51
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Kawai K, Miyata T, Shimada N, Ito S, Miyasaka H, Maruyama A. Single-Molecule Monitoring of the Structural Switching Dynamics of Nucleic Acids through Controlling Fluorescence Blinking. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201708705] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Kiyohiko Kawai
- The Institute of Scientific and Industrial Research (SANKEN); Osaka University; Mihogaoka 8-1 Ibaraki Osaka 567-0047 Japan
| | - Takafumi Miyata
- Department of Life Science and Technology; Tokyo Institute of Technology; 4259 B-57 Nagatsuta Midori-ku, Yokohama Kanagawa 226-8501 Japan
| | - Naohiko Shimada
- Department of Life Science and Technology; Tokyo Institute of Technology; 4259 B-57 Nagatsuta Midori-ku, Yokohama Kanagawa 226-8501 Japan
| | - Syoji Ito
- Division of Frontier Materials Science and Center for Promotion of Advanced Interdisciplinary Research; Graduate School of Engineering Science; Osaka University; Toyonaka, 567-8531 226-8501 Japan
| | - Hiroshi Miyasaka
- Division of Frontier Materials Science and Center for Promotion of Advanced Interdisciplinary Research; Graduate School of Engineering Science; Osaka University; Toyonaka, 567-8531 226-8501 Japan
| | - Atsushi Maruyama
- Department of Life Science and Technology; Tokyo Institute of Technology; 4259 B-57 Nagatsuta Midori-ku, Yokohama Kanagawa 226-8501 Japan
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52
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Piras L, Avitabile C, D'Andrea LD, Saviano M, Romanelli A. Detection of oligonucleotides by PNA-peptide conjugates recognizing the biarsenical fluorescein complex FlAsH-EDT 2. Biochem Biophys Res Commun 2017; 493:126-131. [PMID: 28919425 DOI: 10.1016/j.bbrc.2017.09.064] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 09/13/2017] [Indexed: 12/31/2022]
Abstract
We report the application of the arsenical complex FlAsH-EDT2 for the identification of oligonucleotide sequences. We designed PNA sequences conjugated to either a tetracysteine motif and to split tetracysteine sequences, that are recognized by FlAsH. The effect of conjugation of the PNA to the tetracysteine peptide and RNA hybridization on the fluorescence of the arsenical complex has been investigated. The reconstitution of the tetracysteine motif, starting from 15-mer PNAs conjugated to split tetracysteine sequences and hybridized to a complementary oligonucleotide was also explored.
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Affiliation(s)
- Linda Piras
- Institute of Crystallography (IC), CNR, Via Amendola 122/O, 70126, Bari, Italy
| | - Concetta Avitabile
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Napoli, Italy
| | - Luca Domenico D'Andrea
- Institute of Biostructures and Bioimaging (IBB), CNR, via Mezzocannone 16, 80134, Napoli, Italy
| | - Michele Saviano
- Institute of Crystallography (IC), CNR, Via Amendola 122/O, 70126, Bari, Italy
| | - Alessandra Romanelli
- Department of Pharmacy, University of Naples "Federico II", via Mezzocannone 16, 80134, Napoli, Italy.
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53
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Zhou CY, Alexander SC, Devaraj NK. Fluorescent turn-on probes for wash-free mRNA imaging via covalent site-specific enzymatic labeling. Chem Sci 2017; 8:7169-7173. [PMID: 29081948 PMCID: PMC5635419 DOI: 10.1039/c7sc03150e] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 08/28/2017] [Indexed: 11/21/2022] Open
Abstract
Investigating the many roles RNA plays in cellular regulation and function has increased demand for tools to explore RNA tracking and localization within cells.
Investigating the many roles RNA plays in cellular regulation and function has increased demand for tools to explore RNA tracking and localization within cells. Our recently reported RNA-TAG (transglycosylation at guanine) approach uses an RNA-modifying enzyme, tRNA-guanine transglycosylase (TGT), to accomplish covalent labeling of an RNA of interest with fluorescent tracking agents in a highly selective and efficient manner. Unfortunately, labeling by this method currently suffers from a high nonspecific fluorescent background and is currently unsuitable for imaging RNA within complex cellular environments. Herein we report the design and synthesis of novel fluorogenic thiazole orange probes that significantly lower nonspecific binding and background fluorescence and, as a result, provide up to a 100-fold fluorescence intensity increase after labeling. Using these fluorogenic labeling agents, we were able to image mRNA expressed in Chinese Hamster Ovary cells in a wash-free manner.
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Affiliation(s)
- Cun Yu Zhou
- Department of Chemistry and Biochemistry , University of California , 9500 Gilman Dr La Jolla , San Diego , CA 92093 , USA .
| | - Seth C Alexander
- Department of Chemistry and Biochemistry , University of California , 9500 Gilman Dr La Jolla , San Diego , CA 92093 , USA .
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry , University of California , 9500 Gilman Dr La Jolla , San Diego , CA 92093 , USA .
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54
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Alexander SC, Devaraj NK. Developing a Fluorescent Toolbox To Shed Light on the Mysteries of RNA. Biochemistry 2017; 56:5185-5193. [PMID: 28671838 DOI: 10.1021/acs.biochem.7b00510] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Technologies that detect and image RNA have illuminated the complex roles played by RNA, redefining the traditional and superficial role first outlined by the central dogma of biology. Because there is such a wide diversity of RNA structure arising from an assortment of functions within biology, a toolbox of approaches have emerged for investigation of this important class of biomolecules. These methods are necessary to detect and elucidate the localization and dynamics of specific RNAs and in doing so unlock our understanding of how RNA dysregulation leads to disease. Current methods for detecting and imaging RNA include in situ hybridization techniques, fluorescent aptamers, RNA binding proteins fused to fluorescent reporters, and covalent labeling strategies. Because of the inherent diversity of these methods, each approach comes with a set of strengths and limitations that leave room for future improvement. This perspective seeks to highlight the most recent advances and remaining challenges for the wide-ranging toolbox of technologies that illuminate RNA's contribution to cellular complexity.
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Affiliation(s)
- Seth C Alexander
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego , La Jolla, California 92093, United States
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55
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van Gijtenbeek LA, Kok J. Illuminating Messengers: An Update and Outlook on RNA Visualization in Bacteria. Front Microbiol 2017; 8:1161. [PMID: 28690601 PMCID: PMC5479882 DOI: 10.3389/fmicb.2017.01161] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 06/07/2017] [Indexed: 01/04/2023] Open
Abstract
To be able to visualize the abundance and spatiotemporal features of RNAs in bacterial cells would permit obtaining a pivotal understanding of many mechanisms underlying bacterial cell biology. The first methods that allowed observing single mRNA molecules in individual cells were introduced by Bertrand et al. (1998) and Femino et al. (1998). Since then, a plethora of techniques to image RNA molecules with the aid of fluorescence microscopy has emerged. Many of these approaches are useful for the large eukaryotic cells but their adaptation to study RNA, specifically mRNA molecules, in bacterial cells progressed relatively slow. Here, an overview will be given of fluorescent techniques that can be used to reveal specific RNA molecules inside fixed and living single bacterial cells. It includes a critical evaluation of their caveats as well as potential solutions.
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Affiliation(s)
- Lieke A van Gijtenbeek
- Department of Molecular Genetics, Faculty of Science and Engineering, University of GroningenGroningen, Netherlands
| | - Jan Kok
- Department of Molecular Genetics, Faculty of Science and Engineering, University of GroningenGroningen, Netherlands
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56
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Xia Y, Zhang R, Wang Z, Tian J, Chen X. Recent advances in high-performance fluorescent and bioluminescent RNA imaging probes. Chem Soc Rev 2017; 46:2824-2843. [PMID: 28345687 PMCID: PMC5472208 DOI: 10.1039/c6cs00675b] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
RNA plays an important role in life processes. Imaging of messenger RNAs (mRNAs) and micro-RNAs (miRNAs) not only allows us to learn the formation and transcription of mRNAs and the biogenesis of miRNAs involved in various life processes, but also helps in detecting cancer. High-performance RNA imaging probes greatly expand our view of life processes and enhance the cancer detection accuracy. In this review, we summarize the state-of-the-art high-performance RNA imaging probes, including exogenous probes that can image RNA sequences with special modification and endogeneous probes that can directly image endogenous RNAs without special treatment. For each probe, we review its structure and imaging principle in detail. Finally, we summarize the application of mRNA and miRNA imaging probes in studying life processes as well as in detecting cancer. By correlating the structures and principles of various probes with their practical uses, we compare different RNA imaging probes and offer guidance for better utilization of the current imaging probes and the future design of higher-performance RNA imaging probes.
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Affiliation(s)
- Yuqiong Xia
- Engineering Research Center of Molecular-imaging and Neuro-imaging of Ministry of Education, School of Life Science and Technology, Xidian University, Xi'an, Shaanxi 710126, China.
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57
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Varizhuk AM, Zatsepin TS, Golovin AV, Belyaev ES, Kostyukevich YI, Dedkov VG, Shipulin GA, Shpakovski GV, Aralov AV. Synthesis of oligonucleotides containing novel G-clamp analogue with C8-tethered group in phenoxazine ring: Implication to qPCR detection of the low-copy Kemerovo virus dsRNA. Bioorg Med Chem 2017; 25:3597-3605. [PMID: 28396019 DOI: 10.1016/j.bmc.2017.03.062] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Revised: 03/27/2017] [Accepted: 03/29/2017] [Indexed: 01/20/2023]
Abstract
Nowadays modified oligonucleotides are widely used in diagnostics and as novel therapeutics. Introduction of modified or unnatural residues into oligonucleotides allows fine tuning of their binding properties to complementary nucleic acids and leads to improved stability both in vitro and in vivo. Previously it was demonstrated that insertion of phenoxazine nucleotides with various groups in C9-position into oligonucleotides leads to a significant increase of duplex stability with complementary DNA and RNA. Here the synthesis of a novel G-clamp nucleoside analogue (G8AE-clamp) bearing 2-aminoethyl tether at C8-atom is presented. Introduction of such modified residues into oligonucleotides lead to enhanced specificity of duplex formation towards complementary DNA and RNA targets with increased thermal and 3'-exonuclease stability. According to CD-spectroscopy studies G8AE-clamp does not substantially disrupt helix geometry. Primers containing G8AE-clamp demonstrated superior sensitivity in qPCR detection of dsRNA of Kemerovo virus in comparison to native oligonucleotides.
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Affiliation(s)
- Anna M Varizhuk
- Research and Clinical Center for Physical Chemical Medicine, 119435 Moscow, Russia; Department of Structure-Functional Analysis of Biopolymers, Engelhardt Institute of Molecular Biology, Vavilov Str. 32, Moscow 119991, Russia
| | - Timofei S Zatsepin
- Chemistry Department, Lomonosov Moscow State University, Leninskie Gory, Moscow 119991, Russia; Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia; Skolkovo Institute of Science and Technology, 3 Nobel Street, Skolkovo, Moscow Region 143026, Russia.
| | - Andrey V Golovin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Evgeny S Belyaev
- Institute for Energy Problems of Chemical Physics of RAS, Leninskij pr. 38/2, Moscow 119334, Russia
| | - Yury I Kostyukevich
- Skolkovo Institute of Science and Technology, 3 Nobel Street, Skolkovo, Moscow Region 143026, Russia
| | - Vladimir G Dedkov
- Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia
| | - German A Shipulin
- Central Research Institute of Epidemiology, Novogireevskaya 3a, Moscow 111123, Russia
| | - George V Shpakovski
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, Moscow 117997, Russia
| | - Andrey V Aralov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, Moscow 117997, Russia.
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58
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Klymchenko AS. Solvatochromic and Fluorogenic Dyes as Environment-Sensitive Probes: Design and Biological Applications. Acc Chem Res 2017; 50:366-375. [PMID: 28067047 DOI: 10.1021/acs.accounts.6b00517] [Citation(s) in RCA: 643] [Impact Index Per Article: 91.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Fluorescent environment-sensitive probes are specially designed dyes that change their fluorescence intensity (fluorogenic dyes) or color (e.g., solvatochromic dyes) in response to change in their microenvironment polarity, viscosity, and molecular order. The studies of the past decade, including those of our group, have shown that these molecules become universal tools in fluorescence sensing and imaging. In fact, any biomolecular interaction or change in biomolecular organization results in modification of the local microenvironment, which can be directly monitored by these types of probes. In this Account, the main examples of environment-sensitive probes are summarized according to their design concepts. Solvatochromic dyes constitute a large class of environment-sensitive probes which change their color in response to polarity. Generally, they are push-pull dyes undergoing intramolecular charge transfer. Emission of their highly polarized excited state shifts to the red in more polar solvents. Excited-state intramolecular proton transfer is the second key concept to design efficient solvatochromic dyes, which respond to the microenvironment by changing relative intensity of the two emissive tautomeric forms. Due to their sensitivity to polarity and hydration, solvatochromic dyes have been successfully applied to biological membranes for studying lipid domains (rafts), apoptosis and endocytosis. As fluorescent labels, solvatochromic dyes can detect practically any type of biomolecular interactions, involving proteins, nucleic acids and biomembranes, because the binding event excludes local water molecules from the interaction site. On the other hand, fluorogenic probes usually exploit intramolecular rotation (conformation change) as a design concept, with molecular rotors being main representatives. These probes were particularly efficient for imaging viscosity and lipid order in biomembranes as well as to light up biomolecular targets, such as antibodies, aptamers and receptors. The emerging concepts to achieve fluorogenic response to the microenvironment include ground-state isomerization, aggregation-caused quenching, and aggregation-induced emission. The ground-state isomerization exploits, for instance, polarity-dependent spiro-lactone formation in silica-rhodamines. The aggregation-caused quenching uses disruption of the self-quenched dimers and nanoassemblies of dyes in less polar environments of lipid membranes and biomolecules. The aggregation-induced emission couples target recognition with formation of highly fluorescent dye aggregates. Overall, solvatochromic and fluorogenic probes enable background-free bioimaging in wash-free conditions as well as quantitative analysis when combined with advanced microscopy, such as fluorescence lifetime (FLIM) and ratiometric imaging. Further development of fluorescent environment-sensitive probes should address some remaining problems: (i) improving their optical properties, especially brightness, photostability, and far-red to near-infrared operating range; (ii) minimizing nonspecific interactions of the probes in biological systems; (iii) their adaptation for advanced microscopies, notably for superresolution and in vivo imaging.
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Affiliation(s)
- Andrey S. Klymchenko
- Laboratoire de Biophotonique et Pharmacologie,
UMR 7213 CNRS, Université de Strasbourg, F-67000 Strasbourg, France
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59
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Murayama K, Asanuma H. Effect of Methyl Group on Acyclic Serinol Scaffold for Tethering Dyes on the DNA Duplex Stability. Chembiochem 2016; 18:142-149. [DOI: 10.1002/cbic.201600558] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Indexed: 12/19/2022]
Affiliation(s)
- Keiji Murayama
- Graduate School of Engineering; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8603 Japan
| | - Hiroyuki Asanuma
- Graduate School of Engineering; Nagoya University; Furo-cho Chikusa-ku Nagoya 464-8603 Japan
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60
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Rapid nuclear import of short nucleic acids. Bioorg Med Chem Lett 2016; 26:4568-4570. [PMID: 27597250 DOI: 10.1016/j.bmcl.2016.08.085] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 08/23/2016] [Accepted: 08/26/2016] [Indexed: 01/12/2023]
Abstract
Exogenous short-chain nucleic acids undergo rapid import into the nucleus. Fluorescence-labeled dT1-13 DNA microinjected into the cytoplasm domain of a HeLa cell was rapidly imported into the nucleus domain within 1min. This is much more rapid than what has been observed for intracellular diffusion of small molecules. In contrast, import of longer nucleic acids with a length of over 30nt into the nucleus was suppressed.
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61
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Ohmachi M, Fujiwara Y, Muramatsu S, Yamada K, Iwata O, Suzuki K, Wang DO. A modified single-cell electroporation method for molecule delivery into a motile protist, Euglena gracilis. J Microbiol Methods 2016; 130:106-111. [PMID: 27558617 DOI: 10.1016/j.mimet.2016.08.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/19/2016] [Accepted: 08/19/2016] [Indexed: 12/31/2022]
Abstract
Single-cell transfection is a powerful technique for delivering chemicals, drugs, or probes into arbitrary, specific single cells. This technique is especially important when the analysis of molecular function and cellular behavior in individual microscopic organisms such as protists requires the precise identification of the target cell, as fluorescence labeling of bulk populations makes tracking of individual motile protists virtually impossible. Herein, we have modified current single-cell electroporation techniques for delivering fluorescent markers into single Euglena gracilis, a motile photosynthetic microalga. Single-cell electroporation introduced molecules into individual living E. gracilis cells after a negative pressure was applied through a syringe connected to the micropipette to the target cell. The new method achieves high transfection efficiency and viability after electroporation. With the new technique, we successfully introduced a variety of molecules such as GFP, Alexa Fluor 488, and exciton-controlled hybridization-sensitive fluorescent oligonucleotide (ECHO) RNA probes into individual motile E. gracilis cells. We demonstrate imaging of endogenous mRNA in living E. gracilis without interfering with their physiological functions, such as swimming or division, over an extended period of time. Thus the modified single-cell electroporation technique is suitable for delivering versatile functional molecules into individual motile protists.
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Affiliation(s)
- Masashi Ohmachi
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Yoshie Fujiwara
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan
| | - Shuki Muramatsu
- Research & Development Department, euglena Co., Ltd., Shiba, Minato-ku, Tokyo 108-0014, Japan
| | - Koji Yamada
- Research & Development Department, euglena Co., Ltd., Shiba, Minato-ku, Tokyo 108-0014, Japan
| | - Osamu Iwata
- Research & Development Department, euglena Co., Ltd., Shiba, Minato-ku, Tokyo 108-0014, Japan
| | - Kengo Suzuki
- Research & Development Department, euglena Co., Ltd., Shiba, Minato-ku, Tokyo 108-0014, Japan
| | - Dan Ohtan Wang
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto 606-8501, Japan.
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62
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Wu TW, Lee FH, Gao RC, Chew CY, Tan KT. Fluorescent Probe Encapsulated in Avidin Protein to Eliminate Nonspecific Fluorescence and Increase Detection Sensitivity in Blood Serum. Anal Chem 2016; 88:7873-7. [DOI: 10.1021/acs.analchem.6b02111] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Ting-Wei Wu
- Department of Chemistry, National Tsing Hua University, 101 Section
2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Fang-Hong Lee
- Department of Chemistry, National Tsing Hua University, 101 Section
2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Ruo-Cing Gao
- Department of Chemistry, National Tsing Hua University, 101 Section
2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Chee Ying Chew
- Department of Chemistry, National Tsing Hua University, 101 Section
2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
| | - Kui-Thong Tan
- Department of Chemistry, National Tsing Hua University, 101 Section
2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
- Frontier Research Center on Fundamental and Applied Sciences
of Matters, National Tsing Hua University, 101 Section 2, Kuang Fu Road, Hsinchu 30013, Taiwan, Republic of China
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63
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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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64
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Kumar Verma R, Takei F, Nakatani K. Synthesis and Photophysical Properties of Fluorescence Molecular Probe for Turn-ON-Type Detection of Cytosine Bulge DNA. Org Lett 2016; 18:3170-3. [DOI: 10.1021/acs.orglett.6b01378] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Rajiv Kumar Verma
- Department
of Regulatory Bioorganic Chemistry, The Institute of Scientific and
Industrial Research, Osaka University, Mihogaoka, 8-1,
Ibaraki, Osaka 567-0047, Japan
| | - Fumie Takei
- National Defense Medical College, Namiki, 3-2, Tokorozawa, Saitama 359-8513, Japan
| | - Kazuhiko Nakatani
- Department
of Regulatory Bioorganic Chemistry, The Institute of Scientific and
Industrial Research, Osaka University, Mihogaoka, 8-1,
Ibaraki, Osaka 567-0047, Japan
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65
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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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66
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Zakharova GV, Konstantinov RR, Odinokov AV, Chibisov AK, Alfimov MV, Kasheverov IE, Utkin YN, Zhmak MN, Tsetlin VI. Effect of a peptide modeling the nicotinic receptor binding site on the spectral and luminescent properties of dye complexes with cucurbit[8]uril. HIGH ENERGY CHEMISTRY 2016. [DOI: 10.1134/s0018143916020090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Kimura Y, Soma T, Kasahara N, Delobel D, Hanami T, Tanaka Y, de Hoon MJL, Hayashizaki Y, Usui K, Harbers M. Edesign: Primer and Enhanced Internal Probe Design Tool for Quantitative PCR Experiments and Genotyping Assays. PLoS One 2016; 11:e0146950. [PMID: 26863543 PMCID: PMC4749234 DOI: 10.1371/journal.pone.0146950] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Accepted: 12/22/2015] [Indexed: 01/13/2023] Open
Abstract
Analytical PCR experiments preferably use internal probes for monitoring the amplification reaction and specific detection of the amplicon. Such internal probes have to be designed in close context with the amplification primers, and may require additional considerations for the detection of genetic variations. Here we describe Edesign, a new online and stand-alone tool for designing sets of PCR primers together with an internal probe for conducting quantitative real-time PCR (qPCR) and genotypic experiments. Edesign can be used for selecting standard DNA oligonucleotides like for instance TaqMan probes, but has been further extended with new functions and enhanced design features for Eprobes. Eprobes, with their single thiazole orange-labelled nucleotide, allow for highly sensitive genotypic assays because of their higher DNA binding affinity as compared to standard DNA oligonucleotides. Using new thermodynamic parameters, Edesign considers unique features of Eprobes during primer and probe design for establishing qPCR experiments and genotyping by melting curve analysis. Additional functions in Edesign allow probe design for effective discrimination between wild-type sequences and genetic variations either using standard DNA oligonucleotides or Eprobes. Edesign can be freely accessed online at http://www.dnaform.com/edesign2/, and the source code is available for download.
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Affiliation(s)
- Yasumasa Kimura
- K.K. DNAFORM, 75–1, Ono-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0046, Japan
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Takahiro Soma
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Naoko Kasahara
- RIKEN Omics Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Diane Delobel
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Takeshi Hanami
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Yuki Tanaka
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Michiel J. L. de Hoon
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine & Diagnosis Innovation Program, 2–1 Hirosawa, Wako-shi, Saitama, 351–0198, Japan
| | - Kengo Usui
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
- RIKEN Preventive Medicine & Diagnosis Innovation Program, 2–1 Hirosawa, Wako-shi, Saitama, 351–0198, Japan
| | - Matthias Harbers
- RIKEN Center for Life Science Technologies, Division of Genomic Technologies, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230–0045, Japan
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Lugovski AА, Samtsov MP, Kaplevsky KN, Tarasau D, Voropay ES, Petrov PT, Istomin YP. Novel indotricarbocyanine dyes covalently bonded to polyethylene glycol for theranostics. J Photochem Photobiol A Chem 2016. [DOI: 10.1016/j.jphotochem.2015.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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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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70
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Tokugawa M, Masaki Y, Canggadibrata JC, Kaneko K, Shiozawa T, Kanamori T, Grøtli M, Wilhelmsson LM, Sekine M, Seio K. 7-(Benzofuran-2-yl)-7-deazadeoxyguanosine as a fluorescence turn-ON probe for single-strand DNA binding protein. Chem Commun (Camb) 2016; 52:3809-12. [DOI: 10.1039/c5cc09700b] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
7-(Benzofuran-2-yl)-7-deazadeoxyguanosine (BFdG) was synthesized and incorporated into an oligodeoxynucleotide (ODN).
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Affiliation(s)
- Munefumi Tokugawa
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Yoshiaki Masaki
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | | | - Kazuhei Kaneko
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Takashi Shiozawa
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Takashi Kanamori
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Morten Grøtli
- Department of Chemistry and Molecular Biology
- University of Gothenburg
- S-41296 Gothenburg
- Sweden
| | - L. Marcus Wilhelmsson
- Department of Chemistry and Chemical Engineering/Chemistry and Biochemistry
- Chalmers University of Technology
- S-41296 Gothenburg
- Sweden
| | - Mitsuo Sekine
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
| | - Kohji Seio
- Department of Life Science
- Tokyo Institute of Technology
- Midori-ku
- Japan
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71
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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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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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73
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Rombouts K, Braeckmans K, Remaut K. Fluorescent Labeling of Plasmid DNA and mRNA: Gains and Losses of Current Labeling Strategies. Bioconjug Chem 2015; 27:280-97. [PMID: 26670733 DOI: 10.1021/acs.bioconjchem.5b00579] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Live-cell imaging has provided the life sciences with insights into the cell biology and dynamics. Fluorescent labeling of target molecules proves to be indispensable in this regard. In this Review, we focus on the current fluorescent labeling strategies for nucleic acids, and in particular mRNA (mRNA) and plasmid DNA (pDNA), which are of interest to a broad range of scientific fields. By giving a background of the available techniques and an evaluation of the pros and cons, we try to supply scientists with all the information needed to come to an informed choice of nucleic acid labeling strategy aimed at their particular needs.
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Affiliation(s)
- K Rombouts
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Braeckmans
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Remaut
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
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Abstract
Biosensors first appeared several decades ago to address the need for monitoring physiological parameters such as oxygen or glucose in biological fluids such as blood. More recently, a new wave of biosensors has emerged in order to provide more nuanced and granular information about the composition and function of living cells. Such biosensors exist at the confluence of technology and medicine and often strive to connect cell phenotype or function to physiological or pathophysiological processes. Our review aims to describe some of the key technological aspects of biosensors being developed for cell analysis. The technological aspects covered in our review include biorecognition elements used for biosensor construction, methods for integrating cells with biosensors, approaches to single-cell analysis, and the use of nanostructured biosensors for cell analysis. Our hope is that the spectrum of possibilities for cell analysis described in this review may pique the interest of biomedical scientists and engineers and may spur new collaborations in the area of using biosensors for cell analysis.
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Affiliation(s)
- Qing Zhou
- Department of Biomedical Engineering, University of California, Davis, California 95616;
| | - Kyungjin Son
- Department of Biomedical Engineering, University of California, Davis, California 95616;
| | - Ying Liu
- Department of Biomedical Engineering, University of California, Davis, California 95616;
| | - Alexander Revzin
- Department of Biomedical Engineering, University of California, Davis, California 95616;
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75
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Takei F, Chen X, Yu G, Shibata T, Dohno C, Nakatani K. Cytosine-bulge-dependent fluorescence quenching for the real-time hairpin primer PCR. Chem Commun (Camb) 2015; 50:15195-8. [PMID: 25338232 DOI: 10.1039/c4cc06780k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The progress of a polymerase chain reaction (PCR) was sensitively monitored based on the increase in fluorescence of N,N'-bis(3-aminopropyl)-2,7-diamino-1,8-naphthyridine, which was covalently anchored on the cytosine bulge directly neighbouring the 5'-T_G-3'/5'-CCA-3' sequence in the hairpin tag at the 5' end of the PCR primer.
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Affiliation(s)
- F Takei
- The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, 567-0047 Japan.
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76
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Saito Y, Suzuki A, Yamauchi T, Saito I. Design and synthesis of 7-naphthyl-8-aza-7-deaza-2′-deoxyadenosines as environmentally sensitive fluorescent nucleosides. Tetrahedron Lett 2015. [DOI: 10.1016/j.tetlet.2014.10.116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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77
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Barrois S, Wörner S, Wagenknecht HA. The role of duplex stability for wavelength-shifting fluorescent DNA probes: energy transfer vs. exciton interactions in DNA "traffic lights". Photochem Photobiol Sci 2015; 13:1126-9. [PMID: 25000916 DOI: 10.1039/c4pp00153b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Exciton interactions between thiazole orange and thiazole red as nucleotide substitutes in DNA hairpins interfere with efficient energy transfer and fluorescence color change as readout. This interference can be tuned by two structural parameters that control the hairpin duplex stability.
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Affiliation(s)
- Sebastian Barrois
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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78
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Fontenete S, Leite M, Guimarães N, Madureira P, Ferreira RM, Figueiredo C, Wengel J, Azevedo NF. Towards Fluorescence In Vivo Hybridization (FIVH) Detection of H. pylori in Gastric Mucosa Using Advanced LNA Probes. PLoS One 2015; 10:e0125494. [PMID: 25915865 PMCID: PMC4410960 DOI: 10.1371/journal.pone.0125494] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 03/12/2015] [Indexed: 12/13/2022] Open
Abstract
In recent years, there have been several attempts to improve the diagnosis of infection caused by Helicobacter pylori. Fluorescence in situ hybridization (FISH) is a commonly used technique to detect H. pylori infection but it requires biopsies from the stomach. Thus, the development of an in vivo FISH-based method (FIVH) that directly detects and allows the visualization of the bacterium within the human body would significantly reduce the time of analysis, allowing the diagnosis to be performed during endoscopy. In a previous study we designed and synthesized a phosphorothioate locked nucleic acid (LNA)/ 2’ O-methyl RNA (2’OMe) probe using standard phosphoramidite chemistry and FISH hybridization was then successfully performed both on adhered and suspended bacteria at 37°C. In this work we simplified, shortened and adapted FISH to work at gastric pH values, meaning that the hybridization step now takes only 30 minutes and, in addition to the buffer, uses only urea and probe at non-toxic concentrations. Importantly, the sensitivity and specificity of the FISH method was maintained in the range of conditions tested, even at low stringency conditions (e.g., low pH). In conclusion, this methodology is a promising approach that might be used in vivo in the future in combination with a confocal laser endomicroscope for H. pylori visualization.
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Affiliation(s)
- Sílvia Fontenete
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
- ICBAS, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
- * E-mail:
| | - Marina Leite
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Nuno Guimarães
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Odense M, Denmark
| | - Pedro Madureira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- ICBAS, Institute of Biomedical Sciences Abel Salazar, University of Porto, Porto, Portugal
- IBMC, Institute for Molecular Biology and Cell Biology, Porto, Portugal
| | - Rui Manuel Ferreira
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Céu Figueiredo
- Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- FMUP, Faculty of Medicine of Porto University, Porto, Portugal
| | - Jesper Wengel
- IPATIMUP, Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
| | - Nuno Filipe Azevedo
- LEPABE, Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
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79
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Hayashi G, Yanase M, Takeda K, Sakakibara D, Sakamoto R, Wang DO, Okamoto A. Hybridization-sensitive fluorescent oligonucleotide probe conjugated with a bulky module for compartment-specific mRNA monitoring in a living cell. Bioconjug Chem 2015; 26:412-7. [PMID: 25710491 DOI: 10.1021/acs.bioconjchem.5b00090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Live-cell RNA imaging at specific intracellular locations is technically limited because of the diffusive nature of small oligonucleotide probes. The bulky fluorescent light-up probes that possess streptavidin or gold nanoparticles at the end of oligonucleotides were designed and synthesized. The bulky probes allowed nucleus- and cytoplasm-selective monitoring of endogenous mRNAs through nuclear and cytoplasmic microinjection, respectively. Simultaneous use of bulky and unbulky probes conjugated with different fluorescent dyes enabled dual color imaging of mRNAs present in nucleus and cytoplasm. Furthermore, we observed that the fluorescence near the cell edge in a living HeLa cell traveled over time in coordination with the dynamic formation and deformation of the pseudopodial protrusions after lipofection of the bulky probes.
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Affiliation(s)
- Gosuke Hayashi
- †Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Masafumi Yanase
- †Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Katsuya Takeda
- †Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Daisuke Sakakibara
- †Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Ryosuke Sakamoto
- †Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Dan Ohtan Wang
- ‡Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto, 606-8501, Japan
| | - Akimitsu Okamoto
- †Department of Chemistry and Biotechnology, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan.,§Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo 153-8904, Japan
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80
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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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81
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Wang DO, Okamoto A. Visualization of nucleic acids with synthetic exciton-controlled fluorescent oligonucleotide probes. Methods Mol Biol 2015; 1262:69-87. [PMID: 25555576 DOI: 10.1007/978-1-4939-2253-6_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Engineered probes to adapt new photochemical properties upon recognition of target nucleic acids offer powerful tools to DNA and RNA visualization technologies. Herein, we describe a rapid and effective visualization method of nucleic acids in both fixed and living cells with hybridization-sensitive fluorescent oligonucleotide probes. These probes are efficiently quenched in an aqueous environment due to the homodimeric, excitonic interactions between fluorophores but become highly fluorescent upon hybridization to DNA or RNA with complementary sequences. The fast hybridization kinetics and quick fluorescence activation of the new probes allow applications to simplify the conventional fluorescent in situ hybridization protocols and reduce the amount of time to process the samples. Furthermore, hybridization-sensitive fluorescence emission of the probes allows monitoring dynamic behaviors of RNA in living cells.
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Affiliation(s)
- Dan Ohtan Wang
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Yoshida-Honmachi, Sakyo-ku, Kyoto, 606-8501, Japan,
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82
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Wu H, Cisneros BT, Cole C, Devaraj NK. Bioorthogonal tetrazine-mediated transfer reactions facilitate reaction turnover in nucleic acid-templated detection of microRNA. J Am Chem Soc 2014; 136:17942-5. [PMID: 25495860 PMCID: PMC4291768 DOI: 10.1021/ja510839r] [Citation(s) in RCA: 118] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Indexed: 12/17/2022]
Abstract
Tetrazine ligations have proven to be a powerful bioorthogonal technique for the detection of many labeled biomolecules, but the ligating nature of these reactions can limit reaction turnover in templated chemistry. We have developed a transfer reaction between 7-azabenzonorbornadiene derivatives and fluorogenic tetrazines that facilitates turnover amplification of the fluorogenic response in nucleic acid-templated reactions. Fluorogenic tetrazine-mediated transfer (TMT) reaction probes can be used to detect DNA and microRNA (miRNA) templates to 0.5 and 5 pM concentrations, respectively. The endogenous oncogenic miRNA target mir-21 could be detected in crude cell lysates and detected by imaging in live cells. Remarkably, the technique is also able to differentiate between miRNA templates bearing a single mismatch with high signal to background. We imagine that TMT reactions could find wide application for amplified fluorescent detection of clinically relevant nucleic acid templates.
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Affiliation(s)
- Haoxing Wu
- Department
of Chemistry and
Biochemistry, University of California,
San Diego, La Jolla, California 92093, United States
| | - Brandon T. Cisneros
- Department
of Chemistry and
Biochemistry, University of California,
San Diego, La Jolla, California 92093, United States
| | - Christian
M. Cole
- Department
of Chemistry and
Biochemistry, University of California,
San Diego, La Jolla, California 92093, United States
| | - Neal K. Devaraj
- Department
of Chemistry and
Biochemistry, University of California,
San Diego, La Jolla, California 92093, United States
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83
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Karpenko IA, Collot M, Richert L, Valencia C, Villa P, Mély Y, Hibert M, Bonnet D, Klymchenko AS. Fluorogenic Squaraine Dimers with Polarity-Sensitive Folding As Bright Far-Red Probes for Background-Free Bioimaging. J Am Chem Soc 2014; 137:405-12. [DOI: 10.1021/ja5111267] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Iuliia A. Karpenko
- Laboratoire
d’Innovation Thérapeutique, UMR 7200 CNRS/Université de Strasbourg, Labex MEDALIS, Faculté de Pharmacie, 74
route du Rhin, 67401 Illkirch, France
| | - Mayeul Collot
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213 CNRS/Université de Strasbourg,
Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Ludovic Richert
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213 CNRS/Université de Strasbourg,
Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Christel Valencia
- Platform
of Integrative Chemical Biology of Strasbourg (PCBIS), FMTS, UMS 3286 CNRS/Université de Strasbourg, ESBS Pôle API, Bld Sébastien Brant, 67401 Illkirch, France
| | - Pascal Villa
- Platform
of Integrative Chemical Biology of Strasbourg (PCBIS), FMTS, UMS 3286 CNRS/Université de Strasbourg, ESBS Pôle API, Bld Sébastien Brant, 67401 Illkirch, France
| | - Yves Mély
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213 CNRS/Université de Strasbourg,
Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
| | - Marcel Hibert
- Laboratoire
d’Innovation Thérapeutique, UMR 7200 CNRS/Université de Strasbourg, Labex MEDALIS, Faculté de Pharmacie, 74
route du Rhin, 67401 Illkirch, France
| | - Dominique Bonnet
- Laboratoire
d’Innovation Thérapeutique, UMR 7200 CNRS/Université de Strasbourg, Labex MEDALIS, Faculté de Pharmacie, 74
route du Rhin, 67401 Illkirch, France
| | - Andrey S. Klymchenko
- Laboratoire
de Biophotonique et Pharmacologie, UMR 7213 CNRS/Université de Strasbourg,
Faculté de Pharmacie, 74 route du Rhin, 67401 Illkirch, France
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84
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Kanamori T, Ohzeki H, Masaki Y, Ohkubo A, Takahashi M, Tsuda K, Ito T, Shirouzu M, Kuwasako K, Muto Y, Sekine M, Seio K. Controlling the fluorescence of benzofuran-modified uracil residues in oligonucleotides by triple-helix formation. Chembiochem 2014; 16:167-76. [PMID: 25469677 DOI: 10.1002/cbic.201402346] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Indexed: 12/16/2022]
Abstract
We developed fluorescent turn-on probes containing a fluorescent nucleoside, 5-(benzofuran-2-yl)deoxyuridine (dU(BF)) or 5-(3-methylbenzofuran-2-yl)deoxyuridine (dU(MBF)), for the detection of single-stranded DNA or RNA by utilizing DNA triplex formation. Fluorescence measurements revealed that the probe containing dU(MBF) achieved superior fluorescence enhancement than that containing dU(BF). NMR and fluorescence analyses indicated that the fluorescence intensity increased upon triplex formation partly as a consequence of a conformational change at the bond between the 3-methylbenzofuran and uracil rings. In addition, it is suggested that the microenvironment around the 3-methylbenzofuran ring contributed to the fluorescence enhancement. Further, we developed a method for detecting RNA by rolling circular amplification in combination with triplex-induced fluorescence enhancement of the oligonucleotide probe containing dU(MBF).
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Affiliation(s)
- Takashi Kanamori
- Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501 (Japan)
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85
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Bohländer PR, Wagenknecht HA. Synthesis of a Photostable Energy-Transfer Pair for “DNA Traffic Lights”. European J Org Chem 2014. [DOI: 10.1002/ejoc.201403119] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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86
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Bohländer PR, Wagenknecht HA. Synthesis and evaluation of cyanine-styryl dyes with enhanced photostability for fluorescent DNA staining. Org Biomol Chem 2014; 11:7458-62. [PMID: 24088963 DOI: 10.1039/c3ob41717d] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The photostability of cyanine-styryl dyes of the indole-quinolinium type can be significantly improved by structural variations while the excellent optical properties including the bright fluorescence in the presence of DNA can be maintained or even improved, too.
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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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87
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Zou T, Liu J, Lum CT, Ma C, Chan RCT, Lok CN, Kwok WM, Che CM. Luminescent Cyclometalated Platinum(II) Complex Forms Emissive Intercalating Adducts with Double-Stranded DNA and RNA: Differential Emissions and Anticancer Activities. Angew Chem Int Ed Engl 2014; 53:10119-23. [DOI: 10.1002/anie.201405384] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Indexed: 12/21/2022]
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88
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Zou T, Liu J, Lum CT, Ma C, Chan RCT, Lok CN, Kwok WM, Che CM. Luminescent Cyclometalated Platinum(II) Complex Forms Emissive Intercalating Adducts with Double-Stranded DNA and RNA: Differential Emissions and Anticancer Activities. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405384] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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89
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Stubinitzky C, Vilaivan T, Wagenknecht HA. The base discriminating potential of pyrrolidinyl PNA demonstrated by magnetic Fe(x)O(y) particles. Org Biomol Chem 2014; 12:3586-9. [PMID: 24777755 DOI: 10.1039/c4ob00487f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Pyrrolidinyl PNA was immobilized on Fe(x)O(y) magnetic particles and was able to capture and thereby discriminate single base alterations in DNA counterstrands better than DNA. The selectivities of matched vs. mismatched oligonucleotides measured by the absorption differences were up to 10-12 which are remarkable values for linear probes.
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Affiliation(s)
- Claudia Stubinitzky
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany.
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90
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Kim KT, Kim HW, Moon D, Rhee YM, Kim BH. (DNS)C: a fluorescent, environmentally sensitive cytidine derivative for the direct detection of GGG triad sequences. Org Biomol Chem 2014; 11:5605-14. [PMID: 23846401 DOI: 10.1039/c3ob41222a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
With the goal of developing a fluorescent nucleoside sensitive to its environment, in this study we synthesized (DNS)C, a novel modified 2'-deoxycytidine bearing a 5-(dimethylamino)naphthalene-1-sulfonyl (dansyl) moiety at the N4 position, and tested its properties in monomeric and oligomeric states. (DNS)C undergoes intramolecular photoinduced electron transfer between its dansyl and cytosine units, resulting in remarkable changes in fluorescence that depend on the choice of solvent. In addition, the fluorescence behavior and thermal stability of oligonucleotides containing (DNS)C are dependent on the nature of the flanking and neighboring bases. Notably, (DNS)C exhibits fluorescence enhancement only in fully matched duplex DNA containing a GGG triad sequence. The environmental sensitivity of (DNS)C can be exploited as a fluorescence tool for monitoring the interactions of DNA with other biomolecules, including DNA, RNA, and proteins.
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Affiliation(s)
- Ki Tae Kim
- Department of Chemistry, BK School of Molecular Science, Pohang University of Science and Technology, Pohang 790-784, South Korea
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91
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Zhai D, Xu W, Zhang L, Chang YT. The role of "disaggregation" in optical probe development. Chem Soc Rev 2014; 43:2402-11. [PMID: 24514005 DOI: 10.1039/c3cs60368g] [Citation(s) in RCA: 124] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
"Aggregation-caused signal change" is a well-established mechanism by now and has been widely used as the basis for optical probe and sensor development. Compared to aggregation, its reverse process, disaggregation, has received much less attention and is not properly discussed in the literature so far. With the less established paradigm or mechanism, although some of the reported sensors and probes seem to work through disaggregation phenomena, the proper interpretation of the results and applying the concept to novel probe development is seriously hampered. The process from aggregation to disaggregation generally causes a recovery or enhancement of fluorescence signals, and thus provides an interesting new path to design "turn-on" probes. This tutorial review will provide the balanced comparison between aggregation and disaggregation mechanism, and focuses on the less explored advantages of "disaggregation" as a novel sensing mechanism and its recent applications in probe development.
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Affiliation(s)
- Duanting Zhai
- Department of Chemistry and MedChem Program, Life Sciences Institude, National University of Singapore, 3 Science Drive 3, Singapore117543.
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92
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Göhring J, Jacak J, Barta A. Imaging of endogenous messenger RNA splice variants in living cells reveals nuclear retention of transcripts inaccessible to nonsense-mediated decay in Arabidopsis. THE PLANT CELL 2014; 26:754-64. [PMID: 24532591 PMCID: PMC3967038 DOI: 10.1105/tpc.113.118075] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 01/14/2014] [Accepted: 01/26/2014] [Indexed: 05/18/2023]
Abstract
Alternative splicing (AS) is an important regulatory process that leads to the creation of multiple RNA transcripts from a single gene. Alternative transcripts often carry premature termination codons (PTCs), which trigger nonsense-mediated decay (NMD), a cytoplasmic RNA degradation pathway. However, intron retention, the most prevalent AS event in plants, often leads to PTC-carrying splice variants that are insensitive to NMD; this led us to question the fate of these special RNA variants. Here, we present an innovative approach to monitor and characterize endogenous mRNA splice variants within living plant cells. This method combines standard confocal laser scanning microscopy for molecular beacon detection with a robust statistical pipeline for sample comparison. We demonstrate this technique on the localization of NMD-insensitive splice variants of two Arabidopsis thaliana genes, RS2Z33 and the SEF factor. The experiments reveal that these intron-containing splice variants remain within the nucleus, which allows them to escape the NMD machinery. Moreover, fluorescence recovery after photobleaching experiments in the nucleoplasm show a decreased mobility of intron-retained mRNAs compared with fully spliced RNAs. In addition, differences in mobility were observed for an mRNA dependent on its origin from an intron-free or an intron-containing gene.
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93
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Lou C, Dallmann A, Marafini P, Gao R, Brown T. Enhanced H-bonding and π-stacking in DNA: a potent duplex-stabilizing and mismatch sensing nucleobase analogue. Chem Sci 2014. [DOI: 10.1039/c4sc00948g] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Combining enhanced π-stacking, H-bonding and electrostatic attraction in a single C-monomer greatly increases DNA duplex stability and massively destabilises mismatches.
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Affiliation(s)
- Chenguang Lou
- School of Chemistry
- University of Southampton
- Highfield
- Southampton SO17 1BJ, UK
| | - Andre Dallmann
- Institute of Structural Biology
- Helmholtz Zentrum München, 85764 Neuherberg, Germany
- Center for Integrated Protein Science Munich and Chair of Biomolecular NMR
- TU München
- 85747 Garching, Germany
| | - Pietro Marafini
- School of Chemistry
- University of Southampton
- Highfield
- Southampton SO17 1BJ, UK
- Department of Chemistry
| | - Rachel Gao
- School of Chemistry
- University of Southampton
- Highfield
- Southampton SO17 1BJ, UK
| | - Tom Brown
- School of Chemistry
- University of Southampton
- Highfield
- Southampton SO17 1BJ, UK
- Department of Chemistry
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94
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Tanaka M, Shigi N, Sumaoka J, Komiyama M. Thiazole orange-conjugated peptide nucleic acid for fluorescent detection of specific DNA sequences and site-selective photodamage. RSC Adv 2014. [DOI: 10.1039/c4ra13780a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Conjugates of thiazole orange (TO) with a pseudo-complementary peptide nucleic acid (pcPNA) functioned as (i) fluorescent detector of specific DNA and (ii) site-selective photodamage inducer through generation of 1O2.
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Affiliation(s)
- Makiko Tanaka
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
| | - Narumi Shigi
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
| | - Jun Sumaoka
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
| | - Makoto Komiyama
- Life Science Center of Tsukuba Advanced Research Alliance
- University of Tsukuba
- Tsukuba, Japan
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95
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Doluca O, Hale TK, Edwards PJB, González C, Filichev VV. Assembly Dependent Fluorescence Enhancing Nucleic Acids in Sequence-Specific Detection of Double-Stranded DNA. Chempluschem 2013; 79:58-66. [PMID: 31986766 DOI: 10.1002/cplu.201300310] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Revised: 10/29/2013] [Indexed: 12/19/2022]
Abstract
In this study the position of the thiazole orange derivative in triplex-forming oligonucleotides (TFOs) is varied and the fluorescence of the resulting complexes with DNA duplexes, single-stranded DNAs and RNAs are evaluated. Under similar conditions single attachment of the TO-dye to 2'-O-propargyl nucleotides in the TFOs (assembly dependent fluorescence enhancing nucleic acids, AFENA) led to probes with low fluorescent intensity in the single-stranded state with fluorescence quantum yield (ΦF ) of 0.9 %-1.5 %. Significant increase in fluorescence intensity was detected after formation of DNA triplexes (ΦF =23.5 %-34.9 %). Under similar conditions, Watson-Crick-type duplexes formed by the probes with single stranded (ss) RNA and ssDNA showed lower fluorescence intensities. Bugle insertions of twisted intercalating nucleic acid (TINA) monomers were shown to improve the fluorescent characteristics of GT/GA-containing antiparallel AFENA-TFOs. Self-aggregation of TFOs caused by guanosines was eliminated by TINA insertion which also promoted DNA triplex formation at pH 7.2. Importantly these AFENA-TINA-TFOs can bind to the duplex in the presence of complementary RNA at 37 °C.
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Affiliation(s)
- Osman Doluca
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North (New Zealand), Fax: (+64) 6-3505682.,International Burch University, Francuske Revolucije, 71210 Sarajevo (Bosnia and Herzegovina)
| | - Tracy K Hale
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North (New Zealand), Fax: (+64) 6-3505682
| | - Patrick J B Edwards
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North (New Zealand), Fax: (+64) 6-3505682
| | - Carlos González
- Instituto de Química Física Rocasalano, CSIC, Serrano 119, 28006 Madrid (Spain)
| | - Vyacheslav V Filichev
- College of Sciences, Institute of Fundamental Sciences, Massey University, Private Bag 11-222, 4442 Palmerston North (New Zealand), Fax: (+64) 6-3505682
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96
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Holzhauser C, Rubner MM, Wagenknecht HA. Energy-transfer-based wavelength-shifting DNA probes with "clickable" cyanine dyes. Photochem Photobiol Sci 2013; 12:722-4. [PMID: 23314253 DOI: 10.1039/c2pp25366f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The insertion of cyanine dye azides as energy donor dyes via postsynthetic "click"-type cycloaddition chemistry with e.g. a new thiazole orange azide combined with thiazole red yields dual emitting DNA probes with good fluorescence readout properties.
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Affiliation(s)
- Carolin Holzhauser
- Institute of Organic Chemistry, Karlsruhe Institute of Technology, Fritz-Haber-Weg 6, 76131 Karlsruhe, Germany
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97
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Eprobe mediated real-time PCR monitoring and melting curve analysis. PLoS One 2013; 8:e70942. [PMID: 23951046 PMCID: PMC3737233 DOI: 10.1371/journal.pone.0070942] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 06/25/2013] [Indexed: 01/10/2023] Open
Abstract
Real-time monitoring of PCR is one of the most important methods for DNA and RNA detection widely used in research and medical diagnostics. Here we describe a new approach for combined real-time PCR monitoring and melting curve analysis using a 3′ end-blocked Exciton-Controlled Hybridization-sensitive fluorescent Oligonucleotide (ECHO) called Eprobe. Eprobes contain two dye moieties attached to the same nucleotide and their fluorescent signal is strongly suppressed as single-stranded oligonucleotides by an excitonic interaction between the dyes. Upon hybridization to a complementary DNA strand, the dyes are separated and intercalate into the double-strand leading to strong fluorescence signals. Intercalation of dyes can further stabilize the DNA/DNA hybrid and increase the melting temperature compared to standard DNA oligonucleotides. Eprobes allow for specific real-time monitoring of amplification reactions by hybridizing to the amplicon in a sequence-dependent manner. Similarly, Eprobes allow for analysis of reaction products by melting curve analysis. The function of different Eprobes was studied using the L858R mutation in the human epidermal growth factor receptor (EGFR) gene, and multiplex detection was demonstrated for the human EGFR and KRAS genes using Eprobes with two different dyes. Combining amplification and melting curve analysis in a single-tube reaction provides powerful means for new mutation detection assays. Functioning as “sequence-specific dyes”, Eprobes hold great promises for future applications not only in PCR but also as hybridization probes in other applications.
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98
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Holzhauser C, Wagenknecht HA. DNA and RNA “Traffic Lights”: Synthetic Wavelength-Shifting Fluorescent Probes Based on Nucleic Acid Base Substitutes for Molecular Imaging. J Org Chem 2013; 78:7373-9. [DOI: 10.1021/jo4010102] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Carolin Holzhauser
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), D-76131 Karlsruhe,
Germany
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), D-76131 Karlsruhe,
Germany
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99
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Seckute J, Yang J, Devaraj NK. Rapid oligonucleotide-templated fluorogenic tetrazine ligations. Nucleic Acids Res 2013; 41:e148. [PMID: 23775794 PMCID: PMC3753649 DOI: 10.1093/nar/gkt540] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Template driven chemical ligation of fluorogenic probes represents a powerful method for DNA and RNA detection and imaging. Unfortunately, previous techniques have been hampered by requiring chemistry with sluggish kinetics and background side reactions. We have developed fluorescent DNA probes containing quenched fluorophore-tetrazine and methyl-cyclopropene groups that rapidly react by bioorthogonal cycloaddition in the presence of complementary DNA or RNA templates. Ligation increases fluorescence with negligible background signal in the absence of hybridization template. Reaction kinetics depend heavily on template length and linker structure. Using this technique, we demonstrate rapid discrimination between single template mismatches both in buffer and cell media. Fluorogenic bioorthogonal ligations offer a promising route towards the fast and robust fluorescent detection of specific DNA or RNA sequences.
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Affiliation(s)
- Jolita Seckute
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
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100
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Bortolozzi R, Ihmels H, Thomas L, Tian M, Viola G. 9-(4-Dimethylaminophenyl)benzo[b]quinolizinium: a near-infrared fluorophore for the multicolor analysis of proteins and nucleic acids in living cells. Chemistry 2013; 19:8736-41. [PMID: 23703698 DOI: 10.1002/chem.201301164] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Indexed: 01/08/2023]
Affiliation(s)
- Roberta Bortolozzi
- Dipartimento di Salute della Donna e del Bambino, Laboratorio di Oncoematologia, University of Padova, via Giustiniani 3, I-35128 Padova, Italy
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