberg, 69117 Heidelberg, Germany
| | - Oliver Seitz
- Institut für Chemie der Humboldt-Universität zu Berlin, 12489 Berlin, Germany
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25
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Abstract
The last past decade has witnessed a revolution in our appreciation of transcriptome complexity and regulation. This remarkable expansion in our knowledge largely originates from the advent of high-throughput methodologies, and the consecutive discovery that up to 90% of eukaryotic genomes are transcribed, thus generating an unanticipated large range of noncoding RNAs (Hangauer et al., 15(4):112, 2014). Besides leading to the identification of new noncoding RNA species, transcriptome-wide studies have uncovered novel layers of posttranscriptional regulatory mechanisms controlling RNA processing, maturation or translation, and each contributing to the precise and dynamic regulation of gene expression. Remarkably, the development of systems-level studies has been accompanied by tremendous progress in the visualization of individual RNA molecules in single cells, such that it is now possible to image RNA species with a single-molecule resolution from birth to translation or decay. Monitoring quantitatively, with unprecedented spatiotemporal resolution, the fate of individual molecules has been key to understanding the molecular mechanisms underlying the different steps of RNA regulation. This has also revealed biologically relevant, intracellular and intercellular heterogeneities in RNA distribution or regulation. More recently, the convergence of imaging and high-throughput technologies has led to the emergence of spatially resolved transcriptomic techniques that provide a means to perform large-scale analyses while preserving spatial information. By generating transcriptome-wide data on single-cell RNA content, or even subcellular RNA distribution, these methodologies are opening avenues to a wide range of network-level studies at the cell and organ-level, and promise to strongly improve disease diagnostic and treatment.In this introductory chapter, we highlight how recently developed technologies aiming at detecting and visualizing RNA molecules have contributed to the emergence of entirely new research fields, and to dramatic progress in our understanding of gene expression regulation.
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Affiliation(s)
- Caroline Medioni
- Université Côte d'Azur, CNRS, Inserm, iBV, Parc Valrose, 06100, Nice, France
| | - Florence Besse
- Université Côte d'Azur, CNRS, Inserm, iBV, Parc Valrose, 06100, Nice, France.
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26
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Fang GM, Seitz O. Synthesis of Bipartite Tetracysteine PNA Probes for DNA In Situ Fluorescent Labeling. ACTA ACUST UNITED AC 2017; 71:4.78.1-4.78.14. [PMID: 29275539 DOI: 10.1002/cpnc.44] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
"Label-free" fluorescent probes that avoid additional steps or building blocks for conjugation of fluorescent dyes with oligonucleotides can significantly reduce the time and cost of parallel bioanalysis of a large number of nucleic acid samples. A method for the synthesis of "label-free" bicysteine-modified PNA probes using solid-phase synthesis and procedures for sequence-specific DNA in situ fluorescent labeling is described here. The concept is based on the adjacent alignment of two bicysteine-modified peptide nucleic acids on a DNA target to form a structurally optimized bipartite tetracysteine motif, which induces a sequence-specific fluorogenic reaction with commercially available biarsenic dyes, even in complex media such as cell lysate. This unit will help researchers to quickly synthesize bipartite tetracysteine PNA probes and carry out low-cost DNA in situ fluorescent labeling experiments. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Ge-Min Fang
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
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27
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In Vivo Visualization and Function Probing of Transport mRNPs Using Injected FIT Probes. Methods Mol Biol 2017. [PMID: 29130204 DOI: 10.1007/978-1-4939-7213-5_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Fluorogenic hybridization methods, such as the use of FIT probes, enable the in vivo detection of specific mRNAs transcribed from their endogenous, genetically nonmodified loci. Here, we describe the design, synthesis and injection of nuclease resistant FIT probes into developing Drosophila oocytes to detect endogenous localizing mRNAs as wells as to probe function of structural RNA elements.
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28
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Zhou CY, Alexander SC, Devaraj NK. Fluorescent turn-on probes for wash-free mRNA imaging via covalent site-specific enzymatic labeling. Chem Sci 2017; 8:7169-7173. [PMID: 29081948 PMCID: PMC5635419 DOI: 10.1039/c7sc03150e] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 08/28/2017] [Indexed: 11/21/2022] Open
Abstract
Investigating the many roles RNA plays in cellular regulation and function has increased demand for tools to explore RNA tracking and localization within cells.
Investigating the many roles RNA plays in cellular regulation and function has increased demand for tools to explore RNA tracking and localization within cells. Our recently reported RNA-TAG (transglycosylation at guanine) approach uses an RNA-modifying enzyme, tRNA-guanine transglycosylase (TGT), to accomplish covalent labeling of an RNA of interest with fluorescent tracking agents in a highly selective and efficient manner. Unfortunately, labeling by this method currently suffers from a high nonspecific fluorescent background and is currently unsuitable for imaging RNA within complex cellular environments. Herein we report the design and synthesis of novel fluorogenic thiazole orange probes that significantly lower nonspecific binding and background fluorescence and, as a result, provide up to a 100-fold fluorescence intensity increase after labeling. Using these fluorogenic labeling agents, we were able to image mRNA expressed in Chinese Hamster Ovary cells in a wash-free manner.
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Affiliation(s)
- Cun Yu Zhou
- Department of Chemistry and Biochemistry , University of California , 9500 Gilman Dr La Jolla , San Diego , CA 92093 , USA .
| | - Seth C Alexander
- Department of Chemistry and Biochemistry , University of California , 9500 Gilman Dr La Jolla , San Diego , CA 92093 , USA .
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry , University of California , 9500 Gilman Dr La Jolla , San Diego , CA 92093 , USA .
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29
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Alexander SC, Devaraj NK. Developing a Fluorescent Toolbox To Shed Light on the Mysteries of RNA. Biochemistry 2017; 56:5185-5193. [PMID: 28671838 DOI: 10.1021/acs.biochem.7b00510] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Technologies that detect and image RNA have illuminated the complex roles played by RNA, redefining the traditional and superficial role first outlined by the central dogma of biology. Because there is such a wide diversity of RNA structure arising from an assortment of functions within biology, a toolbox of approaches have emerged for investigation of this important class of biomolecules. These methods are necessary to detect and elucidate the localization and dynamics of specific RNAs and in doing so unlock our understanding of how RNA dysregulation leads to disease. Current methods for detecting and imaging RNA include in situ hybridization techniques, fluorescent aptamers, RNA binding proteins fused to fluorescent reporters, and covalent labeling strategies. Because of the inherent diversity of these methods, each approach comes with a set of strengths and limitations that leave room for future improvement. This perspective seeks to highlight the most recent advances and remaining challenges for the wide-ranging toolbox of technologies that illuminate RNA's contribution to cellular complexity.
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Affiliation(s)
- Seth C Alexander
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
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30
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Haralampiev I, Schade M, Chamiolo J, Jolmes F, Prisner S, Witkowski PT, Behrent M, Hövelmann F, Wolff T, Seitz O, Herrmann A. A Fluorescent RNA Forced-Intercalation Probe as a Pan-Selective Marker for Influenza A Virus Infection. Chembiochem 2017; 18:1589-1592. [PMID: 28557173 DOI: 10.1002/cbic.201700271] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Indexed: 11/08/2022]
Abstract
The influenza A virus (IAV) genome is segmented into eight viral ribonucleoproteins, each expressing a negatively oriented viral RNA (vRNA). Along the infection cycle, highly abundant single-stranded small viral RNAs (svRNA) are transcribed in a segment-specific manner. The sequences of svRNAs and of the vRNA 5'-ends are identical and highly conserved among all IAV strains. Here, we demonstrate that these sequences can be used as a target for a pan-selective sensor of IAV infection. To this end, we used a complementary fluorescent forced-intercalation RNA (IAV QB-FIT) probe with a single locked nucleic acid substitution to increase brightness. We demonstrated by fluorescence in situ hybridization (FISH) that this probe is suitable and easy to use to detect infection of different cell types by a broad variety of avian, porcine, and human IAV strains, but not by other influenza virus types. IAV QB-FIT also provides a useful tool to characterize different infection states of the host cell.
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Affiliation(s)
- Ivan Haralampiev
- Institut für Biologie, Molekulare Biophysik, IRI Life Sciences, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115, Berlin, Germany
| | - Matthias Schade
- Institut für Biologie, Molekulare Biophysik, IRI Life Sciences, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115, Berlin, Germany
| | - Jasmine Chamiolo
- Institut für Chemie, Bioorganische Synthese, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
| | - Fabian Jolmes
- Institut für Biologie, Molekulare Biophysik, IRI Life Sciences, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115, Berlin, Germany
| | - Simon Prisner
- Institut für Biologie, Molekulare Biophysik, IRI Life Sciences, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115, Berlin, Germany
| | | | - Marie Behrent
- Institut für Biologie, Molekulare Biophysik, IRI Life Sciences, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115, Berlin, Germany
| | - Felix Hövelmann
- Institut für Chemie, Bioorganische Synthese, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
| | - Thorsten Wolff
- Fachgebiet 17, Influenza und weitere Viren des Respirationstraktes, Seestrasse 10, 13353, Berlin, Germany
| | - Oliver Seitz
- Institut für Chemie, Bioorganische Synthese, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
| | - Andreas Herrmann
- Institut für Biologie, Molekulare Biophysik, IRI Life Sciences, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115, Berlin, Germany
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31
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Tan X, Constantin TP, Sloane KL, Waggoner AS, Bruchez MP, Armitage BA. Fluoromodules Consisting of a Promiscuous RNA Aptamer and Red or Blue Fluorogenic Cyanine Dyes: Selection, Characterization, and Bioimaging. J Am Chem Soc 2017. [PMID: 28644615 DOI: 10.1021/jacs.7b04211] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
An RNA aptamer selected for binding to the fluorogenic cyanine dye, dimethylindole red (DIR), also binds and activates another cyanine, oxazole thiazole blue (OTB), giving two well-resolved emission colors. The aptamer binds to each dye with submicromolar KD values, and the resulting fluoromodules exhibit fluorescence quantum yields ranging from 0.17 to 0.51 and excellent photostability. The aptamer was fused to a second aptamer previously selected for binding to the epidermal growth factor receptor (EGFR) to create a bifunctional aptamer that labels cell-surface EGFR on mammalian cells. The fluorescent color of the aptamer-labeled EGFR can be switched between blue and red in situ simply by exchanging the dye in the medium. The promiscuity of the aptamer can also be used to distinguish between cell-surface and internalized EGFR on the basis of the addition of red or blue fluorogen at different times.
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Affiliation(s)
- Xiaohong Tan
- Departments of Chemistry and Biological Sciences, Molecular Biosensor and Imaging Center, and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Tudor P Constantin
- Departments of Chemistry and Biological Sciences, Molecular Biosensor and Imaging Center, and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Kelly L Sloane
- Departments of Chemistry and Biological Sciences, Molecular Biosensor and Imaging Center, and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Alan S Waggoner
- Departments of Chemistry and Biological Sciences, Molecular Biosensor and Imaging Center, and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Marcel P Bruchez
- Departments of Chemistry and Biological Sciences, Molecular Biosensor and Imaging Center, and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
| | - Bruce A Armitage
- Departments of Chemistry and Biological Sciences, Molecular Biosensor and Imaging Center, and Center for Nucleic Acids Science and Technology, Carnegie Mellon University , 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, United States
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32
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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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Xia Y, Zhang R, Wang Z, Tian J, Chen X. Recent advances in high-performance fluorescent and bioluminescent RNA imaging probes. Chem Soc Rev 2017; 46:2824-2843. [PMID: 28345687 PMCID: PMC5472208 DOI: 10.1039/c6cs00675b] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RNA plays an important role in life processes. Imaging of messenger RNAs (mRNAs) and micro-RNAs (miRNAs) not only allows us to learn the formation and transcription of mRNAs and the biogenesis of miRNAs involved in various life processes, but also helps in detecting cancer. High-performance RNA imaging probes greatly expand our view of life processes and enhance the cancer detection accuracy. In this review, we summarize the state-of-the-art high-performance RNA imaging probes, including exogenous probes that can image RNA sequences with special modification and endogeneous probes that can directly image endogenous RNAs without special treatment. For each probe, we review its structure and imaging principle in detail. Finally, we summarize the application of mRNA and miRNA imaging probes in studying life processes as well as in detecting cancer. By correlating the structures and principles of various probes with their practical uses, we compare different RNA imaging probes and offer guidance for better utilization of the current imaging probes and the future design of higher-performance RNA imaging probes.
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Affiliation(s)
- Yuqiong Xia
- Engineering Research Center of Molecular-imaging and Neuro-imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi 710126, China.
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Sato T, Sato Y, Nishizawa S. Optimization of the Alkyl Linker of TO Base Surrogate in Triplex-Forming PNA for Enhanced Binding to Double-Stranded RNA. Chemistry 2017; 23:4079-4088. [PMID: 27897343 DOI: 10.1002/chem.201604676] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Indexed: 12/24/2022]
Abstract
A series of triplex-forming peptide nucleic acid (TFP) probes carrying a thiazole orange (TO) base surrogate through an alkyl linker was synthesized, and the interactions between these so-called tFIT probes and purine-rich sequences within double-stranded RNA (dsRNA) were examined. We found that the TO base surrogate linker significantly affected both the binding affinity and the fluorescence response upon triplex formation with the target dsRNA. Among the probes examined, the TO base surrogate connected through the propyl linker in the tFIT probes increased the binding affinity by a factor of ten while maintaining its function as the fluorescent universal base. Isothermal titration calorimetry experiments revealed that the increased binding affinity resulted from the gain in the binding enthalpy, which could be explained by the enhanced π-stacking interaction between the TO base surrogate and the dsRNA part of the triplex. We expect that these results will provide a molecular basis for designing strong binding tFIT probes for fluorescence sensing of various kinds of purine-rich dsRNAs sequences including those carrying a pyrimidine-purine inversion. The obtained data also offers a new insight into further development of the universal bases incorporated in TFP.
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Affiliation(s)
- Takaya Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, 980-8578, Japan
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Gáspár I, Sysoev V, Komissarov A, Ephrussi A. An RNA-binding atypical tropomyosin recruits kinesin-1 dynamically to oskar mRNPs. EMBO J 2016; 36:319-333. [PMID: 28028052 PMCID: PMC5286366 DOI: 10.15252/embj.201696038] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 11/14/2022] Open
Abstract
Localization and local translation of oskar mRNA at the posterior pole of the Drosophila oocyte directs abdominal patterning and germline formation in the embryo. The process requires recruitment and precise regulation of motor proteins to form transport‐competent mRNPs. We show that the posterior‐targeting kinesin‐1 is loaded upon nuclear export of oskar mRNPs, prior to their dynein‐dependent transport from the nurse cells into the oocyte. We demonstrate that kinesin‐1 recruitment requires the DmTropomyosin1‐I/C isoform, an atypical RNA‐binding tropomyosin that binds directly to dimerizing oskar 3′UTRs. Finally, we show that a small but dynamically changing subset of oskar mRNPs gets loaded with inactive kinesin‐1 and that the motor is activated during mid‐oogenesis by the functionalized spliced oskar RNA localization element. This inefficient, dynamic recruitment of Khc decoupled from cargo‐dependent motor activation constitutes an optimized, coordinated mechanism of mRNP transport, by minimizing interference with other cargo‐transport processes and between the cargo‐associated dynein and kinesin‐1.
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Affiliation(s)
- Imre Gáspár
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Vasiliy Sysoev
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Artem Komissarov
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Anne Ephrussi
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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Fang GM, Seitz O. Bivalent Display of Dicysteine on Peptide Nucleic Acids for Homogenous DNA/RNA Detection through in Situ Fluorescence Labelling. Chembiochem 2016; 18:189-194. [PMID: 27883258 DOI: 10.1002/cbic.201600623] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Indexed: 01/06/2023]
Abstract
Fluorogenic probes that signal the presence of specific DNA or RNA sequences are key enabling tools for molecular disease diagnosis and imaging studies. Usually, at least one fluorophore is attached through covalent bonding to an oligonucleotide probe. However, the additional conjugation step increases costs. Here we introduce a method that avoids the requirement for the preparation of fluorescence-labelled oligonucleotides and provides the opportunity to alter the fluorogenic reporter dye without resynthesis. The method is based on adjacent hybridization of two dicysteine-containing peptide nucleic acid (PNA) probes to form a bipartite tetracysteine motif that binds profluorescent bisarsenical dyes such as FIAsH, ReAsH or CrAsH. Binding is accompanied by strong increases in fluorescence emission (with response factors of up to 80-fold and high brightness up to 50 mL mol-1 cm-1 ). The detection system provides sub-nanomolar limits of detection and allows discrimination of single nucleotide variations through more than 20-fold changes in fluorescence intensity. To demonstrate its usefulness, the FIAsH-based readout of the bivalent CysCys-PNA display was interfaced with a rolling-circle amplification (RCA) assay used to detect disease-associated microRNA let-7a.
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Affiliation(s)
- Ge-Min Fang
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
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37
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Chen J, Wu J, Hong Y. The morpholino molecular beacon for specific RNA visualization in vivo. Chem Commun (Camb) 2016; 52:3191-4. [PMID: 26810703 DOI: 10.1039/c5cc07124k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A non-invasive fluorescent probe, morpholino molecular beacon (MO-MB), was designed for RNA visualization in vivo. Featuring negligible toxicity, stability, and high target specificity in living embryos, MO-MB is superior to conventional probes and has the potential for specific RNA visualization in basic biological and clinical research.
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Affiliation(s)
- Jianbin Chen
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
| | - Jikui Wu
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore. and College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Yunhan Hong
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore.
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38
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Kolevzon N, Hashoul D, Naik S, Rubinstein A, Yavin E. Single point mutation detection in living cancer cells by far-red emitting PNA-FIT probes. Chem Commun (Camb) 2016; 52:2405-7. [PMID: 26735489 DOI: 10.1039/c5cc07502e] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peptide nucleic acid bis-quinoline conjugates are reported as attractive far-red emitting probes that detect mutated mRNA in living cells at SNP resolution.
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Affiliation(s)
- N Kolevzon
- The Institute for Drug Research, The School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem 91120, Israel.
| | - D Hashoul
- The Institute for Drug Research, The School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem 91120, Israel.
| | - S Naik
- The Institute for Drug Research, The School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem 91120, Israel.
| | - A Rubinstein
- The Institute for Drug Research, The School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem 91120, Israel.
| | - E Yavin
- The Institute for Drug Research, The School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem 91120, Israel.
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DNA-Dye-Conjugates: Conformations and Spectra of Fluorescence Probes. PLoS One 2016; 11:e0160229. [PMID: 27467071 PMCID: PMC4965132 DOI: 10.1371/journal.pone.0160229] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 07/16/2016] [Indexed: 02/04/2023] Open
Abstract
Extensive molecular-dynamics (MD) simulations have been used to investigate DNA-dye and DNA-photosensitizer conjugates, which act as reactants in templated reactions leading to the generation of fluorescent products in the presence of specific desoxyribonucleic acid sequences (targets). Such reactions are potentially suitable for detecting target nucleic acids in live cells by fluorescence microscopy or flow cytometry. The simulations show how the attached dyes/photosensitizers influence DNA structure and reveal the relative orientations of the chromophores with respect to each other. Our results will help to optimize the reactants for the templated reactions, especially length and structure of the spacers used to link reporter dyes or photosensitizers to the oligonucleotides responsible for target recognition. Furthermore, we demonstrate that the structural ensembles obtained from the simulations can be used to calculate steady-state UV-vis absorption and emission spectra. We also show how important quantities describing the quenching of the reporter dye via fluorescence resonance energy transfer (FRET) can be calculated from the simulation data, and we compare these for different relative chromophore geometries.
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40
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Kashida H, Morimoto K, Asanuma H. A stem-less probe using spontaneous pairing between Cy3 and quencher for RNA detection. SCIENCE AND TECHNOLOGY OF ADVANCED MATERIALS 2016; 17:267-273. [PMID: 27877879 PMCID: PMC5101869 DOI: 10.1080/14686996.2016.1182412] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 03/30/2016] [Accepted: 04/05/2016] [Indexed: 05/26/2023]
Abstract
We herein report a stem-less probe for the detection of RNA that depends on pairing between Cy3 and nitro methyl red. In our design, two Cy3 residues and two nitro methyl red residues were introduced into an oligonucleotide. In the absence of the target, these dyes formed a complex, and emission of Cy3 was efficiently quenched. Hybridization with the target RNA disrupted this interaction and resulted in Cy3 emission. Under optimized conditions, the signal to background ratio was as high as 180. We demonstrated specific detection of target RNA in cells using a wash-free FISH protocol.
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Affiliation(s)
- Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya464-8603, Japan
- Japan Science and Technology Agency, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama332-0012, Japan
| | - Kazuhiro Morimoto
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya464-8603, Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya464-8603, Japan
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41
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Hövelmann F, Seitz O. DNA Stains as Surrogate Nucleobases in Fluorogenic Hybridization Probes. Acc Chem Res 2016; 49:714-23. [PMID: 26963493 DOI: 10.1021/acs.accounts.5b00546] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The increasing importance assigned to RNA dynamics in cells and tissues calls for probe molecules that enable fluorescence microscopy imaging in live cells. To achieve this goal, fluorescence dyes are conjugated with oligonucleotides so as to provide strong emission upon hybridization with the target molecule. The impressive 10(3)-fold fluorescence intensification observed when DNA stains such as thiazole orange (TO) interact with double-stranded DNA is intriguing and prompted the exploration of oligonucleotide conjugates. However, nonspecific interactions of DNA stains with polynucleotides tend to increase background, which would affect the contrast achievable in live-cell imaging. This Account describes the development of DNA-stain-labeled hybridization probes that provide high signal-to-background. We focus on our contributions in context with related advances from other laboratories. The emphasis will be on the requirements of RNA imaging in live cells. To reduce background, intercalator dyes such as TO were appended to peptide nucleic acid (PNA), which is less avidly recognized by DNA stains than DNA/RNA. Constraining the TO dye as a nucleobase surrogate in "forced intercalation (FIT) probes" improved the target specificity, presumably by helping to prevent unspecific interactions. The enforcement of TO intercalation between predetermined base pairs upon formation of the probe-target duplex provided for high brightness and enabled match/mismatch selectivity beyond stringency of hybridization. We show examples that highlight the use of PNA FIT probes in the imaging of mRNA, miRNA, and lncRNA in living cells. The "FIT approach" was recently extended to DNA probes. Signal brightness can become limiting when low-abundance targets ought to be visualized over cellular autofluorescence. We discuss strategies that further the brightness of signaling by FIT probes. Multilabeling with identical dyes does not solve the brightness issue. To avoid self-quenching, we combined two different yet spectrally overlapping fluorescent base surrogates. A hybridization-sensitive dye serves as a light collector that transfers energy to a brightly emissive acceptor dye. To improve the brilliance of single-dye probes, the "TO-nucleotide" was accompanied by an adjacent locked nucleic acid (LNA) unit. The LNA-constrained FIT probes are responsive and bright, enabling the tracking of mRNA transport in living tissue. We also show that the color repertoire of FIT probes is not restricted to the green-emissive TO but can be expanded to cyan and red. A new base surrogate (4,4-linked bisquinoline) provided up to 195-fold enhancement of the fluorescence.
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Affiliation(s)
- Felix Hövelmann
- Department of Chemistry, Humboldt University Berlin, Brook-Taylor-Str.
2, 12489 Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt University Berlin, Brook-Taylor-Str.
2, 12489 Berlin, Germany
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42
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Fontenete S, Leite M, Cappoen D, Santos R, Ginneken CV, Figueiredo C, Wengel J, Cos P, Azevedo NF. Fluorescence In Vivo Hybridization (FIVH) for Detection of Helicobacter pylori Infection in a C57BL/6 Mouse Model. PLoS One 2016; 11:e0148353. [PMID: 26848853 PMCID: PMC4743915 DOI: 10.1371/journal.pone.0148353] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 01/18/2016] [Indexed: 12/30/2022] Open
Abstract
INTRODUCTION In this study, we applied fluorescence in vivo hybridization (FIVH) using locked nucleic acid (LNA) probes targeting the bacterial rRNA gene for in vivo detection of H. pylori infecting the C57BL/6 mouse model. A previously designed Cy3_HP_LNA/2OMe_PS probe, complementary to a sequence of the H. pylori 16S rRNA gene, was used. First, the potential cytotoxicity and genotoxicity of the probe was assessed by commercial assays. Further, the performance of the probe for detecting H. pylori at different pH conditions was tested in vitro, using fluorescence in situ hybridization (FISH). Finally, the efficiency of FIVH to detect H. pylori SS1 strain in C57BL/6 infected mice was evaluated ex vivo in mucus samples, in cryosections and paraffin-embedded sections by epifluorescence and confocal microscopy. RESULTS H. pylori SS1 strain infecting C57BL/6 mice was successfully detected by the Cy3_HP_LNA/2OMe_PS probe in the mucus, attached to gastric epithelial cells and colonizing the gastric pits. The specificity of the probe for H. pylori was confirmed by microscopy. CONCLUSIONS In the future this methodology can be used in combination with a confocal laser endomicroscope for in vivo diagnosis of H. pylori infection using fluorescent LNA probes, which would be helpful to obtain an immediate diagnosis. Our results proved for the first time that FIVH method is applicable inside the body of a higher-order animal.
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Affiliation(s)
- Sílvia Fontenete
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
- ICBAS, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
| | - Marina Leite
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Davie Cappoen
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Rita Santos
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Laboratory of General Biochemistry and Physical Pharmacy, Ghent University, Gent, Belgium
| | - Chris Van Ginneken
- Laboratory of Applied Veterinary Morphology, Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Céu Figueiredo
- i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- FMUP, Faculty of Medicine of the University of Porto, University, Porto, Portugal
| | - Jesper Wengel
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Paul Cos
- Laboratory of Microbiology, Parasitology and Hygiene (LMPH), Faculty of Pharmaceutical, Biomedical and Veterinary Sciences, University of Antwerp, Antwerp, Belgium
| | - Nuno Filipe Azevedo
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
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Hövelmann F, Gaspar I, Chamiolo J, Kasper M, Steffen J, Ephrussi A, Seitz O. LNA-enhanced DNA FIT-probes for multicolour RNA imaging. Chem Sci 2016; 7:128-135. [PMID: 29861973 PMCID: PMC5950760 DOI: 10.1039/c5sc03053f] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 11/01/2015] [Indexed: 01/04/2023] Open
Abstract
The simultaneous imaging of different RNA molecules in homogeneous solution is a challenge and requires optimisation to enable unambiguous staining of intracellular RNA targets. Our approach relies on single dye forced intercalation (FIT) probes, in which a visco-sensitive reporter of the thiazole orange (TO) family serves as a surrogate nucleobase and provides enhancements of fluorescence upon hybridisation. Previous FIT probes spanned the cyan and green emission range. Herein, we report for the first time chromophores for FIT probes that emit in the red range (above 600 nm). Such probes are valuable to overcome cellular auto-fluorescent background and enable multiplexed detection. In order to find suitable chromophores, we developed a submonomer approach that facilitated the rapid analysis of different TO family dyes in varied sequence positions. A carboxymethylated 4,4'-methine linked cyanine, which we named quinoline blue (QB), provided exceptional response characteristics at the 605 nm emission maximum. Exceeding previously reported base surrogates, the emission of the QB nucleotide intensified by up to 195-fold upon binding of complementary RNA. Owing to large extinction coefficients and quantum yields (up to ε = 129.000 L mol-1 cm-1 and Φ = 0.47, respectively) QB-FIT probes enable imaging of intracellular mRNA. A mixture of BO-, TO- and QB-containing FIT probes allowed the simultaneous detection of three different RNA targets in homogenous solution. TO- and QB-FIT probes were used to localize oskar mRNA and other polyadenylated mRNA molecules in developing oocytes from Drosphila melanogaster by means of wash-free fluorescent in situ hybridisation and super resolution microscopy (STED).
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Affiliation(s)
- F Hövelmann
- Department of Chemistry , Humboldt University Berlin , Brook-Taylor-Str. 2 , D-12489 Berlin , Germany .
- European Molecular Biology Laboratory (EMBL) Heidelberg , Meyerhofstr. 1 , 69117 Heidelberg , Germany
| | - I Gaspar
- European Molecular Biology Laboratory (EMBL) Heidelberg , Meyerhofstr. 1 , 69117 Heidelberg , Germany
| | - J Chamiolo
- Department of Chemistry , Humboldt University Berlin , Brook-Taylor-Str. 2 , D-12489 Berlin , Germany .
| | - M Kasper
- Department of Chemistry , Humboldt University Berlin , Brook-Taylor-Str. 2 , D-12489 Berlin , Germany .
| | - J Steffen
- Department of Chemistry , Humboldt University Berlin , Brook-Taylor-Str. 2 , D-12489 Berlin , Germany .
| | - A Ephrussi
- European Molecular Biology Laboratory (EMBL) Heidelberg , Meyerhofstr. 1 , 69117 Heidelberg , Germany
| | - O Seitz
- Department of Chemistry , Humboldt University Berlin , Brook-Taylor-Str. 2 , D-12489 Berlin , Germany .
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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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Rastede EE, Tanha M, Yaron D, Watkins SC, Waggoner AS, Armitage BA. Spectral fine tuning of cyanine dyes: electron donor-acceptor substituted analogues of thiazole orange. Photochem Photobiol Sci 2015; 14:1703-12. [PMID: 26171668 PMCID: PMC4557812 DOI: 10.1039/c5pp00117j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Accepted: 07/02/2015] [Indexed: 12/21/2022]
Abstract
The introduction of electron donor and acceptor groups at strategic locations on a fluorogenic cyanine dye allows fine-tuning of the absorption and emission spectra while preserving the ability of the dye to bind to biomolecular hosts such as double-stranded DNA and a single-chain antibody fragment originally selected for binding to the parent unsubstituted dye, thiazole orange (TO). The observed spectral shifts are consistent with calculated HOMO-LUMO energy gaps and reflect electron density localization on the quinoline half of TO in the LUMO. A dye bearing donating methoxy and withdrawing trifluoromethyl groups on the benzothiazole and quinoline rings, respectively, shifts the absorption spectrum to sufficiently longer wavelengths to allow excitation at green wavelengths as opposed to the parent dye, which is optimally excited in the blue.
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Affiliation(s)
- Elizabeth E Rastede
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.
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46
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Oomoto I, Suzuki-Hirano A, Umeshima H, Han YW, Yanagisawa H, Carlton P, Harada Y, Kengaku M, Okamoto A, Shimogori T, Wang DO. ECHO-liveFISH: in vivo RNA labeling reveals dynamic regulation of nuclear RNA foci in living tissues. Nucleic Acids Res 2015; 43:e126. [PMID: 26101260 PMCID: PMC4627062 DOI: 10.1093/nar/gkv614] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2015] [Accepted: 06/01/2015] [Indexed: 02/07/2023] Open
Abstract
Elucidating the dynamic organization of nuclear RNA foci is important for understanding and manipulating these functional sites of gene expression in both physiological and pathological states. However, such studies have been difficult to establish in vivo as a result of the absence of suitable RNA imaging methods. Here, we describe a high-resolution fluorescence RNA imaging method, ECHO-liveFISH, to label endogenous nuclear RNA in living mice and chicks. Upon in vivo electroporation, exciton-controlled sequence-specific oligonucleotide probes revealed focally concentrated endogenous 28S rRNA and U3 snoRNA at nucleoli and poly(A) RNA at nuclear speckles. Time-lapse imaging reveals steady-state stability of these RNA foci and dynamic dissipation of 28S rRNA concentrations upon polymerase I inhibition in native brain tissue. Confirming the validity of this technique in a physiological context, the in vivo RNA labeling did not interfere with the function of target RNA nor cause noticeable cytotoxicity or perturbation of cellular behavior.
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Affiliation(s)
- Ikumi Oomoto
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan Graduate School of Biostudies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Asuka Suzuki-Hirano
- Brain Science Institute, RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan JSPS Research fellow, Japan Society of Promotion of Science, 5-3-1 Kojimachi, Chiyoda-ku,Tokyo 102-0083, Japan
| | - Hiroki Umeshima
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yong-Woon Han
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Hiroyuki Yanagisawa
- Advanced Science Institute, RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan
| | - Peter Carlton
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshie Harada
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan Graduate School of Biostudies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Mineko Kengaku
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan Graduate School of Biostudies, Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Akimitsu Okamoto
- Advanced Science Institute, RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan Research Center for Advanced Science and Technology, University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8904, Japan
| | - Tomomi Shimogori
- Brain Science Institute, RIKEN, Hirosawa, Wako City, Saitama 351-0198, Japan
| | - Dan Ohtan Wang
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
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47
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Gaspar I, Ephrussi A. Strength in numbers: quantitative single-molecule RNA detection assays. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2015; 4:135-50. [PMID: 25645249 PMCID: PMC5024021 DOI: 10.1002/wdev.170] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 12/02/2014] [Indexed: 01/19/2023]
Abstract
Gene expression is a fundamental process that underlies development, homeostasis, and behavior of organisms. The fact that it relies on nucleic acid intermediates, which can specifically interact with complementary probes, provides an excellent opportunity for studying the multiple steps—transcription, RNA processing, transport, translation, degradation, and so forth—through which gene function manifests. Over the past three decades, the toolbox of nucleic acid science has expanded tremendously, making high‐precision in situ detection of DNA and RNA possible. This has revealed that many—probably the vast majority of—transcripts are distributed within the cytoplasm or the nucleus in a nonrandom fashion. With the development of microscopy techniques we have learned not only about the qualitative localization of these molecules but also about their absolute numbers with great precision. Single‐molecule techniques for nucleic acid detection have been transforming our views of biology with elementary power: cells are not average members of their population but are highly distinct individuals with greatly and suddenly changing gene expression, and this behavior of theirs can be measured, modeled, and thus predicted and, finally, comprehended. WIREs Dev Biol 2015, 4:135–150. doi: 10.1002/wdev.170 For further resources related to this article, please visit the
WIREs website. Conflict of interest: The authors have declared no conflicts of interest for this article.
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Affiliation(s)
- Imre Gaspar
- Developmental Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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48
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Murayama K, Kashida H, Asanuma H. Acyclic
l-threoninol nucleic acid (l-aTNA) with suitable structural rigidity cross-pairs with DNA and RNA. Chem Commun (Camb) 2015; 51:6500-3. [DOI: 10.1039/c4cc09244a] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We newly synthesized l-aTNA, which showed the best affinity to DNA and RNA among acyclic nucleic acids with phosphodiester linkages.
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Affiliation(s)
- Keiji Murayama
- Department of Molecular Design and Engineering
- Graduate School of Engineering
- Nagoya University
- Nagoya 464-8603
- Japan
| | - Hiromu Kashida
- Department of Molecular Design and Engineering
- Graduate School of Engineering
- Nagoya University
- Nagoya 464-8603
- Japan
| | - Hiroyuki Asanuma
- Department of Molecular Design and Engineering
- Graduate School of Engineering
- Nagoya University
- Nagoya 464-8603
- Japan
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49
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Spille JH, Kubitscheck U. Labelling and imaging of single endogenous messenger RNA particles in vivo. J Cell Sci 2015; 128:3695-706. [DOI: 10.1242/jcs.166728] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
ABSTRACT
RNA molecules carry out widely diverse functions in numerous different physiological processes in living cells. The RNA life cycle from transcription, through the processing of nascent RNA, to the regulatory function of non-coding RNA and cytoplasmic translation of messenger RNA has been studied extensively using biochemical and molecular biology techniques. In this Commentary, we highlight how single molecule imaging and particle tracking can yield further insight into the dynamics of RNA particles in living cells. In the past few years, a variety of bright and photo-stable labelling techniques have been developed to generate sufficient contrast for imaging of single endogenous RNAs in vivo. New imaging modalities allow determination of not only lateral but also axial positions with high precision within the cellular context, and across a wide range of specimen from yeast and bacteria to cultured cells, and even multicellular organisms or live animals. A whole range of methods to locate and track single particles, and to analyze trajectory data are available to yield detailed information about the kinetics of all parts of the RNA life cycle. Although the concepts presented are applicable to all types of RNA, we showcase here the wealth of information gained from in vivo imaging of single particles by discussing studies investigating dynamics of intranuclear trafficking, nuclear pore transport and cytoplasmic transport of endogenous messenger RNA.
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Affiliation(s)
- Jan-Hendrik Spille
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegeler Str. 12, Bonn 53115, Germany
| | - Ulrich Kubitscheck
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms-University Bonn, Wegeler Str. 12, Bonn 53115, Germany
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50
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Sato SI, Watanabe M, Katsuda Y, Murata A, Wang DO, Uesugi M. Live-Cell Imaging of Endogenous mRNAs with a Small Molecule. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201410339] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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