1
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Kim Y, Jang S, Chang C, Kim KT. Facile Strategy to Output Fluorescein from Nucleic Acid Interactions. Bioconjug Chem 2023; 34:1606-1612. [PMID: 37639511 DOI: 10.1021/acs.bioconjchem.3c00276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Biomolecular operations, which involve the conversion of molecular signals or interactions into specific functional outputs, are fundamental to the field of biology and serve as the important foundation for the design of diagnostic and therapeutic systems. To maximize their functionalities and broaden their applicability, it is crucial to develop novel outputs and facile chemical transformation methods. With this aim, in this study, we present a straightforward method for converting nucleic acid signals into fluorescein outputs that exhibit a wide range of functionalities. This operation is designed through a DNA-templated reaction based on riboflavin-photocatalyzed oxidation of dihydrofluorescein, which is readily prepared by simple NaBH4 reduction of the fluorescein with no complicated chemical caging steps. The templated photooxidation exhibits high efficiency (kapp = 2.7 × 10-3/s), generating a clear fluorescein output signal distinguishable from a low background, originating from the high stability of the synthesized dihydrofluorescein. This facile and efficient operation allows the nucleic acid-initiated activation of various fluorescein functions, such as fluorescence and artificial oxidase activity, which are applied in the design of novel bioanalytical systems, including fluorescent and colorimetric DNA sensors. The operation presented herein would expand the scope of biomolecular circuit systems for diagnostic and therapeutic applications.
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Affiliation(s)
- Yeojin Kim
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Sarah Jang
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Chuljoo Chang
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Republic of Korea
| | - Ki Tae Kim
- Department of Chemistry, Chungbuk National University, Cheongju 28644, Republic of Korea
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2
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Houska R, Stutz MB, Seitz O. Expanding the scope of native chemical ligation - templated small molecule drug synthesis via benzanilide formation. Chem Sci 2021; 12:13450-13457. [PMID: 34777764 PMCID: PMC8528049 DOI: 10.1039/d1sc00513h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 09/10/2021] [Indexed: 12/15/2022] Open
Abstract
We describe a reaction system that enables the synthesis of Bcr–Abl tyrosine kinase inhibitors (TKI) via benzanilide formation in water. The reaction is based on native chemical ligation (NCL). In contrast to previous applications, we used the NCL chemistry to establish aromatic rather than aliphatic amide bonds in coupling reactions between benzoyl and o-mercaptoaniline fragments. The method was applied for the synthesis of thiolated ponatinib and GZD824 derivatives. Acid treatment provided benzothiazole structures, which opens opportunities for diversification. Thiolation affected the affinity for Abl1 kinase only moderately. Of note, a ponatinib-derived benzothiazole also showed nanomolar affinity. NCL-enabled benzanilide formation may prove useful for fragment-based drug discovery. To show that benzanilide synthesis can be put under the control of a template, we connected the benzoyl and o-mercaptoaniline fragments to DNA and peptide nucleic acid (PNA) oligomers. Complementary RNA templates enabled adjacent binding of reactive conjugates triggering a rapid benzoyl transfer from a thioester-linked DNA conjugate to an o-mercaptoaniline-DNA or -PNA conjugate. We evaluated the influence of linker length and unpaired spacer nucleotides within the RNA template on the product yield. The data suggest that nucleic acid-templated benzanilide formation could find application in the establishment of DNA-encoded combinatorial libraries (DEL). The templated native chemical ligation between benzoyl thioesters and o-mercaptoaniline fragments proceeds in water and provides benzanilides that have nanomolar affinity for Abl1 kinase.![]()
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Affiliation(s)
- Richard Houska
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Marvin Björn Stutz
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin Brook-Taylor-Strasse 2 12489 Berlin Germany
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3
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Janett E, Diep KL, Fromm KM, Bochet CG. A Simple Reaction for DNA Sensing and Chemical Delivery. ACS Sens 2020; 5:2338-2343. [PMID: 32804492 DOI: 10.1021/acssensors.0c00988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reactions templated by nucleic acids are currently at the heart of applications in biosensing and drug release. The number of chemical reactions selectively occurring only in the presence of the template, in aqueous solutions, and at room temperature and able to release a chemical moiety is still very limited. Here, we report the use of the p-nitrophenyl carbonate (NPC) as a new reactive moiety for DNA templated reactions releasing a colored reporter by reaction with a simple amine. The easily synthesized p-nitrophenyl carbonate was integrated in an oligonucleotide and showed a very good stability as well as a high reactivity toward amines, without the need for any supplementary reagent, quantitatively releasing the red p-nitrophenolate with a half-life of about 1 h.
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Affiliation(s)
- Elia Janett
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Kim-Long Diep
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Katharina M. Fromm
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
| | - Christian G. Bochet
- Department of Chemistry, University of Fribourg, Chemin du Musée 9, CH-1700 Fribourg, Switzerland
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4
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Fujita H, Oikawa R, Hayakawa M, Tomoike F, Kimura Y, Okuno H, Hatashita Y, Fiallos Oliveros C, Bito H, Ohshima T, Tsuneda S, Abe H, Inoue T. Quantification of native mRNA dynamics in living neurons using fluorescence correlation spectroscopy and reduction-triggered fluorescent probes. J Biol Chem 2020; 295:7923-7940. [PMID: 32341124 PMCID: PMC7278347 DOI: 10.1074/jbc.ra119.010921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 04/22/2020] [Indexed: 11/06/2022] Open
Abstract
RNA localization in subcellular compartments is essential for spatial and temporal regulation of protein expression in neurons. Several techniques have been developed to visualize mRNAs inside cells, but the study of the behavior of endogenous and nonengineered mRNAs in living neurons has just started. In this study, we combined reduction-triggered fluorescent (RETF) probes and fluorescence correlation spectroscopy (FCS) to investigate the diffusion properties of activity-regulated cytoskeleton-associated protein (Arc) and inositol 1,4,5-trisphosphate receptor type 1 (Ip3r1) mRNAs. This approach enabled us to discriminate between RNA-bound and unbound fluorescent probes and to quantify mRNA diffusion parameters and concentrations in living rat primary hippocampal neurons. Specifically, we detected the induction of Arc mRNA production after neuronal activation in real time. Results from computer simulations with mRNA diffusion coefficients obtained in these analyses supported the idea that free diffusion is incapable of transporting mRNA of sizes close to those of Arc or Ip3r1 to distal dendrites. In conclusion, the combined RETF-FCS approach reported here enables analyses of the dynamics of endogenous, unmodified mRNAs in living neurons, affording a glimpse into the intracellular dynamics of RNA in live cells.
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Affiliation(s)
- Hirotaka Fujita
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Ryota Oikawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Aichi, Japan
| | - Mayu Hayakawa
- Department of Chemistry, Graduate School of Science, Nagoya University, Aichi, Japan
| | - Fumiaki Tomoike
- Department of Chemistry, Graduate School of Science, Nagoya University, Aichi, Japan
| | - Yasuaki Kimura
- Department of Chemistry, Graduate School of Science, Nagoya University, Aichi, Japan
| | - Hiroyuki Okuno
- Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima, Japan
| | - Yoshiki Hatashita
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Carolina Fiallos Oliveros
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Haruhiko Bito
- Department of Neurochemistry, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Toshio Ohshima
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Satoshi Tsuneda
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Hiroshi Abe
- Department of Chemistry, Graduate School of Science, Nagoya University, Aichi, Japan
| | - Takafumi Inoue
- Department of Life Science and Medical Bioscience, School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
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5
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Li J, Quan K, Yang Y, Yang X, Meng X, Huang J, Wang K. Engineering DNAzyme cascade for signal transduction and amplification. Analyst 2020; 145:1925-1932. [PMID: 31989119 DOI: 10.1039/c9an02003a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Inspired by the natural enzyme cascade reaction, a multiple DNAzyme cascade platform is engineered to imitate the intracellular process of signal transduction and signal amplification. In this design, when particular stimuli appear, an activated upstream DNAzyme will cleave a well-designed intermediary S1, releasing a downstream DNAzyme that can cleave the reporter substrate S2 to output signals. Thus, the signal is passed from the upstream DNAzyme to the downstream DNAzyme through a well-designed intermediary, accomplishing signal transduction and signal amplification. According to the experimental results, the DNAzyme cascades are capable of improving sensitivity for bioassays compared with that for single DNAzyme-based biocatalysis, which holds promise for potential applications, such as biomolecular computing, logic circuits and precision medicine.
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Affiliation(s)
- Jing Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China.
| | - Ke Quan
- School of Chemistry and Food Engineering, Changsha University of Science and Technology, Changsha, P. R. China
| | - Yanjing Yang
- College of Chemistry and Chemical Engineering, Central South University, Changsha, P. R. China
| | - Xiaohai Yang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China.
| | - Xiangxian Meng
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China.
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China.
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province, Hunan University, Changsha, P. R. China.
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6
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7
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RNA imaging by chemical probes. Adv Drug Deliv Rev 2019; 147:44-58. [PMID: 31398387 DOI: 10.1016/j.addr.2019.08.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 07/02/2019] [Accepted: 08/02/2019] [Indexed: 12/29/2022]
Abstract
Sequence-specific detection of intracellular RNA is one of the most important approaches to understand life phenomena. However, it is difficult to detect RNA in living cells because of its variety and scarcity. In the last three decades, several chemical probes have been developed for RNA detection in living cells. These probes are composed of DNA or artificial nucleic acid and hybridize with the target RNA in a sequence-specific manner. This hybridization triggers a change of fluorescence or a chemical reaction. In this review, we classify the probes according to the associated fluorogenic mechanism, that is, interaction between fluorophore and quencher, environmental change of fluorophore, and template reaction with/without ligation. In addition, we introduce examples of RNA imaging in living cells.
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8
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Abstract
Bioorthogonal reactions that proceed readily under physiological conditions without interference from biomolecules have found widespread application in the life sciences. Complementary to the bioorthogonal reactions that ligate two molecules, reactions that release a molecule or cleave a linker are increasingly attracting interest. Such dissociative bioorthogonal reactions have a broad spectrum of uses, for example, in controlling bio-macromolecule activity, in drug delivery, and in diagnostic assays. This review article summarizes the developed bioorthogonal reactions linked to a release step, outlines representative areas of the applications of such reactions, and discusses aspects that require further improvement.
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Affiliation(s)
- Julian Tu
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah, 84112, USA
| | - Minghao Xu
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah, 84112, USA
| | - Raphael M Franzini
- Department of Medicinal Chemistry, University of Utah, 30 S 2000 E, Salt Lake City, Utah, 84112, USA
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9
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Stewart MP, Langer R, Jensen KF. Intracellular Delivery by Membrane Disruption: Mechanisms, Strategies, and Concepts. Chem Rev 2018; 118:7409-7531. [PMID: 30052023 PMCID: PMC6763210 DOI: 10.1021/acs.chemrev.7b00678] [Citation(s) in RCA: 399] [Impact Index Per Article: 66.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Intracellular delivery is a key step in biological research and has enabled decades of biomedical discoveries. It is also becoming increasingly important in industrial and medical applications ranging from biomanufacture to cell-based therapies. Here, we review techniques for membrane disruption-based intracellular delivery from 1911 until the present. These methods achieve rapid, direct, and universal delivery of almost any cargo molecule or material that can be dispersed in solution. We start by covering the motivations for intracellular delivery and the challenges associated with the different cargo types-small molecules, proteins/peptides, nucleic acids, synthetic nanomaterials, and large cargo. The review then presents a broad comparison of delivery strategies followed by an analysis of membrane disruption mechanisms and the biology of the cell response. We cover mechanical, electrical, thermal, optical, and chemical strategies of membrane disruption with a particular emphasis on their applications and challenges to implementation. Throughout, we highlight specific mechanisms of membrane disruption and suggest areas in need of further experimentation. We hope the concepts discussed in our review inspire scientists and engineers with further ideas to improve intracellular delivery.
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Affiliation(s)
- Martin P. Stewart
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Robert Langer
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
- The Koch Institute for Integrative Cancer Research,
Massachusetts Institute of Technology, Cambridge, USA
| | - Klavs F. Jensen
- Department of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, USA
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10
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Abstract
Probes that detect specific biological materials are indispensable tools for deepening our understanding of various cellular phenomena. In live cell imaging, the probe must emit fluorescence only when a specific substance is detected. In this paper, we introduce a new probe we developed for live cell imaging. Glutathione S-transferase (GST) activity is higher in tumor cells than in normal cells and is involved in the development of resistance to various anticancer drugs. We previously reported the development of a general strategy for the synthesis of probes for detection of GST enzymes, including fluorogenic, bioluminogenic, and 19F-NMR probes. Arylsulfonyl groups were used as caging groups during probe design. The fluorogenic probes were successfully used to quantitate very low levels of GST activity in cell extracts and were also successfully applied to the imaging of microsomal MGST1 activity in living cells. The bioluminogenic and 19F-NMR probes were able to detect GST activity in Escherichia coli cells. Oligonucleotide-templated reactions are powerful tools for nucleic acid sensing. This strategy exploits the target strand as a template for two functionalized probes and provides a simple molecular mechanism for multiple turnover reactions. We developed a nucleophilic aromatic substitution reaction-triggered fluorescent probe. The probe completed its reaction within 30 s of initiation and amplified the fluorescence signal from 0.5 pM target oligonucleotide by 1500 fold under isothermal conditions. Additionally, we applied the oligonucleotide-templated reaction for molecular releasing and peptide detection.
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11
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Chang D, Kim KT, Lindberg E, Winssinger N. Accelerating Turnover Frequency in Nucleic Acid Templated Reactions. Bioconjug Chem 2017; 29:158-163. [PMID: 29178795 DOI: 10.1021/acs.bioconjchem.7b00663] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nucleic acid templated reactions have attracted attention as an important technology to sense oligonucleotides and to translate nucleic acid-based instructions into diverse outputs. Great progress has been made in accelerating the reaction in order to improve signal amplification, reaching rates where substrate turnover rather than chemical reaction is rate limiting. Herein we explore the utility of architectures inspired by three-way junction that yield a cleavage of a strand thus accelerating substrate turnover. We demonstrate that such design can overcome product inhibition in templated reactions and operate close to the rate of hybridization.
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Affiliation(s)
- Dalu Chang
- Department of Organic chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva , 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Ki Tae Kim
- Department of Organic chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva , 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Eric Lindberg
- Department of Organic chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva , 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic chemistry, NCCR Chemical Biology, Faculty of Science, University of Geneva , 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
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12
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Yu H, Zheng J, Yang S, Asiri AM, Alamry KA, Sun M, Zhang K, Wang S, Yang R. Use of a small molecule as an initiator for interchain staudinger reaction: A new ATP sensing platform using product fluorescence. Talanta 2017; 178:282-286. [PMID: 29136823 DOI: 10.1016/j.talanta.2017.09.051] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 09/15/2017] [Accepted: 09/17/2017] [Indexed: 10/18/2022]
Abstract
We demonstrated that a small molecule induced interchain Staudinger reaction can be employed for highly selective detection of adenosine triphosphate (ATP), an important energy-storage biomolecule. A designed ATP split aptamer (A1) was first functionalized with a weakly fluorescent coumarin derivative due to an azide group (azido-coumarin). The second DNA strand (A2) was covalently linked with triphenylphosphine, which could selectively and efficiently reduce azido to amino group through the Staudinger reaction. The A2 was then hybridized with a half of another designed longer DNA strand (T1). The second half of T1 was a split aptamer and selectively recognized ATP with A1 to form a sandwich structure. The specific interaction between ATP and the aptamers drew the two functionalized DNA strands (A1 and A2) together to initiate the interchain Staudinger reduction at fmol-nmol concentration level, hence produced fluorescent 7-aminocoumarin which could be used as an indicator for the presence of trace ATP. The reaction process had a concentration dependent manner with ATP in a large concentration range. Such a strategy of interchain Staudinger reaction can be extended to construct biosensors for other small functional molecules on the basis of judiciously designed aptamers.
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Affiliation(s)
- Huan Yu
- Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China; Department of Materials Science and Engineering, University of Science and Technology of China, Hefei, Anhui 230026, PR China
| | - Jing Zheng
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, PR China
| | - Sheng Yang
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, PR China
| | - Abdullah M Asiri
- NAAM Research Group, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Khalid A Alamry
- NAAM Research Group, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Mingtai Sun
- Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China
| | - Kui Zhang
- Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, Anhui 230031, PR China
| | - Suhua Wang
- School of Environment and Chemical Engineering, North China Electric Power University, Beijing 102206, China.
| | - Ronghua Yang
- Hunan Provincial Key Laboratory of Materials Protection for Electric Power and Transportation, School of Chemistry and Biological Engineering, Changsha University of Science and Technology, Changsha 410114, PR China.
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13
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George JT, Srivatsan SG. Vinyluridine as a Versatile Chemoselective Handle for the Post-transcriptional Chemical Functionalization of RNA. Bioconjug Chem 2017; 28:1529-1536. [PMID: 28406614 DOI: 10.1021/acs.bioconjchem.7b00169] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The development of modular and efficient methods to functionalize RNA with biophysical probes is very important in advancing the understanding of the structural and functional relevance of RNA in various cellular events. Herein, we demonstrate a two-step bioorthogonal chemical functionalization approach for the conjugation of multiple probes onto RNA transcripts using a 5-vinyl-modified uridine nucleotide analog (VUTP). VUTP, containing a structurally noninvasive and versatile chemoselective handle, was efficiently incorporated into RNA transcripts by in vitro transcription reactions. Furthermore, we show for the first time the use of a palladium-mediated oxidative Heck reaction in functionalizing RNA with fluorogenic probes by reacting vinyl-labeled RNA transcripts with appropriate boronic acid substrates. The vinyl label also permitted the post-transcriptional functionalization of RNA by a reagent-free inverse electron demand Diels-Alder (IEDDA) reaction in the presence of tetrazine substrates. Collectively, our results demonstrate that the incorporation of VUTP provides newer possibilities for the modular functionalization of RNA with variety of reporters.
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Affiliation(s)
- Jerrin Thomas George
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
| | - Seergazhi G Srivatsan
- Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune , Dr. Homi Bhabha Road, Pashan, Pune 411008, India
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14
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Chang D, Lindberg E, Winssinger N. Critical Analysis of Rate Constants and Turnover Frequency in Nucleic Acid-Templated Reactions: Reaching Terminal Velocity. J Am Chem Soc 2017; 139:1444-1447. [DOI: 10.1021/jacs.6b12764] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dalu Chang
- Department of Organic Chemistry,
NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, 1205 Geneva, Switzerland
| | - Eric Lindberg
- Department of Organic Chemistry,
NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, 1205 Geneva, Switzerland
| | - Nicolas Winssinger
- Department of Organic Chemistry,
NCCR Chemical Biology, Faculty of Science, University of Geneva, 30 quai Ernest-Ansermet, 1205 Geneva, Switzerland
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15
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Sawant AA, Mukherjee PP, Jangid RK, Galande S, Srivatsan SG. A clickable UTP analog for the posttranscriptional chemical labeling and imaging of RNA. Org Biomol Chem 2016; 14:5832-42. [PMID: 27173127 DOI: 10.1039/c6ob00576d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The development of robust tools and practical RNA labeling strategies that would facilitate the biophysical analysis of RNA in both cell-free and cellular systems will have profound implications in the discovery of new RNA diagnostic tools and therapeutic strategies. In this context, we describe the development of a new alkyne-modified UTP analog, 5-(1,7-octadinyl)uridine triphosphate (ODUTP), which serves as an efficient substrate for the introduction of a clickable alkyne label into RNA transcripts by bacteriophage T7 RNA polymerase and mammalian cellular RNA polymerases. The ODU-labeled RNA is effectively used by reverse transcriptase to produce cDNA, a property which could be utilized in expanding the chemical space of a RNA library in the aptamer selection scheme. Further, the alkyne label on RNA provides a convenient tool for the posttranscriptional chemical functionalization with a variety of biophysical tags (fluorescent, affinity, amino acid and sugar) by using alkyne-azide cycloaddition reaction. Importantly, the ability of endogenous RNA polymerases to specifically incorporate ODUTP into cellular RNA transcripts enabled the visualization of newly transcribing RNA in cells by microscopy using click reactions. In addition to a clickable alkyne group, ODU contains a Raman scattering label (internal disubstituted alkyne), which exhibits characteristic Raman shifts that fall in the Raman-silent region of cells. Our results indicate that an ODU label could potentially facilitate two-channel visualization of RNA in cells by using click chemistry and Raman spectroscopy. Taken together, ODU represents a multipurpose ribonucleoside tool, which is expected to provide new avenues to study RNA in cell-free and cellular systems.
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Affiliation(s)
- Anupam A Sawant
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, Dr Homi Bhabha Road, Pashan, Pune 411008, India.
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16
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Lv Y, Cui L, Peng R, Zhao Z, Qiu L, Chen H, Jin C, Zhang XB, Tan W. Entropy Beacon: A Hairpin-Free DNA Amplification Strategy for Efficient Detection of Nucleic Acids. Anal Chem 2015; 87:11714-20. [PMID: 26505212 PMCID: PMC4898272 DOI: 10.1021/acs.analchem.5b02654] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
![]()
Here, we propose an efficient strategy
for enzyme- and hairpin-free
nucleic acid detection called an entropy beacon (abbreviated as Ebeacon).
Different from previously reported DNA hybridization/displacement-based
strategies, Ebeacon is driven forward by increases in the entropy
of the system, instead of free energy released from new base-pair
formation. Ebeacon shows high sensitivity, with a detection limit
of 5 pM target DNA in buffer and 50 pM in cellular homogenate. Ebeacon
also benefits from the hairpin-free amplification strategy and zero-background,
excellent thermostability from 20 °C to 50 °C, as well as
good resistance to complex environments. In particular, based on the
huge difference between the breathing rate of a single base pair and
two adjacent base pairs, Ebeacon also shows high selectivity toward
base mutations, such as substitution, insertion, and deletion and,
therefore, is an efficient nucleic acid detection method, comparable
to most reported enzyme-free strategies.
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Affiliation(s)
- Yifan Lv
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Liang Cui
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Ruizi Peng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Zilong Zhao
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Liping Qiu
- Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Shands Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida , Gainesville, Florida 32611-7200, United States
| | - Huapei Chen
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Cheng Jin
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Xiao-Bing Zhang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, College of Biology, Collaborative Innovation Center for Chemistry and Molecular Medicine, Hunan University , Changsha, 410082, China.,Department of Chemistry and Department of Physiology and Functional Genomics, Center for Research at the Bio/Nano Interface, Shands Cancer Center, UF Genetics Institute, McKnight Brain Institute, University of Florida , Gainesville, Florida 32611-7200, United States
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17
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Cserép GB, Herner A, Kele P. Bioorthogonal fluorescent labels: a review on combined forces. Methods Appl Fluoresc 2015; 3:042001. [DOI: 10.1088/2050-6120/3/4/042001] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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18
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Yan L, Zhou J, Zheng Y, Gamson AS, Roembke BT, Nakayama S, Sintim HO. Isothermal amplified detection of DNA and RNA. MOLECULAR BIOSYSTEMS 2014; 10:970-1003. [PMID: 24643211 DOI: 10.1039/c3mb70304e] [Citation(s) in RCA: 282] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review highlights various methods that can be used for a sensitive detection of nucleic acids without using thermal cycling procedures, as is done in PCR or LCR. Topics included are nucleic acid sequence-based amplification (NASBA), strand displacement amplification (SDA), loop-mediated amplification (LAMP), Invader assay, rolling circle amplification (RCA), signal mediated amplification of RNA technology (SMART), helicase-dependent amplification (HDA), recombinase polymerase amplification (RPA), nicking endonuclease signal amplification (NESA) and nicking endonuclease assisted nanoparticle activation (NENNA), exonuclease-aided target recycling, Junction or Y-probes, split DNAZyme and deoxyribozyme amplification strategies, template-directed chemical reactions that lead to amplified signals, non-covalent DNA catalytic reactions, hybridization chain reactions (HCR) and detection via the self-assembly of DNA probes to give supramolecular structures. The majority of these isothermal amplification methods can detect DNA or RNA in complex biological matrices and have great potential for use at point-of-care.
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Affiliation(s)
- Lei Yan
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA.
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19
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Vázquez O, Seitz O. Templated native chemical ligation: peptide chemistry beyond protein synthesis. J Pept Sci 2014; 20:78-86. [PMID: 24395765 DOI: 10.1002/psc.2602] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 11/22/2013] [Accepted: 11/22/2013] [Indexed: 12/11/2022]
Abstract
Native chemical ligation (NCL) is a powerful method for the convergent synthesis of proteins and peptides. In its original format, NCL between a peptide containing a C-terminal thioester and another peptide offering an N-terminal cysteine has been used to enable protein synthesis of unprotected peptide fragments. However, the applications of NCL extend beyond the scope of protein synthesis. For instance, NCL can be put under the control of template molecules. In such a scenario, NCL enables the design of conditional reaction systems in which, peptide bond formation occurs only when a specific third party molecule is present. In this review, we will show how templates can be used to control the reactivity and chemoselectivity of NCL reactions. We highlight peptide and nucleic-acid-templated NCL reactions and discuss potential applications in nucleic acid diagnosis, origin-of-life studies and gene-expression-specific therapies.
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Affiliation(s)
- Olalla Vázquez
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489, Berlin, Germany
| | - Oliver Seitz
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489, Berlin, Germany
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20
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Gorska K, Winssinger N. Rapid miRNA imaging in cells using fluorogenic templated Staudinger reaction between PNA-based probes. Methods Mol Biol 2014; 1050:179-192. [PMID: 24297360 DOI: 10.1007/978-1-62703-553-8_15] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Reactions templated by a specific nucleic acid sequence have emerged as an attractive strategy for nucleic acid sensing. The Staudinger reaction using an azide-quenched fluorophore and a phosphine is particularly well suited by virtue of its bioorthogonality and biocompatibility. The reaction is promoted by a complementary nucleic acid that aligns the phosphine with the azide-quenched fluorophore. Cellular RNAs can catalyze the Staudinger reaction and signal amplification can be achieved through multiple turnover of the template. Peptide nucleic acids (PNA) provide a convenient platform for the preparation of specific probes as they combine desirable hybridization properties, robust synthesis, ease of fluorophore conjugation, and high biochemical stability. Herein, we describe protocols for fast fluorescent detection of miRNAs in human cells with PNA-based probes via reductive unquenching of bis-azidorhodamine by trialkylphosphine.
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Affiliation(s)
- Katarzyna Gorska
- Laboratoire de Chemie Organique et Bioorganique, Institut de Science et d'Ingénierie Supramoléculaires, Université Louis Pasteur, Strasbourg, France
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21
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Michaelis J, Roloff A, Seitz O. Amplification by nucleic acid-templated reactions. Org Biomol Chem 2014; 12:2821-33. [DOI: 10.1039/c4ob00096j] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Nucleic acid-templated reactions that proceed with turnover provide a means for signal amplification, which facilitates the use and detection of biologically occurring DNA/RNA molecules.
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Affiliation(s)
- Julia Michaelis
- Institut für Chemie der Humboldt-Universität zu Berlin
- 12489-Berlin, Germany
| | - Alexander Roloff
- Institut für Chemie der Humboldt-Universität zu Berlin
- 12489-Berlin, Germany
| | - Oliver Seitz
- Institut für Chemie der Humboldt-Universität zu Berlin
- 12489-Berlin, Germany
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22
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Michaelis J, van der Heden van Noort GJ, Seitz O. DNA-Triggered Dye Transfer on a Quantum Dot. Bioconjug Chem 2013; 25:18-23. [DOI: 10.1021/bc400494j] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Julia Michaelis
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Str. 2, 12489 Berlin, Germany
| | | | - Oliver Seitz
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Str. 2, 12489 Berlin, Germany
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23
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Saneyoshi H, Shimada N, Maruyama A, Ito Y, Abe H. Polycation-assisted DNA detection by reduction triggered fluorescence amplification probe. Bioorg Med Chem Lett 2013; 23:6851-3. [DOI: 10.1016/j.bmcl.2013.10.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 09/28/2013] [Accepted: 10/02/2013] [Indexed: 10/26/2022]
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24
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Roloff A, Seitz O. Reducing product inhibition in nucleic acid-templated ligation reactions: DNA-templated cycligation. Chembiochem 2013; 14:2322-8. [PMID: 24243697 DOI: 10.1002/cbic.201300516] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Indexed: 01/19/2023]
Abstract
Programmable interactions allow nucleic acid molecules to template chemical reactions by increasing the effective molarities of appended reactive groups. DNA/RNA-triggered reactions can proceed, in principle, with turnover in the template. The amplification provided by the formation of many product molecules per template is a valuable asset when the availability of the DNA or RNA target is limited. However, turnover is usually impeded by reaction products that block access to the template. Product inhibition is most severe in ligation reactions, where products after ligation have dramatically increased template affinities. We introduce a potentially generic approach to reduce product inhibition in nucleic acid-programmed ligation reactions. A DNA-triggered ligation-cyclization sequence ("cycligation") of bifunctional peptide nucleic acid (PNA) conjugates affords cyclic ligation products. Melting experiments revealed that product cyclization is accompanied by a pronounced decrease in template affinity compared to linear ligation products. The reaction system relies upon haloacetylated PNA-thioesters and isocysteinyl-PNA-cysteine conjugates, which were ligated on a DNA template according to a native chemical ligation mechanism. Dissociation of the resulting linear product-template duplex (induced by, for example, thermal cycling) enabled product cyclization through sulfur-halide substitution. Both ligation and cyclization are fast reactions (ligation: 86 % yield after 20 min, cyclization: quantitative after 5 min). Under thermocycling conditions, the DNA template was able to trigger the formation of new product molecules when fresh reactants were added. Furthermore, cycligation produced 2-3 times more product than a conventional ligation reaction with substoichiometric template loads (0.25-0.01 equiv). We believe that cyclization of products from DNA-templated reactions could ultimately afford systems that completely overcome product inhibition.
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Affiliation(s)
- Alexander Roloff
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489-Berlin (Germany)
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25
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Shibata A, Uzawa T, Nakashima Y, Ito M, Nakano Y, Shuto S, Ito Y, Abe H. Very rapid DNA-templated reaction for efficient signal amplification and its steady-state kinetic analysis of the turnover cycle. J Am Chem Soc 2013; 135:14172-8. [PMID: 24015779 DOI: 10.1021/ja404743m] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligonucleotide-templated reactions are powerful tools for the detection of nucleic acid sequences. One of the major scientific challenges associated with this technique is the rational design of non-enzyme-mediated catalytic templated reactions capable of multiple turnovers that provide high levels of signal amplification. Herein, we report the development of a nucleophilic aromatic substitution reaction-triggered fluorescent probe. The probe underwent a rapid templated reaction without any of the undesired background reactions. The fluorogenic reaction conducted in the presence of a template provided a 223-fold increase in fluorescence after 30 s compared with the nontemplated reaction. The probe provided an efficient level of signal amplification that ultimately enabled particularly sensitive levels of detection. Assuming a simple model for the templated reactions, it was possible to estimate the rate constants of the chemical reaction in the presence and in the absence of the template. From these kinetic analyses, it was possible to confirm that an efficient turnover cycle had been achieved, on the basis of the dramatic enhancement in the rate of the chemical reaction considered to be the rate-determining step. With maximized turnover efficiency, it was demonstrated that the probe could offer a high turnover number of 1500 times to enable sensitive levels of detection with a detection limit of 0.5 pM in the catalytic templated reactions.
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Affiliation(s)
- Aya Shibata
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute , 2-1, Hirosawa, Wako-Shi, Saitama 351-0198, Japan
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26
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Saneyoshi H, Ito Y, Abe H. Long-lived luminogenic probe for detection of RNA in a crude solution of living bacterial cells. J Am Chem Soc 2013; 135:13632-5. [PMID: 24010717 DOI: 10.1021/ja406724k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A pre-type sensitizer for a lanthanide complex on an oligonucleotide was successfully converted to a perfect final structure in a target DNA/RNA-templated reaction, without any chemical reagent or enzyme, under neutral conditions. The final form of the lanthanide-oligonucleotide provided a long-lived luminescence signal, appropriate for time-gated luminescence analysis and signal amplification. Target DNA/RNA-assisted time-gated luminescence analysis is a powerful tool for elimination of autofluorescence and detection of target RNA in living bacterial cells.
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Affiliation(s)
- Hisao Saneyoshi
- Nano Medical Engineering Laboratory, RIKEN , 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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27
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Barluenga S, Winssinger N. Picture Perfect: DNA-Templated Photoaffinity Labeling. Chembiochem 2013; 14:1927-8. [DOI: 10.1002/cbic.201300416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Indexed: 12/18/2022]
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28
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Gorska K, Winssinger N. Reactions templated by nucleic acids: more ways to translate oligonucleotide-based instructions into emerging function. Angew Chem Int Ed Engl 2013; 52:6820-43. [PMID: 23794204 DOI: 10.1002/anie.201208460] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Indexed: 12/30/2022]
Abstract
The programmability of oligonucleotide recognition offers an attractive platform to direct the assembly of reactive partners that can engage in chemical reactions. Recently, significant progress has been made in both the breadth of chemical transformations and in the functional output of the reaction. Herein we summarize these recent progresses and illustrate their applications to translate oligonucleotide instructions into functional materials and novel architectures (conductive polymers, nanopatterns, novel oligonucleotide junctions); into fluorescent or bioactive molecule using cellular RNA; to interrogate secondary structures or oligonucelic acids; or a synthetic oligomer.
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Affiliation(s)
- Katarzyna Gorska
- Institut de Science et Ingénierie Supramoléculaires (ISIS-UMR 7006), Universite de Strasbourg-CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
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29
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Gorska K, Winssinger N. Reaktionen an Nucleinsäuretemplaten: mehr Methoden zur Übersetzung Oligonucleotid-basierter Informationen in neue Funktionen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208460] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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30
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Sadhu KK, Winssinger N. Detection of miRNA in live cells by using templated RuII-catalyzed unmasking of a fluorophore. Chemistry 2013; 19:8182-9. [PMID: 23633397 DOI: 10.1002/chem.201300060] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Indexed: 12/21/2022]
Abstract
Reactions templated by cellular nucleic acids are attractive for nucleic acid sensing or responsive systems. Herein we report the use of a photocatalyzed reductive cleavage of an immolative linker to unmask a rhodamine fluorophore, and its application to miRNA imaging. The reaction was found to proceed with a very high turnover (>4000) and provided reliable detection down to 5 pM of template by using γ-serine-modified peptide nucleic acid (PNA) probes. The reaction was used for the selective detection of miR-21 in BT474 cells and miR-31 in HeLa cells following irradiation for 30 min. The probes were introduced by using reversible permeation with streptolysin-O (SLO) or a transfection technique.
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Affiliation(s)
- Kalyan K Sadhu
- Institut de Science et Ingénierie Supramoléculaires (ISIS-UMR 7006), Université de Strasbourg, CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
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31
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Hayashi G, Okamoto A. Probe design for the effective fluorescence imaging of intracellular RNA. CHEM REC 2013; 13:209-17. [PMID: 23495145 DOI: 10.1002/tcr.201200026] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Indexed: 01/18/2023]
Abstract
Over the past two decades, the spatiotemporal analysis of fluorescently labeled single RNA species has provided a broad insight into the synthesis, localization, degradation, and transport of RNA. To elucidate the dynamic behavior of functional RNAs in living cells, researchers throughout the world have proposed numerous fluorometric strategies for intracellular RNA imaging. Because, like most other biological molecules, RNA is intrinsically nonfluorescent, the development of methods for the labeling of RNAs of interest with fluorescent molecules is essential. Several artificial tag sequences have been attached onto the 3' end of target RNAs and used as scaffolds for interacting with their fluorescent counterparts. In this Personal Account, we focus on the methods that have been developed to show how RNAs expressed in cells can be labeled and visualized by fluorescent proteins, small molecules, or nucleic acids. Each of these methods is designed to increase the sensitivity and specificity for imaging or to decrease the background fluorescence.
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Affiliation(s)
- Gosuke Hayashi
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Tokyo 153-8904, Japan
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32
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Sadhu KK, Röthlingshöfer M, Winssinger N. DNA as a Platform to Program Assemblies with Emerging Functions in Chemical Biology. Isr J Chem 2013. [DOI: 10.1002/ijch.201200100] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Kalyan K. Sadhu
- Institut de Science et Ingénierie Supramoléculaires (ISIS – UMR 7006), Université de Strasbourg – CNRS, 8 allée Gaspard Monge, F67000 Strasbourg (France)
| | - Manuel Röthlingshöfer
- Institut de Science et Ingénierie Supramoléculaires (ISIS – UMR 7006), Université de Strasbourg – CNRS, 8 allée Gaspard Monge, F67000 Strasbourg (France)
| | - Nicolas Winssinger
- Institut de Science et Ingénierie Supramoléculaires (ISIS – UMR 7006), Université de Strasbourg – CNRS, 8 allée Gaspard Monge, F67000 Strasbourg (France)
- Department of Organic Chemistry, University of Geneva, 30 quai Ernest Ansermet, CH‐1211 Geneva 4 (Switzerland) phone: +41‐22‐379‐61‐05 fax: +41‐22‐379‐32‐15
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33
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Stoop M, Désiron C, Leumann CJ. Nucleic acid sensing by an orthogonal reporter system based on homo-DNA. ARTIFICIAL DNA, PNA & XNA 2013; 4:28-33. [PMID: 23507698 PMCID: PMC3654727 DOI: 10.4161/adna.24227] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have developed an assay for single strand DNA or RNA detection which is based on the homo-DNA templated Staudinger reduction of the profluorophore rhodamine-azide. The assay is based on a three component system, consisting of a homo-DNA/DNA hybrid probe, a set of homo-DNA reporter strands and the target DNA or RNA. We present two different formats of the assay (Omega probe and linear probe) in which the linear probe was found to perform best with catalytic turnover of the reporter strands (TON: 8) and a match/mismatch discrimination of up to 19. The advantage of this system is that the reporting (homo-DNA) and sensing (DNA) domain are decoupled from each other since the two pairing systems are bioorthogonal. This allows independent optimization of either domain which may lead to higher selectivity in in vivo imaging.
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Affiliation(s)
- Matthias Stoop
- University of Bern, Department of Chemistry and Biochemistry, Bern, Switzerland
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34
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Shibata A, Ito Y, Abe H. RNA-templated molecule release induced protein expression in bacterial cells. Chem Commun (Camb) 2013; 49:270-2. [DOI: 10.1039/c2cc37826d] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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35
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Detection of pre-mRNA splicing in vitro by an RNA-templated fluorogenic reaction. Bioorg Med Chem Lett 2012; 22:7248-51. [DOI: 10.1016/j.bmcl.2012.09.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 09/10/2012] [Accepted: 09/11/2012] [Indexed: 11/19/2022]
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36
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Sadhu KK, Eierhoff T, Römer W, Winssinger N. Photoreductive uncaging of fluorophore in response to protein oligomers by templated reaction in vitro and in cellulo. J Am Chem Soc 2012. [PMID: 23186060 DOI: 10.1021/ja310171s] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The photoreduction of azide-based immolative linker by Ru(II) conjugates to uncage rhodamine was achieved using different oligomeric protein templates. The generality of the approach was validated with three sets of ligand having varying affinity to their target (biotin, desthiobiotin and raloxifene). The reaction rates of the templated reaction was found to be at least 30-fold faster than the untemplated reaction providing a clear fluorescent signal in response to the protein oligomer within 30 min. The templated reaction was found to also proceed in cellulo and could be used to identify acetyl coenzyme A carboxylase (ACC) in Pseudomonas aeruginosa and human cell lines as well the and estrogen receptor (ER).
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Affiliation(s)
- Kalyan K Sadhu
- Institut de Science et Ingénierie Supramoléculaires (ISIS-UMR 7006), Université de Strasbourg-CNRS, 8 allée Gaspard Monge, F67000 Strasbourg, France
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37
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Kashida H, Asanuma* H. Oligonucleotide Conjugates for Detection of Specific Nucleic Acid Sequences. DNA CONJUGATES AND SENSORS 2012. [DOI: 10.1039/9781849734936-00242] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In this chapter, we summarise the designs of fluorophore-modified nucleic acids used as probes for the detection of target DNA/RNA. Recently, there has been an increasing demand for the sequence-specific detection of DNA and RNA in biology and biotechnology. Fluorescent probes based on nucleic acids are useful because of their simplicity and ease of handling. Here, we described three types of fluorescent probe: 1) linear probes, 2) binary probes, and 3) molecular beacons. Each can have one or more fluorophores. Mechanisms for the fluorescence responses of these probes are also discussed in detail. These fluorescent probes have been used in real-time polymerase chain reaction (PCR), genetic analyses, and messenger RNA (mRNA) imaging in living cells. Improvements in sensitivity, selectivity, and nuclease resistance of these probes will lead to more widespread applications in chemical biology, biotechnology, and medicine.
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Affiliation(s)
- Hiromu Kashida
- 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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38
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Prusty DK, Kwak M, Wildeman J, Herrmann A. Modular assembly of a Pd catalyst within a DNA scaffold for the amplified colorimetric and fluorimetric detection of nucleic acids. Angew Chem Int Ed Engl 2012; 51:11894-8. [PMID: 23076826 PMCID: PMC3533772 DOI: 10.1002/anie.201206006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Indexed: 11/10/2022]
Affiliation(s)
- Deepak K Prusty
- University of Groningen, Zernike Institute for Advanced Materials, Department of Polymer Chemistry, Nijenborgh 4, 9747 AG Groningen, Netherlands
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39
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Prusty DK, Kwak M, Wildeman J, Herrmann A. Modular Assembly of a Pd Catalyst within a DNA Scaffold for the Amplified Colorimetric and Fluorimetric Detection of Nucleic Acids. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201206006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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40
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Kummer S, Knoll A, Socher E, Bethge L, Herrmann A, Seitz O. PNA FIT-probes for the dual color imaging of two viral mRNA targets in influenza H1N1 infected live cells. Bioconjug Chem 2012; 23:2051-60. [PMID: 22946435 DOI: 10.1021/bc300249f] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Fluorogenic hybridization probes that allow RNA imaging provide information as to how the synthesis and transport of particular RNA molecules is orchestrated in living cells. In this study, we explored the peptide nucleic acid (PNA)-based FIT-probes in the simultaneous imaging of two different viral mRNA molecules expressed during the replication cycle of the H1N1 influenza A virus. PNA FIT-probes are non-nucleotidic, nonstructured probes and contain a single asymmetric cyanine dye which serves as a fluorescent base surrogate. The fluorochrome acts as a local intercalator probe and reports hybridization of target DNA/RNA by enhancement of fluorescence. Though multiplexed hybridization probes are expected to facilitate the analysis of RNA expression, there are no previous reports on the dual color imaging of two different viral mRNA targets. In this work, we developed a set of two differently colored PNA FIT-probes that allow the spectrally resolved imaging of mRNA coding for neuraminidase (NA) and matrix protein 1 (M1); proteins which execute distinct functions during the replication of the influenza A virus. The probes are characterized by a wide range of applicable hybridization temperatures. The same probe sequence enabled live-cell RNA imaging (at 37 °C) as well as real-time PCR measurements (at 60 °C annealing temperature). This facilitated a comprehensive analysis of RNA expression by quantitative (qPCR) and qualitative (imaging) means. Confocal laser scanning microscopy showed that the viral-RNA specific PNA FIT-probes neither stained noninfected cells nor cells infected by a control virus. The joint use of differently colored PNA FIT-probes in this feasibility study revealed significant differences in the expression pattern of influenza H1N1 mRNAs coding for NA or M1. These experiments provide evidence for the usefulness of PNA FIT-probes in investigations on the temporal and spatial progression of mRNA synthesis in living cells for two mRNA species.
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Affiliation(s)
- Susann Kummer
- Department of Biology, Humboldt University Berlin, Invalidenstr. 42, D-10115 Berlin, Germany
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41
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Lee SH, Wang S, Kool ET. Templated chemistry for monitoring damage and repair directly in duplex DNA. Chem Commun (Camb) 2012; 48:8069-71. [PMID: 22782065 DOI: 10.1039/c2cc34060g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We report the fluorogenic detection of the product of base excision repair (an abasic site) in a specific sequence of duplex DNA. This is achieved by DNA-templated chemistry, employing triple helix-forming probes that contain unnatural nucleobases designed to selectively recognize the site of a missing base. Light-up signals of up to 36-fold were documented, and probes could be used to monitor enzymatic removal of a damaged base.
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Affiliation(s)
- Seoung Ho Lee
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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42
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Photochemically relevant DNA-based molecular systems enabling chemical and signal transductions and their analytical applications. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2012. [DOI: 10.1016/j.jphotochemrev.2012.03.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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43
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Rao H, Tanpure AA, Sawant AA, Srivatsan SG. Enzymatic incorporation of an azide-modified UTP analog into oligoribonucleotides for post-transcriptional chemical functionalization. Nat Protoc 2012; 7:1097-112. [PMID: 22576108 DOI: 10.1038/nprot.2012.046] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol describes the detailed experimental procedure for the synthesis of an azide-modified uridine triphosphate analog and its effective incorporation into an oligoribonucleotide by in vitro transcription reactions. Furthermore, procedures for labeling azide-modified oligoribonucleotides post-transcriptionally with biophysical probes by copper(I)-catalyzed alkyne-azide cycloaddition (CuAAC) and Staudinger reactions are also provided. This post-transcriptional chemical modification protocol is simple and modular, and it affords labeled oligonucleotides in reasonable amounts for biophysical assays. The procedure for enzymatic incorporation of the monophosphate of azide-modified UTP into an oligoribonucleotide transcript takes ∼2 d, and subsequent post-transcriptional chemical functionalization of the transcript takes about 2 d.
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Affiliation(s)
- Harita Rao
- Department of Chemistry, Indian Institute of Science Education and Research, Pune, India
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44
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Oligonucleotide-templated reactions for sensing nucleic acids. Molecules 2012; 17:2446-63. [PMID: 22374329 PMCID: PMC6268776 DOI: 10.3390/molecules17032446] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 02/23/2012] [Accepted: 02/24/2012] [Indexed: 02/07/2023] Open
Abstract
Oligonucleotide-templated reactions are useful for applying nucleic acid sensing. Various chemistries for oligonucleotide-templated reaction have been reported so far. Major scientific interests are focused on the development of signal amplification systems and signal generation systems. We introduce the recent advances of oligonucleotide-templated reaction in consideration of the above two points.
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45
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Tanabe K, Ishizaki J, Ando Y, Ito T, Nishimoto SI. Reductive activation of 5-fluorodeoxyuridine prodrug possessing azide methyl group by hypoxic X-irradiation. Bioorg Med Chem Lett 2012; 22:1682-5. [DOI: 10.1016/j.bmcl.2011.12.106] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 12/21/2011] [Accepted: 12/22/2011] [Indexed: 11/30/2022]
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46
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Röthlingshöfer M, Gorska K, Winssinger N. Nucleic Acid Templated Uncaging of Fluorophores Using Ru-Catalyzed Photoreduction with Visible Light. Org Lett 2011; 14:482-5. [DOI: 10.1021/ol203029t] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Manuel Röthlingshöfer
- Institut de Science et Ingénierie Supramoléculaires (ISIS - UMR 7006), Université de Strasbourg - CNRS, 8 allée Gaspard Monge, F67000 Strasbourg, France
| | - Katarzyna Gorska
- Institut de Science et Ingénierie Supramoléculaires (ISIS - UMR 7006), Université de Strasbourg - CNRS, 8 allée Gaspard Monge, F67000 Strasbourg, France
| | - Nicolas Winssinger
- Institut de Science et Ingénierie Supramoléculaires (ISIS - UMR 7006), Université de Strasbourg - CNRS, 8 allée Gaspard Monge, F67000 Strasbourg, France
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47
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Imaging of RNA in live cells. Curr Opin Chem Biol 2011; 15:806-12. [PMID: 22055496 DOI: 10.1016/j.cbpa.2011.10.006] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 10/11/2011] [Accepted: 10/17/2011] [Indexed: 01/07/2023]
Abstract
Fluorescence microscopy and molecular tagging technologies have ushered in a new era in our understanding of protein localization and function in cells. This review summarizes recent efforts to extend some of these methods (and to create new ones) to imaging of RNA in live cells. Both fluorescent proteins and hybridization probes allow noncovalent labeling of specific RNA molecules with fluorescent dyes that allow detection and tracking in real time.
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48
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Furukawa K, Abe H, Tamura Y, Yoshimoto R, Yoshida M, Tsuneda S, Ito Y. Fluorescence Detection of Intron Lariat RNA with Reduction-Triggered Fluorescent Probes. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201104425] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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49
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Furukawa K, Abe H, Tamura Y, Yoshimoto R, Yoshida M, Tsuneda S, Ito Y. Fluorescence detection of intron lariat RNA with reduction-triggered fluorescent probes. Angew Chem Int Ed Engl 2011; 50:12020-3. [PMID: 22021091 DOI: 10.1002/anie.201104425] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2011] [Revised: 09/22/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Kazuhiro Furukawa
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1, Hirosawa, Wako-Shi, Saitama, 351-0198, Japan
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50
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Röthlingshöfer M, Gorska K, Winssinger N. Nucleic Acid-Templated Energy Transfer Leading to a Photorelease Reaction and its Application to a System Displaying a Nonlinear Response. J Am Chem Soc 2011; 133:18110-3. [DOI: 10.1021/ja2086504] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Manuel Röthlingshöfer
- Institut de Science et Ingénierie Supramoléculaires (ISIS − UMR 7006), Université de Strasbourg − CNRS, 8 allée Gaspard Monge, F67000 Strasbourg, France
| | - Katarzyna Gorska
- Institut de Science et Ingénierie Supramoléculaires (ISIS − UMR 7006), Université de Strasbourg − CNRS, 8 allée Gaspard Monge, F67000 Strasbourg, France
| | - Nicolas Winssinger
- Institut de Science et Ingénierie Supramoléculaires (ISIS − UMR 7006), Université de Strasbourg − CNRS, 8 allée Gaspard Monge, F67000 Strasbourg, France
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