1
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Mannully ST, Mahajna R, Nazzal H, Maree S, Zheng H, Appella DH, Reich R, Yavin E. Detecting the FLJ22447 lncRNA in Ovarian Cancer with Cyclopentane-Modified FIT-PNAs (cpFIT-PNAs). Biomolecules 2024; 14:609. [PMID: 38927013 PMCID: PMC11202290 DOI: 10.3390/biom14060609] [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: 04/01/2024] [Revised: 05/13/2024] [Accepted: 05/16/2024] [Indexed: 06/28/2024] Open
Abstract
Ovarian cancer (OC) is one of the most lethal gynecologic cancers that is typically diagnosed at the very late stage of disease progression. Thus, there is an unmet need to develop diagnostic probes for early detection of OC. One approach may rely on RNA as a molecular biomarker. In this regard, FLJ22447 lncRNA is an RNA biomarker that is over-expressed in ovarian cancer (OC) and in cancer-associated fibroblasts (CAFs). CAFs appear early on in OC as they provide a metastatic niche for OC progression. FIT-PNAs (forced intercalation-peptide nucleic acids) are DNA analogs that are designed to fluoresce upon hybridization to their complementary RNA target sequence. In recent studies, we have shown that the introduction of cyclopentane PNAs into FIT-PNAs (cpFIT-PNA) results in superior RNA sensors. Herein, we report the design and synthesis of cpFIT-PNAs for the detection of this RNA biomarker in living OC cells (OVCAR8) and in CAFs. cpFIT-PNA was compared to FIT-PNA and the cell-penetrating peptide (CPP) of choice was either a simple one (four L-lysines) or a CPP with enhanced cellular uptake (CLIP6). The combination of CLIP6 with cpFIT-PNA resulted in a superior sensing of FLJ22447 lncRNA in OVCAR8 cells as well as in CAFs. Moreover, incubation of CLIP6-cpFIT-PNA in OVCAR8 cells leads to a significant decrease (ca. 60%) in FLJ22447 lncRNA levels and in cell viability, highlighting the potential theranostic use of such molecules.
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Affiliation(s)
- Sheethal Thomas Mannully
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem 91120, Israel; (S.T.M.); (R.M.); (H.N.); (S.M.); (R.R.)
| | - Rawan Mahajna
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem 91120, Israel; (S.T.M.); (R.M.); (H.N.); (S.M.); (R.R.)
| | - Huda Nazzal
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem 91120, Israel; (S.T.M.); (R.M.); (H.N.); (S.M.); (R.R.)
| | - Salam Maree
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem 91120, Israel; (S.T.M.); (R.M.); (H.N.); (S.M.); (R.R.)
| | - 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, MD 20892, USA; (H.Z.); (D.H.A.)
| | - 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, MD 20892, USA; (H.Z.); (D.H.A.)
| | - Reuven Reich
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem 91120, Israel; (S.T.M.); (R.M.); (H.N.); (S.M.); (R.R.)
| | - Eylon Yavin
- Institute for Drug Research, School of Pharmacy, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem 91120, Israel; (S.T.M.); (R.M.); (H.N.); (S.M.); (R.R.)
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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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Shen S, Xu W, Lu J, Wang S, Huang Y, Zeng X, Xiao W, Yin J. Recent progress on fluorescent probes for viruses. CHINESE CHEM LETT 2023. [DOI: 10.1016/j.cclet.2023.108360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2023]
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4
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Swenson C, Argueta-Gonzalez HS, Sterling SA, Robichaux R, Knutson SD, Heemstra JM. Forced Intercalation Peptide Nucleic Acid Probes for the Detection of an Adenosine-to-Inosine Modification. ACS OMEGA 2023; 8:238-248. [PMID: 36643573 PMCID: PMC9835161 DOI: 10.1021/acsomega.2c03568] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
The deamination of adenosine to inosine is an important modification in nucleic acids that functionally recodes the identity of the nucleobase to a guanosine. Current methods to analyze and detect this single nucleotide change, such as sequencing and PCR, typically require time-consuming or costly procedures. Alternatively, fluorescent "turn-on" probes that result in signal enhancement in the presence of target are useful tools for real-time detection and monitoring of nucleic acid modification. Here we describe forced-intercalation PNA (FIT-PNA) probes that are designed to bind to inosine-containing nucleic acids and use thiazole orange (TO), 4-dimethylamino-naphthalimide (4DMN), and malachite green (MG) fluorogenic dyes to detect A-to-I editing events. We show that incorporation of the dye as a surrogate base negatively affects the duplex stability but does not abolish binding to targets. We then determined that the identity of the adjacent nucleobase and temperature affect the overall signal and fluorescence enhancement in the presence of inosine, achieving an 11-fold increase, with a limit of detection (LOD) of 30 pM. We determine that TO and 4DMN probes are viable candidates to enable selective inosine detection for biological applications.
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Affiliation(s)
- Colin
S. Swenson
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | | | - Sierra A. Sterling
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Ryan Robichaux
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Steve D. Knutson
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Jennifer M. Heemstra
- Department
of Chemistry, Emory University, Atlanta, Georgia 30322, United States
- Department
of Chemistry, Washington University, St. Louis, Missouri 63130, United States
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5
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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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6
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Liu B, Vonhausen Y, Schulz A, Höbartner C, Würthner F. Peptide Backbone Directed Self‐Assembly of Merocyanine Oligomers into Duplex Structures. Angew Chem Int Ed Engl 2022; 61:e202200120. [PMID: 35194914 PMCID: PMC9401582 DOI: 10.1002/anie.202200120] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Indexed: 11/10/2022]
Abstract
The pseudopeptide backbone provided by N‐(2‐aminoethyl)‐glycine oligomers with attached nucleobases has been widely utilized in peptide nucleic acids (PNAs) as DNA mimics. Here we demonstrate the suitability of this backbone for the formation of structurally defined dye stacks. Toward this goal a series of peptide merocyanine (PMC) dye oligomers connected to a N‐(2‐aminoethyl)‐glycine backbone were prepared through peptide synthesis. Our concentration‐, temperature‐ and solvent‐dependent UV/Vis absorption studies show that under the control of dipole–dipole interactions, smaller‐sized oligomers consisting of one, two or three dyes self‐assemble into defined duplex structures containing two up to six chromophores. In contrast, upon further extension of the oligomer, the chosen peptide backbone cannot direct the formation of a defined duplex architecture anymore due to intramolecular aggregation between the dyes. For all aggregate species a moderate aggregation‐induced emission enhancement is observed.
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Affiliation(s)
- Bin Liu
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Yvonne Vonhausen
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Alexander Schulz
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Claudia Höbartner
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC) Universität Würzburg Theodor-Boveri-Weg 97074 Würzburg Germany
| | - Frank Würthner
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC) Universität Würzburg Theodor-Boveri-Weg 97074 Würzburg Germany
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7
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Liu B, Vonhausen Y, Schulz A, Höbartner C, Würthner F. Peptide Backbone Directed Self‐Assembly of Merocyanine Oligomers into Duplex Structures. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Bin Liu
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Yvonne Vonhausen
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Alexander Schulz
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
| | - Claudia Höbartner
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC) Universität Würzburg Theodor-Boveri-Weg 97074 Würzburg Germany
| | - Frank Würthner
- Institut für Organische Chemie Universität Würzburg Am Hubland 97074 Würzburg Germany
- Center for Nanosystems Chemistry (CNC) Universität Würzburg Theodor-Boveri-Weg 97074 Würzburg Germany
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8
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Bustamante-Jaramillo LF, Fingal J, Blondot ML, Rydell GE, Kann M. Imaging of Hepatitis B Virus Nucleic Acids: Current Advances and Challenges. Viruses 2022; 14:v14030557. [PMID: 35336964 PMCID: PMC8950347 DOI: 10.3390/v14030557] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 01/30/2022] [Accepted: 03/01/2022] [Indexed: 11/16/2022] Open
Abstract
Hepatitis B virus infections are the main reason for hepatocellular carcinoma development. Current treatment reduces the viral load but rarely leads to virus elimination. Despite its medical importance, little is known about infection dynamics on the cellular level not at least due to technical obstacles. Regardless of infections leading to extreme viral loads, which may reach 1010 virions per mL serum, hepatitis B viruses are of low abundance and productivity in individual cells. Imaging of the infections in cells is thus a particular challenge especially for cccDNA that exists only in a few copies. The review describes the significance of microscopical approaches on genome and transcript detection for understanding hepatitis B virus infections, implications for understanding treatment outcomes, and recent microscopical approaches, which have not been applied in HBV research.
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Affiliation(s)
- Luisa F. Bustamante-Jaramillo
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden; (L.F.B.-J.); (J.F.); (G.E.R.)
| | - Joshua Fingal
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden; (L.F.B.-J.); (J.F.); (G.E.R.)
| | - Marie-Lise Blondot
- Microbiologie Fondamentale et Pathogénicité (MFP), CNRS UMR 5234, University of Bordeaux, 33076 Bordeaux, France;
| | - Gustaf E. Rydell
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden; (L.F.B.-J.); (J.F.); (G.E.R.)
| | - Michael Kann
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden; (L.F.B.-J.); (J.F.); (G.E.R.)
- Region Västra Götaland, Department of Clinical Microbiology, Sahlgrenska University Hospital, 405 30 Gothenburg, Sweden
- Correspondence:
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9
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Tepper O, Peled I, Fastman Y, Heinberg A, Mitesser V, Dzikowski R, Yavin E. FIT-PNAs as RNA-Sensing Probes for Drug-Resistant Plasmodium falciparum. ACS Sens 2022; 7:50-59. [PMID: 34985283 DOI: 10.1021/acssensors.1c01481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Detecting RNA at single-nucleotide resolution is a formidable task. Plasmodium falciparum is the deadliest form of malaria in humans and has shown to gain resistance to essentially all antimalarial drugs including artemisinin and chloroquine. Some of these drug resistances are associated with single-nucleotide polymorphisms (SNPs). Forced-intercalation peptide nucleic acids (FIT-PNAs) are DNA mimics that are designed as RNA-sensing molecules that fluoresce upon hybridization to their complementary (RNA) targets. We have previously designed and synthesized FIT-PNAs that target the C580Y SNP in the K13 gene of P. falciparum. In addition, we have now prepared FIT-PNAs that target the K76T SNP in the CRT gene of P. falciparum. Both SNPs are common ones associated with artemisinin and chloroquine drug resistance, respectively. Our FIT-PNAs are conjugated to a simple cell-penetrating peptide (CPP) that consists of eight d-lysines (dK8), which renders these FIT-PNAs cell-permeable to infected red blood cells (iRBCs). Herein, we demonstrate that FIT-PNAs clearly discriminate between wild-type (WT) strains (NF54-WT: artemisinin-sensitive or chloroquine-sensitive) and mutant strains (NF54-C580Y: artemisinin-resistant or Dd2: chloroquine-resistant) of P. falciparum parasites. Simple incubation of FIT-PNAs with live blood-stage parasites results in a substantial difference in fluorescence as corroborated by FACS analysis and confocal microscopy. We foresee FIT-PNAs as molecular probes that will provide a fast, simple, and cheap means for the assessment of drug resistance in malaria─a tool that would be highly desirable for the optimal choice of antimalarial treatment in endemic countries.
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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
| | - Itamar Peled
- The Institute for Drug Research, The School of Pharmacy, The Faculty of Medicine, The Hebrew University of Jerusalem, Hadassah Ein-Kerem, Jerusalem 9112102, Israel
| | - Yair Fastman
- 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
| | - Adina Heinberg
- 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
| | - Vera Mitesser
- 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
| | - 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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10
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Brodyagin N, Katkevics M, Kotikam V, Ryan CA, Rozners E. Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications. Beilstein J Org Chem 2021; 17:1641-1688. [PMID: 34367346 PMCID: PMC8313981 DOI: 10.3762/bjoc.17.116] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 06/28/2021] [Indexed: 12/23/2022] Open
Abstract
Peptide nucleic acid (PNA) is arguably one of the most successful DNA mimics, despite a most dramatic departure from the native structure of DNA. The present review summarizes 30 years of research on PNA's chemistry, optimization of structure and function, applications as probes and diagnostics, and attempts to develop new PNA therapeutics. The discussion starts with a brief review of PNA's binding modes and structural features, followed by the most impactful chemical modifications, PNA enabled assays and diagnostics, and discussion of the current state of development of PNA therapeutics. While many modifications have improved on PNA's binding affinity and specificity, solubility and other biophysical properties, the original PNA is still most frequently used in diagnostic and other in vitro applications. Development of therapeutics and other in vivo applications of PNA has notably lagged behind and is still limited by insufficient bioavailability and difficulties with tissue specific delivery. Relatively high doses are required to overcome poor cellular uptake and endosomal entrapment, which increases the risk of toxicity. These limitations remain unsolved problems waiting for innovative chemistry and biology to unlock the full potential of PNA in biomedical applications.
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Affiliation(s)
- Nikita Brodyagin
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Martins Katkevics
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga, LV-1006, Latvia
| | - Venubabu Kotikam
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Christopher A Ryan
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, New York 13902, United States
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11
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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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12
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Duan W, Huang F, Bi Y, Zhu L, Wang D, Liu Y, Wu J, Ge Y, Liu D. Design, synthesis and cell imaging of a simple peptide-based probe for the selective detection of RNA. Chem Commun (Camb) 2021; 57:2653-2656. [PMID: 33587737 DOI: 10.1039/d0cc06508k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we present a novel peptide-based fluorescent "turn-on" molecule P1 for detecting RNA, in a double or single strand, AU-rich or CG-rich. Both computational and experimental studies indicate that the detection efficiency depends on the binding affinity of P1 and conformational changes. P1 could be applied for cell imaging without any additional transfection vectors. Selective detection of RNA in cells was determined by RNase digestion. Successful application of P1 for RNA imaging in cell mitosis reveals that it may have broad applications in research, biotechnology and medical science.
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Affiliation(s)
- Wenxiu Duan
- Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, China.
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13
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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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14
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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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15
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Samanta D, Ebrahimi SB, Mirkin CA. Nucleic-Acid Structures as Intracellular Probes for Live Cells. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1901743. [PMID: 31271253 PMCID: PMC6942251 DOI: 10.1002/adma.201901743] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/08/2019] [Indexed: 05/02/2023]
Abstract
The chemical composition of cells at the molecular level determines their growth, differentiation, structure, and function. Probing this composition is powerful because it provides invaluable insight into chemical processes inside cells and in certain cases allows disease diagnosis based on molecular profiles. However, many techniques analyze fixed cells or lysates of bulk populations, in which information about dynamics and cellular heterogeneity is lost. Recently, nucleic-acid-based probes have emerged as a promising platform for the detection of a wide variety of intracellular analytes in live cells with single-cell resolution. Recent advances in this field are described and common strategies for probe design, types of targets that can be identified, current limitations, and future directions are discussed.
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Affiliation(s)
- Devleena Samanta
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Sasha B Ebrahimi
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
| | - Chad A Mirkin
- Department of Chemistry and International Institute for Nanotechnology, Northwestern University, 2145 Sheridan Road, Evanston, IL, 60208, USA
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16
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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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17
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Abdelhameed A, Liao X, McElroy CA, Joice AC, Rakotondraibe L, Li J, Slebodnick C, Guo P, Wilson WD, Werbovetz KA. Synthesis and antileishmanial evaluation of thiazole orange analogs. Bioorg Med Chem Lett 2020; 30:126725. [DOI: 10.1016/j.bmcl.2019.126725] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/26/2019] [Accepted: 09/28/2019] [Indexed: 01/10/2023]
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18
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RNA imaging by chemical probes. Adv Drug Deliv Rev 2019; 147:44-58. [PMID: 31398387 DOI: 10.1016/j.addr.2019.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 07/02/2019] [Accepted: 08/02/2019] [Indexed: 12/29/2022]
Abstract
Sequence-specific detection of intracellular RNA is one of the most important approaches to understand life phenomena. However, it is difficult to detect RNA in living cells because of its variety and scarcity. In the last three decades, several chemical probes have been developed for RNA detection in living cells. These probes are composed of DNA or artificial nucleic acid and hybridize with the target RNA in a sequence-specific manner. This hybridization triggers a change of fluorescence or a chemical reaction. In this review, we classify the probes according to the associated fluorogenic mechanism, that is, interaction between fluorophore and quencher, environmental change of fluorophore, and template reaction with/without ligation. In addition, we introduce examples of RNA imaging in living cells.
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19
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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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20
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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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21
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Steinmeyer J, Walter HK, Bichelberger MA, Schneider V, Kubař T, Rönicke F, Olshausen B, Nienhaus K, Nienhaus GU, Schepers U, Elstner M, Wagenknecht HA. "siRNA traffic lights": arabino-configured 2'-anchors for fluorescent dyes are key for dual color readout in cell imaging. Org Biomol Chem 2019; 16:3726-3731. [PMID: 29565089 DOI: 10.1039/c8ob00417j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Two fluorescent dyes covalently attached in diagonal interstrand orientation to siRNA undergo energy transfer and thereby enable a dual color fluorescence readout (red/green) for hybridization. Three different structural variations were carried out and compared by their optical properties, including (i) the base surrogate approach with an acyclic linker as a substitute of the 2-deoxyriboside between the phosphodiester bridges, (ii) the 2'-modification of conventional ribofuranosides and (iii) the arabino-configured 2'-modification. The double stranded siRNA with the latter type of modification delivered the best energy transfer efficiency, which was explained by molecular dynamics simulations that showed that the two dyes are more flexible at the arabino-configured sugars compared to the completely stacked situation at the ribo-configured ones. Single molecule fluorescence lifetime measurements indicate their application in fluorescence cell imaging, which reveals a red/green fluorescence contrast in particular for the arabino-configured 2'-modification by the two dyes, which is key for tracking of siRNA transport into HeLa cells.
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Affiliation(s)
- Jeannine Steinmeyer
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany. Wagenknecht @kit.edu
| | - Heidi-Kristin Walter
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany. Wagenknecht @kit.edu
| | - Mathilde A Bichelberger
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Violetta Schneider
- Institute of Physical Chemistry and Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Tomáš Kubař
- Institute of Physical Chemistry and Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Franziska Rönicke
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany. Wagenknecht @kit.edu
| | - Bettina Olshausen
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Karin Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Gerd Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany and Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany and Department of Physics, University of Illinois at Urbana-Champaign, 1110 W. Green St, Urbana, IL 61801, USA and Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Ute Schepers
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), Eggenstein-Leopoldshafen, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry and Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany. Wagenknecht @kit.edu
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22
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Schwechheimer C, Doll L, Wagenknecht HA. Synthesis of Dye-Modified Oligonucleotides via Copper(I)-Catalyzed Alkyne Azide Cycloaddition Using On- and Off-Bead Approaches. ACTA ACUST UNITED AC 2019; 72:4.80.1-4.80.13. [PMID: 29927126 DOI: 10.1002/cpnc.47] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Fluorescence molecular imaging is widely used to visualize and observe different biomolecules, in particular DNA and RNA, in vivo and in real time. Typically, DNA strands are tagged with only one fluorophore, and, in the case of molecular beacons, an additional quencher is conjugated, which bears the risk of false-positive or false-negative results because only fluorescence intensities at one fluorescence wavelength (color) are compared. To address this drawback, the concept of "DNA/RNA traffic lights," which is characterized by a fluorescence color change due to energy transfer between two dyes, was developed by our working group. For these DNA and RNA systems, the oligonucleotides are post-synthetically labeled, specifically after solid-phase synthesis by chemical means, with a fluorescent dye using copper(I)-catalyzed cycloaddition at the 2' position of single uridines. In order to functionalize oligonucleotides with several different labels, an on-resin method is required to ensure the necessary selectivity. This unit describes two different CuAAC ("click") approaches-in solution (post-synthetic) and on solid phase (during synthesis)-for the attachment of fluorophores to the 2' position of DNA. © 2018 by John Wiley & Sons, Inc.
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Affiliation(s)
| | - Larissa Doll
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
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23
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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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24
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Sabale P, Ambi UB, Srivatsan SG. Clickable PNA Probes for Imaging Human Telomeres and Poly(A) RNAs. ACS OMEGA 2018; 3:15343-15352. [PMID: 30556003 PMCID: PMC6289544 DOI: 10.1021/acsomega.8b02550] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 10/31/2018] [Indexed: 05/10/2023]
Abstract
The ability to bind strongly to complementary nucleic acid sequences, invade complex nucleic acid structures, and resist degradation by cellular enzymes has made peptide nucleic acid (PNA) oligomers as very useful hybridization probes in molecular diagnosis. For such applications, the PNA oligomers have to be labeled with appropriate reporters as they lack intrinsic labels that can be used in biophysical assays. Although solid-phase synthesis is commonly used to attach reporters onto PNA, development of milder and modular labeling methods will provide access to PNA oligomers labeled with a wider range of biophysical tags. Here, we describe the establishment of a postsynthetic modification strategy based on bioorthogonal chemical reactions in functionalizing PNA oligomers in solution with a variety of tags. A toolbox composed of alkyne- and azide-modified monomers were site-specifically incorporated into PNA oligomers and postsynthetically click-functionalized with various tags, ranging from sugar, amino acid, biotin, to fluorophores, by using copper(I)-catalyzed azide-alkyne cycloaddition, strain-promoted azide-alkyne cycloaddition, and Staudinger ligation reactions. As a proof of utility of this method, fluorescent PNA hybridization probes were developed and used in imaging human telomeres in chromosomes and poly(A) RNAs in cells. Taken together, this simple approach of generating a wide range of functional PNA oligomers will expand the use of PNA in molecular diagnosis.
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25
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Ge C, Huang H, Wang Y, Zhao H, Zhang P, Zhang Q. Near-Infrared Luminescent Osmium(II) Complexes with an Intrinsic RNA-Targeting Capability for Nucleolus Imaging in Living Cells. ACS APPLIED BIO MATERIALS 2018; 1:1587-1593. [DOI: 10.1021/acsabm.8b00455] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Chen Ge
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, People’s Republic of China
| | - Huaiyi Huang
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, United Kingdom
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Guangzhou 510275, People’s Republic of China
| | - Yi Wang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, People’s Republic of China
| | - Hang Zhao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, People’s Republic of China
| | - Pingyu Zhang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, People’s Republic of China
| | - Qianling Zhang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen 518060, People’s Republic of China
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26
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27
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Fang GM, Chamiolo J, Kankowski S, Hövelmann F, Friedrich D, Löwer A, Meier JC, Seitz O. A bright FIT-PNA hybridization probe for the hybridization state specific analysis of a C → U RNA edit via FRET in a binary system. Chem Sci 2018; 9:4794-4800. [PMID: 29910930 PMCID: PMC5982193 DOI: 10.1039/c8sc00457a] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 05/01/2018] [Indexed: 12/24/2022] Open
Abstract
Oligonucleotide probes that show enhanced fluorescence upon nucleic acid hybridization enable the detection and visualization of specific mRNA molecules, in vitro and in cellulo. A challenging problem is the analysis of single nucleotide alterations that occur, for example, when cellular mRNA is subject to C → U editing. Given the length required for uniqueness of the targeted segment, the commonly used probes do not provide the level of sequence specificity needed to discriminate single base mismatched hybridization. Herein we introduce a binary probe system based on fluorescence resonance energy transfer (FRET) that distinguishes three possible states i.e. (i) absence of target, (ii) presence of edited (matched) and (iii) unedited (single base mismatched) target. To address the shortcomings of read-out via FRET, we designed donor probes that avoid bleed through into the acceptor channel and nevertheless provide a high intensity of FRET signaling. We show the combined use of thiazole orange (TO) and an oxazolopyridine analogue (JO), linked as base surrogates in modified PNA FIT-probes that serve as FRET donor for a second, near-infrared (NIR)-labeled strand. In absence of target, donor emission is low and FRET cannot occur in lieu of the lacking co-alignment of probes. Hybridization of the TO/JO-PNA FIT-probe with the (unedited RNA) target leads to high brightness of emission at 540 nm. Co-alignment of the NIR-acceptor strand ensues from recognition of edited RNA inducing emission at 690 nm. We show imaging of mRNA in fixed and live cells and discuss the homogeneous detection and intracellular imaging of a single nucleotide mRNA edit used by nature to post-transcriptionally modify the function of the Glycine Receptor (GlyR).
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Affiliation(s)
- Ge-Min Fang
- Department of Chemistry , Humboldt-Universität zu Berlin , Brook-Taylor-Strasse 2 , D-12489 Berlin , Germany . .,Institute of Physical Science and Information Technology , Anhui University , Hefei , Anhui 230601 , China
| | - Jasmine Chamiolo
- Department of Chemistry , Humboldt-Universität zu Berlin , Brook-Taylor-Strasse 2 , D-12489 Berlin , Germany .
| | - Svenja Kankowski
- Zoological Institute , Technical University Braunschweig , Spielmannstr. 7 , D-38106 Braunschweig , Germany
| | - Felix Hövelmann
- Department of Chemistry , Humboldt-Universität zu Berlin , Brook-Taylor-Strasse 2 , D-12489 Berlin , Germany .
| | - Dhana Friedrich
- Max Delbrück Centrum für Molekulare Medizin , Robert Rössle Straße 10 , 13125 Berlin , Germany.,Technische Universität Darmstadt , Department of Biology , Schnittspahnstraße 13 , 64287 Darmstadt , Germany
| | - Alexander Löwer
- Max Delbrück Centrum für Molekulare Medizin , Robert Rössle Straße 10 , 13125 Berlin , Germany.,Technische Universität Darmstadt , Department of Biology , Schnittspahnstraße 13 , 64287 Darmstadt , Germany
| | - Jochen C Meier
- Zoological Institute , Technical University Braunschweig , Spielmannstr. 7 , D-38106 Braunschweig , Germany
| | - Oliver Seitz
- Department of Chemistry , Humboldt-Universität zu Berlin , Brook-Taylor-Strasse 2 , D-12489 Berlin , Germany .
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28
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Chao XJ, Wang KN, Sun LL, Cao Q, Ke ZF, Cao DX, Mao ZW. Cationic Organochalcogen with Monomer/Excimer Emissions for Dual-Color Live Cell Imaging and Cell Damage Diagnosis. ACS APPLIED MATERIALS & INTERFACES 2018; 10:13264-13273. [PMID: 29616788 DOI: 10.1021/acsami.7b12521] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Studies on the development of fluorescent organic molecules with different emission colors for imaging of organelles and their biomedical application are gaining lots of focus recently. Here, we report two cationic organochalcogens 1 and 2, both of which exhibit very weak green emission (Φ1 = 0.12%; Φ2 = 0.09%) in dilute solution as monomers, but remarkably enhanced green emission upon interaction with nucleic acids and large red-shifted emission in aggregate state by the formation of excimers at high concentration. More interestingly, the monomer emission and excimer-like emission can be used for dual color imaging of different organelles. Upon passively diffusing into cells, both probes selectively stain nucleoli with strong green emission upon 488 nm excitation, whereas upon 405 nm excitation, a completely different stain pattern by staining lysosomes (for 1) or mitochondria (for 2) with distinct red emission is observed because of the highly concentrated accumulation in these organelles. Studies on the mechanism of the accumulation in lysosomes (for 1) or mitochondria (for 2) found that the accumulations of the probes are dependent on the membrane permeabilization, which make the probes have great potential in diagnosing cell damage by sensing lysosomal or mitochondrial membrane permeabilization. The study is demonstrative, for the first time, of two cationic molecules for dual-color imaging nucleoli and lysosomes (1)/mitochondria (2) simultaneously in live cell based on monomer and excimer-like emission, respectively, and more importantly, for diagnosing cell damage.
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Affiliation(s)
- Xi-Juan Chao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry , Sun Yat-Sen University , Guangzhou 510275 , China
| | - Kang-Nan Wang
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry , Sun Yat-Sen University , Guangzhou 510275 , China
| | - Li-Li Sun
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry , Sun Yat-Sen University , Guangzhou 510275 , China
| | - Qian Cao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry , Sun Yat-Sen University , Guangzhou 510275 , China
| | - Zhuo-Feng Ke
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry , Sun Yat-Sen University , Guangzhou 510275 , China
| | - Du-Xia Cao
- School of Materials Science and Engineering , University of Jinan , Jinan 250022 Shandong , China
| | - Zong-Wan Mao
- MOE Key Laboratory of Bioinorganic and Synthetic Chemistry, School of Chemistry , Sun Yat-Sen University , Guangzhou 510275 , China
- College of Materials and Energy , South China Agricultural University , Guangzhou 510642 , China
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29
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Hua XW, Bao YW, Wu FG. Fluorescent Carbon Quantum Dots with Intrinsic Nucleolus-Targeting Capability for Nucleolus Imaging and Enhanced Cytosolic and Nuclear Drug Delivery. ACS APPLIED MATERIALS & INTERFACES 2018; 10:10664-10677. [PMID: 29508612 DOI: 10.1021/acsami.7b19549] [Citation(s) in RCA: 170] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Nucleolus tracking and nucleus-targeted photodynamic therapy are attracting increasing attention due to the importance of nucleolus and the sensitivity of nucleus to various therapeutic stimuli. Herein, a new class of multifunctional fluorescent carbon quantum dots (or carbon dots, CDs) synthesized via the one-pot hydrothermal reaction of m-phenylenediamine and l-cysteine was reported to effectively target nucleolus. The as-prepared CDs possess superior properties, such as low-cost and facile synthesis, good water dispersibility, various surface groups for further modifications, prominent photostability, excellent compatibility, and rapid/convenient/wash-free staining procedures. Besides, as compared with SYTO RNASelect (a commonly used commercial dye for nucleolus imaging) that can only image nucleolus in fixed cells, the CDs can realize high-quality nucleolus imaging in not only fixed cells but also living cells, allowing the real-time tracking of nucleolus-related biological behaviors. Furthermore, after conjugating with protoporphyrin IX (PpIX), a commonly used photosensitizer, the resultant CD-PpIX nanomissiles showed remarkably increased cellular uptake and nucleus-targeting properties and achieved greatly enhanced phototherapeutic efficiency because the nuclei show poor tolerance to reactive oxygen species produced during the photodynamic therapy. The in vivo experiments revealed that the negatively charged CD-PpIX nanomissiles could rapidly and specifically target a tumor site after intravenous injection and cause efficient tumor ablation with no toxic side effects after laser irradiation. It is believed that the present CD-based nanosystem will hold great potential in nucleolus imaging and nucleus-targeted drug delivery and cancer therapy.
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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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31
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Sabale PM, Ambi UB, Srivatsan SG. A Lucifer-Based Environment-Sensitive Fluorescent PNA Probe for Imaging Poly(A) RNAs. Chembiochem 2018; 19:826-835. [PMID: 29396904 PMCID: PMC5972818 DOI: 10.1002/cbic.201700661] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Indexed: 12/14/2022]
Abstract
Fluorescence‐based oligonucleotide (ON) hybridization probes greatly aid the detection and profiling of RNA sequences in cells. However, certain limitations such as target accessibility and hybridization efficiency in cellular environments hamper their broad application because RNAs can form complex and stable structures. In this context, we have developed a robust hybridization probe suitable for imaging RNA in cells by combining the properties of 1) a new microenvironment‐sensitive fluorescent nucleobase analogue, obtained by attaching the Lucifer chromophore (1,8‐naphthalimide) at the 5‐position of uracil, and 2) a peptide nucleic acid (PNA) capable of forming stable hybrids with RNA. The fluorescence of the PNA base analogue labeled with the Lucifer chromophore, when incorporated into PNA oligomers and hybridized to complementary and mismatched ONs, is highly responsive to its neighboring base environment. Notably, the PNA base reports the presence of an adenine repeat in an RNA ON with reasonable enhancement in fluorescence. This feature of the emissive analogue enabled the construction of a poly(T) PNA probe for the efficient visualization of polyadenylated [poly(A)] RNAs in cells—poly(A) being an important motif that plays vital roles in the lifecycle of many types of RNA. Our results demonstrate that such responsive fluorescent nucleobase analogues, when judiciously placed in PNA oligomers, could generate useful hybridization probes to detect nucleic acid sequences in cells and also to image them.
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Affiliation(s)
- Pramod M Sabale
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
| | - Uddhav B Ambi
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pune, 411008, India
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Abstract
Fluorogenic oligonucleotide probes that can produce a change in fluorescence signal upon binding to specific biomolecular targets, including nucleic acids as well as non-nucleic acid targets, such as proteins and small molecules, have applications in various important areas. These include diagnostics, drug development and as tools for studying biomolecular interactions in situ and in real time. The probes usually consist of a labeled oligonucleotide strand as a recognition element together with a mechanism for signal transduction that can translate the binding event into a measurable signal. While a number of strategies have been developed for the signal transduction, relatively little attention has been paid to the recognition element. Peptide nucleic acids (PNA) are DNA mimics with several favorable properties making them a potential alternative to natural nucleic acids for the development of fluorogenic probes, including their very strong and specific recognition and excellent chemical and biological stabilities in addition to their ability to bind to structured nucleic acid targets. In addition, the uncharged backbone of PNA allows for other unique designs that cannot be performed with oligonucleotides or analogues with negatively-charged backbones. This review aims to introduce the principle, showcase state-of-the-art technologies and update recent developments in the areas of fluorogenic PNA probes during the past 20 years.
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Affiliation(s)
- Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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33
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Enzymatic Modification of 5'-Capped RNA and Subsequent Labeling by Click Chemistry. Methods Mol Biol 2017; 1428:45-60. [PMID: 27236791 DOI: 10.1007/978-1-4939-3625-0_3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The combination of enzymatic modification and bioorthogonal click chemistry provides a powerful approach for site-specific labeling of different classes of biomolecules in vitro and even in cellular environments. Herein, we describe a chemoenzymatic method to site specifically label 5'-capped model mRNAs independent of their sequence. A trimethylguanosine synthase was engineered to introduce alkyne, azido, or 4-vinylbenzyl moieties to the 5'-cap. These functional groups were then used for labeling using typical click reactions, such as the azide-alkyne cycloaddition or the tetrazine ligation.
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34
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Yokoyama C, Nakamoto K, Ueno Y. Design and synthesis of novel photoinduced electron transfer-based hybridization probes. Bioorg Med Chem 2017; 25:3574-3582. [DOI: 10.1016/j.bmc.2017.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 05/04/2017] [Accepted: 05/05/2017] [Indexed: 10/19/2022]
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35
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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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36
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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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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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38
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Qiu J, Wilson A, El-Sagheer AH, Brown T. Combination probes with intercalating anchors and proximal fluorophores for DNA and RNA detection. Nucleic Acids Res 2016; 44:e138. [PMID: 27369379 PMCID: PMC5041472 DOI: 10.1093/nar/gkw579] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2016] [Accepted: 06/16/2016] [Indexed: 12/20/2022] Open
Abstract
A new class of modified oligonucleotides (combination probes) has been designed and synthesised for use in genetic analysis and RNA detection. Their chemical structure combines an intercalating anchor with a reporter fluorophore on the same thymine nucleobase. The intercalator (thiazole orange or benzothiazole orange) provides an anchor, which upon hybridisation of the probe to its target becomes fluorescent and simultaneously stabilizes the duplex. The anchor is able to communicate via FRET to a proximal reporter dye (e.g. ROX, HEX, ATTO647N, FAM) whose fluorescence signal can be monitored on a range of analytical devices. Direct excitation of the reporter dye provides an alternative signalling mechanism. In both signalling modes, fluorescence in the unhybridised probe is switched off by collisional quenching between adjacent intercalator and reporter dyes. Single nucleotide polymorphisms in DNA and RNA targets are identified by differences in the duplex melting temperature, and the use of short hybridization probes, made possible by the stabilisation provided by the intercalator, enhances mismatch discrimination. Unlike other fluorogenic probe systems, placing the fluorophore and quencher on the same nucleobase facilitates the design of short probes containing multiple modifications. The ability to detect both DNA and RNA sequences suggests applications in cellular imaging and diagnostics.
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Affiliation(s)
- Jieqiong Qiu
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Adam Wilson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
| | - Afaf H El-Sagheer
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK 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, Chemistry Research Laboratory, 12 Mansfield Road, Oxford, OX1 3TA, UK
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39
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Cheruiyot SK, Rozners E. Fluorescent 2-Aminopyridine Nucleobases for Triplex-Forming Peptide Nucleic Acids. Chembiochem 2016; 17:1558-62. [PMID: 27223320 DOI: 10.1002/cbic.201600182] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Indexed: 01/18/2023]
Abstract
Development of new fluorescent peptide nucleic acids (PNAs) is important for fundamental research and practical applications. The goal of this study was the design of fluorogenic nucleobases for incorporation in triplex-forming PNAs. The underlying design principle was the use of a protonation event that accompanied binding of a 2-aminopyridine (M) nucleobase to a G-C base pair as an on switch for a fluorescence signal. Two fluorogenic nucleobases, 3-(1-phenylethynyl)-M and phenylpyrrolo-M, were designed, synthesized and studied. The new M derivatives provided modest enhancement of fluorescence upon protonation but showed reduced RNA binding affinity and quenching of fluorescence signal upon triple-helix formation with cognate double-stranded RNA. Our study illustrates the principal challenges of design and provides guidelines for future improvement of fluorogenic PNA nucleobases. The 3-(1-phenylethynyl)-M may be used as a fluorescent nucleobase to study PNA-RNA triple-helix formation.
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Affiliation(s)
- Samwel K Cheruiyot
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY, 13902, USA
| | - Eriks Rozners
- Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY, 13902, USA.
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40
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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: 73] [Impact Index Per Article: 9.1] [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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41
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Penas C, Mascareñas JL, Vázquez ME. Coupling the folding of a β-hairpin with chelation-enhanced luminescence of Tb(III) and Eu(III) ions for specific sensing of a viral RNA. Chem Sci 2016; 2016:2674-2678. [PMID: 27293537 PMCID: PMC4898589 DOI: 10.1039/c5sc04501k] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Rational modification of a natural RNA-binding peptide with a lanthanide EDTA chelator, and a phenanthroline ligand yields a highly selective luminescent sensor. The sensing mechanism relies on the RNA-triggered folding of the peptide into a β-hairpin, which promotes the coordination of the phenanthroline sensitizer, and the efficient sensitization of complexed lanthanide ions.
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42
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Kellermann SJ, Rentmeister A. A Genetically Encodable System for Sequence-Specific Detection of RNAs in Two Colors. Chembiochem 2016; 17:895-9. [PMID: 26919688 DOI: 10.1002/cbic.201500705] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Indexed: 12/28/2022]
Abstract
Multicolor readout is an important feature of RNA detection techniques aiming at the investigation of RNA localization. Several detection methods have been developed, however they require either transfection of cells with the probe or prior tagging of the target RNA. We report a fully genetically encodable system for simultaneous detection of two RNAs by using green and yellow fluorescence based on tetramolecular fluorescence complementation (TetFC). To obtain yellow fluorescent protein (YFP), substitution T203Y was introduced into one of the three non-fluorescent GFP fragments; this was fused to different variants of the Homo sapiens Pumilio homology domain. Using different sets of fusion proteins we were able to discriminate between two closely related target RNAs based on the fluorescence signals at the respective wavelengths.
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Affiliation(s)
- Stefanie J Kellermann
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany.,Department of Chemistry, Institute for Biochemistry and Molecular Biology, University of Hamburg, Martin-Luther-King-Platz 6, 20146, Hamburg, Germany
| | - Andrea Rentmeister
- Department of Chemistry and Pharmacy, Institute of Biochemistry, University of Münster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany. .,Cells-in-Motion Cluster of Excellence (EXC 1003-CiM), University of Münster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany.
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43
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Berndl S, Dimitrov SD, Menacher F, Fiebig T, Wagenknecht HA. Thiazole Orange Dimers in DNA: Fluorescent Base Substitutions with Hybridization Readout. Chemistry 2016; 22:2386-95. [DOI: 10.1002/chem.201503849] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Indexed: 01/03/2023]
Affiliation(s)
- Sina Berndl
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
| | - Stoichko D. Dimitrov
- Centre for Plastic Electronics; Department of Chemistry; Imperial College London; Exhibition Road London SW7 2AZ UK
| | - Florian Menacher
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
| | - Torsten Fiebig
- Feinberg School of Medicine; Department of Otolaryngology; Northwestern University; 420 East Superior Street Chicago IL 60611 USA
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
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44
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Okamoto A. Thiazole Orange-Tethered Nucleic Acids and ECHO Probes for Fluorometric Detection of Nucleic Acids. MODIFIED NUCLEIC ACIDS 2016. [DOI: 10.1007/978-3-319-27111-8_3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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45
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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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46
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Takahashi K, Ito S, Nakamoto K, Ito Y, Ueno Y. Photoinduced Electron-Transfer-Based Hybridization Probes for Detection of DNA and RNA. J Org Chem 2015; 80:8561-70. [PMID: 26258850 DOI: 10.1021/acs.joc.5b01132] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Here, we report the synthesis of a hybridization probe for detection of RNA and DNA based on photoinduced electron transfer (PeT). We designed and synthesized an oligonucleotide containing an adenosine analogue with a 9-(N,N-dimethylaminomethyl)anthracenyl moiety at its 6-position via an ethynylene linker as the hybridization probe. When the probe was hybridized with a complementary RNA or DNA, the fluorescence intensity increased 3-fold or 4.5-fold, respectively, compared to the single-stranded state.
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Affiliation(s)
| | | | | | - Yasutomo Ito
- Division for Medical Research Engineering, Nagoya University Graduate School of Medicine , Nagoya 466-8550, Japan
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47
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Murayama K, Kamiya Y, Kashida H, Asanuma H. Ultrasensitive Molecular Beacon Designed with Totally Serinol Nucleic Acid (SNA) for Monitoring mRNA in Cells. Chembiochem 2015; 16:1298-301. [PMID: 25851922 DOI: 10.1002/cbic.201500167] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Indexed: 12/28/2022]
Abstract
An artificial nucleic acid based on acyclic serinol building blocks and termed "serinol nucleic acid" (SNA) was used to construct a fluorescent probe for RNA visualization in cells. The molecular beacon (MB) composed of only SNA with a fluorophore at one terminus and a quencher at the other was resistant to enzymatic digestion, due to its unnatural acyclic scaffold. The SNA-MB could detect its complementary RNA with extremely high sensitivity; the signal-to-background (S/B) ratio was as high as 930 when perylene and anthraquinone were used as the fluorophore and quencher pair. A high S/B ratio was also achieved with SNA-MB tethering the conventional Cy3 fluorophore, and this probe enabled selective visualization of target mRNA in fixed cells. Thus, SNA-MB has potential for use as a biological tool capable of visualizing RNA in living cells.
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Affiliation(s)
- Keiji Murayama
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan)
- Venture business laboratory (VBL), Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan)
| | - Yukiko Kamiya
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan)
- Division of Green Conversion, EcoTopia Science Institute, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan)
| | - Hiromu Kashida
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan).
- PRESTO, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 (Japan).
| | - Hiroyuki Asanuma
- Graduate School of Engineering, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8603 (Japan).
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48
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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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49
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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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50
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Holstein JM, Stummer D, Rentmeister A. Enzymatic modification of 5'-capped RNA with a 4-vinylbenzyl group provides a platform for photoclick and inverse electron-demand Diels-Alder reaction. Chem Sci 2014; 6:1362-1369. [PMID: 29560223 PMCID: PMC5811123 DOI: 10.1039/c4sc03182b] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 11/26/2014] [Indexed: 01/20/2023] Open
Abstract
Enzymatic transfer of 4-vinylbenzyl to the mRNA 5′-cap gives access to the fluorogenic photoclick and the inverse electron-demand Diels–Alder reaction.
Chemo-enzymatic strategies provide a highly selective means to label different classes of biomolecules in vitro, but also in vivo. In the field of RNA, efficient labeling of eukaryotic mRNA with small organic reporter molecules would provide a way to detect endogenous mRNA and is therefore highly attractive. Although more and more bioorthogonal reactions are being reported, they can only be applied to chemo-enzymatic strategies if a suitable (i.e., click compatible) modification can be introduced into the RNA of interest. We report enzymatic site-specific transfer of a 4-vinylbenzyl group to the 5′-cap typical of eukaryotic mRNAs. The 4-vinylbenzyl group gives access to mRNA labeling using the inverse electron-demand Diels–Alder reaction, which does not work with an enzymatically transferred allyl group. The 4-vinylbenzyl-modified 5′-cap can also be converted in a photoclick reaction generating a “turn-on” fluorophore. Both click reactions are bioorthogonal and the two step approach also works in eukaryotic cell lysate. Enzymatic transfer of the 4-vinylbenzyl group addresses the lack of flexibility often attributed to biotransformations and thus advances the potential of chemo-enzymatic approaches for labeling.
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Affiliation(s)
- Josephin Marie Holstein
- Westfälische Wilhelms-Universität Münster , Institute of Biochemistry , 48149 Muenster , Germany .
| | - Daniela Stummer
- Westfälische Wilhelms-Universität Münster , Institute of Biochemistry , 48149 Muenster , Germany . .,Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM) , University of Muenster , 48149 Muenster , Germany
| | - Andrea Rentmeister
- Westfälische Wilhelms-Universität Münster , Institute of Biochemistry , 48149 Muenster , Germany . .,Cells-in-Motion Cluster of Excellence (EXC 1003 - CiM) , University of Muenster , 48149 Muenster , Germany
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