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Ditmangklo B, Taechalertpaisarn J, Siriwong K, Vilaivan T. Clickable styryl dyes for fluorescence labeling of pyrrolidinyl PNA probes for the detection of base mutations in DNA. Org Biomol Chem 2019; 17:9712-9725. [PMID: 31531484 DOI: 10.1039/c9ob01492f] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Fluorescent hybridization probes are important tools for rapid, specific and sensitive analysis of genetic mutations. In this work, we synthesized novel alkyne-modified styryl dyes for conjugation with pyrrolidinyl peptide nucleic acid (acpcPNA) by click chemistry for the development of hybridization responsive fluorescent PNA probes. The free styryl dyes generally exhibited weak fluorescence in aqueous media, and the fluorescence was significantly enhanced (up to 125-fold) upon binding with DNA duplexes. Selected styryl dyes that showed good responses with DNA were conjugated with PNA via sequential reductive alkylation-click chemistry. Although these probes showed little fluorescence change when hybridized to complementary DNA, significant fluorescence enhancements were observed in the presence of structural defects including mismatched, abasic and base-inserted DNA targets. The largest increase in fluorescence quantum yield (up to 14.5-fold) was achieved with DNA carrying base insertion. Although a number of probes were designed to give fluorescence response to complementary DNA targets, probes that are responsive to mutations such as single nucleotide polymorphism (SNP), base insertion/deletion and abasic site are less common. Therefore, styryl-dye-labeled acpcPNA is a unique probe that is responsive to structural defects in the duplexes that may be further applied for diagnostic purposes.
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Affiliation(s)
- Boonsong Ditmangklo
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
| | - Jaru Taechalertpaisarn
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand. and National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency, Pathumthani 12120, Thailand
| | - Khatcharin Siriwong
- Materials Chemistry Research Center, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand.
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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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3
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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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Sakai Y, Islam MS, Adamiak M, Shiu SCC, Tanner JA, Heddle JG. DNA Aptamers for the Functionalisation of DNA Origami Nanostructures. Genes (Basel) 2018; 9:E571. [PMID: 30477184 PMCID: PMC6315403 DOI: 10.3390/genes9120571] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 11/07/2018] [Accepted: 11/19/2018] [Indexed: 01/05/2023] Open
Abstract
DNA origami has emerged in recent years as a powerful technique for designing and building 2D and 3D nanostructures. While the breadth of structures that have been produced is impressive, one of the remaining challenges, especially for DNA origami structures that are intended to carry out useful biomedical tasks in vivo, is to endow them with the ability to detect and respond to molecules of interest. Target molecules may be disease indicators or cell surface receptors, and the responses may include conformational changes leading to the release of therapeutically relevant cargo. Nucleic acid aptamers are ideally suited to this task and are beginning to be used in DNA origami designs. In this review, we consider examples of uses of DNA aptamers in DNA origami structures and summarise what is currently understood regarding aptamer-origami integration. We review three major roles for aptamers in such applications: protein immobilisation, triggering of structural transformation, and cell targeting. Finally, we consider future perspectives for DNA aptamer integration with DNA origami.
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Affiliation(s)
- Yusuke Sakai
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.
| | - Md Sirajul Islam
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.
| | - Martyna Adamiak
- Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Krakow, Poland.
| | - Simon Chi-Chin Shiu
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
| | - Julian Alexander Tanner
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
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5
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Steinmeyer J, Wagenknecht HA. Synthesis of DNA Modified with Boronic Acid: Compatibility to Copper(I)-Catalyzed Azide–Alkyne Cycloaddition. Bioconjug Chem 2018; 29:431-436. [DOI: 10.1021/acs.bioconjchem.7b00765] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jeannine Steinmeyer
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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6
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Röthlisberger P, Gasse C, Hollenstein M. Nucleic Acid Aptamers: Emerging Applications in Medical Imaging, Nanotechnology, Neurosciences, and Drug Delivery. Int J Mol Sci 2017; 18:E2430. [PMID: 29144411 PMCID: PMC5713398 DOI: 10.3390/ijms18112430] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/08/2017] [Accepted: 11/09/2017] [Indexed: 12/25/2022] Open
Abstract
Recent progresses in organic chemistry and molecular biology have allowed the emergence of numerous new applications of nucleic acids that markedly deviate from their natural functions. Particularly, DNA and RNA molecules-coined aptamers-can be brought to bind to specific targets with high affinity and selectivity. While aptamers are mainly applied as biosensors, diagnostic agents, tools in proteomics and biotechnology, and as targeted therapeutics, these chemical antibodies slowly begin to be used in other fields. Herein, we review recent progress on the use of aptamers in the construction of smart DNA origami objects and MRI and PET imaging agents. We also describe advances in the use of aptamers in the field of neurosciences (with a particular emphasis on the treatment of neurodegenerative diseases) and as drug delivery systems. Lastly, the use of chemical modifications, modified nucleoside triphosphate particularly, to enhance the binding and stability of aptamers is highlighted.
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Affiliation(s)
- Pascal Röthlisberger
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris CEDEX 15, France.
| | - Cécile Gasse
- Institute of Systems & Synthetic Biology, Xenome Team, 5 rue Henri Desbruères Genopole Campus 1, University of Evry, F-91030 Evry, France.
| | - Marcel Hollenstein
- Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR3523, 28, rue du Docteur Roux, 75724 Paris CEDEX 15, France.
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7
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Light-induced functions in DNA. Curr Opin Chem Biol 2017; 40:119-126. [DOI: 10.1016/j.cbpa.2017.07.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 06/13/2017] [Accepted: 07/20/2017] [Indexed: 12/30/2022]
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8
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Erdmann RM, Hoffmann A, Walter HK, Wagenknecht HA, Groß-Hardt R, Gehring M. Molecular movement in the Arabidopsis thaliana female gametophyte. PLANT REPRODUCTION 2017; 30:141-146. [PMID: 28695277 PMCID: PMC5599461 DOI: 10.1007/s00497-017-0304-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 07/02/2017] [Indexed: 05/03/2023]
Abstract
Size limits on molecular movement among female gametes. Cellular decisions can be influenced by information communicated from neighboring cells. Communication can occur via signaling or through the direct transfer of molecules. Movement of RNAs and proteins has frequently been observed among symplastically connected plant cells. In flowering plants, the female gametes, the egg cell and central cell, are closely apposed within the female gametophyte. Here we investigated the ability of fluorescently labeled dyes and small RNAs to move from the Arabidopsis thaliana central cell to the egg apparatus following microinjection. These results define a size limit of at least 20 kDa for symplastic movement between the two gametes, somewhat larger than that previously observed in Torenia fournieri. Our results indicate that symplastic connectivity in Arabidopsis thaliana changes after fertilization and suggest that prior to fertilization mechanisms are in place to facilitate small RNA movement from the central cell to the egg cell and synergids.
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Affiliation(s)
- Robert M Erdmann
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Anja Hoffmann
- Department of Plant Molecular Genetics, University of Bremen, 28359, Bremen, Germany
| | - Heidi-Kristin Walter
- Institute for Organic Chemistry, Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Hans-Achim Wagenknecht
- Institute for Organic Chemistry, Karlsruhe Institute of Technology, 76131, Karlsruhe, Germany
| | - Rita Groß-Hardt
- Department of Plant Molecular Genetics, University of Bremen, 28359, Bremen, Germany
| | - Mary Gehring
- Whitehead Institute for Biomedical Research, Cambridge, MA, 02142, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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9
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Steinmeyer J, Rönicke F, Schepers U, Wagenknecht HA. Synthesis of Wavelength-Shifting Fluorescent DNA and RNA with Two Photostable Cyanine-Styryl Dyes as the Base Surrogate Pair. ChemistryOpen 2017; 6:514-518. [PMID: 28794946 PMCID: PMC5542753 DOI: 10.1002/open.201700059] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Indexed: 01/19/2023] Open
Abstract
Two nucleic acid building blocks were synthesized, consisting of two photostable green‐ and red‐emitting cyanine–styryl dyes and (S)‐3‐amino‐1,2‐propanediol as a substitute for the ribofuranoside, and incorporated as base‐pair surrogates by using automated phosphoramidte chemistry in the solid phase. The optical properties and, in particular, the energy‐transfer properties were screened in a range of DNA duplexes, in which the “counter bases” of the two dyes were varied and the distance between the two dyes was enlarged to up to three intervening adenosine–thymidine pairs. The DNA duplex with the best optical properties and the best red/green emission ratio as the readout bore adenosine and thymidine opposite to the dyes, and the two dyes directly adjacent to each other as the base surrogate pair. This structural arrangement can be transferred to RNA to obtain similarly fluorescent RNA probes. Representatively, the positively evaluated DNA duplex was applied to verify the fluorescence readout in living HeLa cells by using fluorescence confocal microscopy.
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Affiliation(s)
- Jeannine Steinmeyer
- Institute of Organic Chemistry Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Franziska Rönicke
- Institute of Organic Chemistry Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Ute Schepers
- Institute of Toxicology and Genetics Karlsruhe Institute of Technology (KIT) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry Karlsruhe Institute of Technology (KIT) Fritz-Haber-Weg 6 76131 Karlsruhe Germany
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10
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Walter HK, Bauer J, Steinmeyer J, Kuzuya A, Niemeyer CM, Wagenknecht HA. "DNA Origami Traffic Lights" with a Split Aptamer Sensor for a Bicolor Fluorescence Readout. NANO LETTERS 2017; 17:2467-2472. [PMID: 28249387 DOI: 10.1021/acs.nanolett.7b00159] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A split aptamer for adenosine triphosphate (ATP) was embedded as a recognition unit into two levers of a nanomechanical DNA origami construct by extension and modification of selected staple strands. An additional optical module in the stem of the split aptamer comprised two different cyanine-styryl dyes that underwent an energy transfer from green (donor) to red (acceptor) emission if two ATP molecules were bound as target molecule to the recognition module and thereby brought the dyes in close proximity. As a result, the ATP as a target triggered the DNA origami shape transition and yielded a fluorescence color change from green to red as readout. Conventional atomic force microscopy (AFM) images confirmed the topology change from the open form of the DNA origami in the absence of ATP into the closed form in the presence of the target molecule. The obtained closed/open ratios in the absence and presence of target molecules tracked well with the fluorescence color ratios and thereby validated the bicolor fluorescence readout. The correct positioning of the split aptamer as the functional unit farthest away from the fulcrum of the DNA origami was crucial for the aptasensing by fluorescence readout. The fluorescence color change allowed additionally to follow the topology change of the DNA origami aptasensor in real time in solution. The concepts of fluorescence energy transfer for bicolor readout in a split aptamer in solution, and AFM on surfaces, were successfully combined in a single DNA origami construct to obtain a bimodal readout. These results are important for future custom DNA devices for chemical-biological and bioanalytical purposes because they are not only working as simple aptamers but are also visible by AFM on the single-molecule level.
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Affiliation(s)
- Heidi-Kristin Walter
- Institute for Organic Chemistry, Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Jens Bauer
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Jeannine Steinmeyer
- Institute for Organic Chemistry, Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Akinori Kuzuya
- Department of Chemistry and Materials Engineering, Kansai University , 3-3-35 Yamate, Suita, Osaka 564-8680, Japan
| | - Christof M Niemeyer
- Institute for Biological Interfaces (IBG 1), Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Hans-Achim Wagenknecht
- Institute for Organic Chemistry, Karlsruhe Institute of Technology (KIT) , Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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11
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Walter HK, Olshausen B, Schepers U, Wagenknecht HA. A postsynthetically 2'-"clickable" uridine with arabino configuration and its application for fluorescent labeling and imaging of DNA. Beilstein J Org Chem 2017; 13:127-137. [PMID: 28228854 PMCID: PMC5302004 DOI: 10.3762/bjoc.13.16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 01/03/2017] [Indexed: 12/24/2022] Open
Abstract
The arabino-configured analog of uridine with a propargyl group at the 2’-position was synthesized and incorporated into DNA by solid-phase chemistry. The fluorescence quantum yields of DNA strands that were postsynthetically modified by blue and green emitting cyanine-styryl dyes were improved due to the arabino-configured anchor. These oligonucleotides were used as energy transfer donors in hybrids with oligonucleotides modified with acceptor dyes that emit in the yellow-red range. These combinations give energy transfer pairs with blue–yellow, blue–red and green–red emission color changes. All combinations of arabino- and ribo-configured donor strands with arabino- and ribo-configured acceptor strands were evaluated. This array of doubly modified hybrids was screened by their emission color contrast and fluorescence quantum yield. Especially mixed combinations, that means donor dyes with arabino-configured anchor with acceptor dyes with ribo-configured anchor, and vice versa, showed significantly improved fluorescence properties. Those were successfully applied for fluorescent imaging of DNA after transport into living cells.
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Affiliation(s)
- Heidi-Kristin Walter
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
| | - Bettina Olshausen
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), H.-v.-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Ute Schepers
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology (KIT), H.-v.-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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12
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Arndt S, Walter HK, Wagenknecht HA. Synthesis of Wavelength-shifting DNA Hybridization Probes by Using Photostable Cyanine Dyes. J Vis Exp 2016:54121. [PMID: 27501433 PMCID: PMC4993372 DOI: 10.3791/54121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
In this protocol, we demonstrate a method for the synthesis of 2'-alkyne modified deoxyribonucleic acid (DNA) strands by automated solid phase synthesis using standard phosphoramidite chemistry. Oligonucleotides are post-synthetically labeled by two new photostable cyanine dyes using copper-catalyzed click-chemistry. The synthesis of both donor and acceptor dye is described and is performed in three consecutive steps. With the DNA as the surrounding architecture, these two dyes undergo an energy transfer when they are brought into close proximity by hybridization. Therefore, annealing of two single stranded DNA strands is visualized by a change of fluorescence color. This color change is characterized by fluorescence spectroscopy but can also be directly observed by using a handheld ultraviolet (UV) lamp. The concept of a dual fluorescence color readout makes these oligonucleotide probes excellent tools for molecular imaging especially when the described photostable dyes are used. Thereby, photobleaching of the imaging probes is prevented, and biological processes can be observed in real time for a longer time period.
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Affiliation(s)
- Stefanie Arndt
- Institute of Organic Chemistry, Karlsruhe Institute of Technology
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13
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Bohländer PR, Abba ML, Bestvater F, Allgayer H, Wagenknecht HA. Two wavelength-shifting molecular beacons for simultaneous and selective imaging of vesicular miRNA-21 and miRNA-31 in living cancer cells. Org Biomol Chem 2016; 14:5001-6. [PMID: 27114268 DOI: 10.1039/c6ob00691d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Two molecular beacons were designed as complementary fluorescent imaging probes for miRNA-21 and miRNA-31. Both beacons were prepared by a combination of solid-phase protocol and Cu(i)-catalyzed cycloaddition chemistry. The four photostable and bright fluorophores were attached to 2'-positions in the stem part of the two beacons. One beacon was labeled by a green-to-red emitting and the other by a blue-to-yellow emitting energy transfer pair. This two by two combination yields the four color emission readout. In vitro experiments demonstrate rapid and highly selective opening of both molecular beacons upon addition of the complementary target RNA and excellent green : red and blue : yellow emission color contrasts. Confocal microscopy of selected cancer cell lines provides evidence that a four color imaging of versicular miRNA-21 and miRNA-31 can be achieved both selectively and simultaneously upon transfection by the beacons, and that the fluorescent readouts track well with miRNA levels determined by PCR.
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Affiliation(s)
- Peggy R Bohländer
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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14
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Bohländer PR, Wagenknecht HA. Bright and photostable cyanine-styryl chromophores with green and red fluorescence colour for DNA staining. Methods Appl Fluoresc 2015; 3:044003. [PMID: 29148508 DOI: 10.1088/2050-6120/3/4/044003] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The synthesis and optical characterisation of a series of green- and red-emitting cyanine and cyanine-styryl dyes is presented that were developed based on the cyanine-indole-quinolinium and based on the thiazole red type structure. For the green emitting fluorophores the quinolinium part was replaced by a pyridinium group. The bridge to the indole group was attached either to the 2-position or to the 4-position of the pyridinium moiety. For the red-emitting dyes the connection to the indole moiety is at the 4-position of the quinolinium part. In each set of dyes a methyl group at the indole-NH and/or a phenyl group at the 2-position of the indole part were introduced to tune the optical properties and photostability. Additionally, two dyes were modified with a cyano group to tune the photophysical properties and to enhance the photostabilities. The developed dyes show good photostabilities and bright green or red fluorescence intensities in the presence of DNA. Thus, these dyes represent important and promising candidates for fluorescent molecular imaging of nucleic acids inside living cells.
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Affiliation(s)
- Peggy R Bohländer
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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