51
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Rao H, Sawant AA, Tanpure AA, Srivatsan SG. Posttranscriptional chemical functionalization of azide-modified oligoribonucleotides by bioorthogonal click and Staudinger reactions. Chem Commun (Camb) 2011; 48:498-500. [PMID: 22006199 DOI: 10.1039/c1cc15659d] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Direct incorporation of azide groups into RNA oligonucleotides by in vitro transcription reactions in the presence of a new azide-modified UTP analogue, and subsequent posttranscriptional chemical labeling of azide-modified oligoribonucleotide transcripts by click and Staudinger reactions are described. This postsynthetic labeling protocol is robust and modular, and offers an alternative access to RNA labeled with biophysical probes.
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Affiliation(s)
- Harita Rao
- Indian Institute of Science Education and Research, Sai Trinity Building, Pashan, Pune 411021, India
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52
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Franzini RM, Kool ET. Improved templated fluorogenic probes enhance the analysis of closely related pathogenic bacteria by microscopy and flow cytometry. Bioconjug Chem 2011; 22:1869-77. [PMID: 21870777 DOI: 10.1021/bc2003567] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Templated fluorescence activation has recently emerged as a promising molecular approach to detect and differentiate nucleic acid sequences in vitro and in cells. Here, we describe the application of a reductive quencher release strategy to the taxonomic analysis of Gram-negative bacteria by targeting a single nucleotide difference in their 16S rRNA in a two-color assay. For this purpose, it was necessary to develop a release linker containing a quencher suitable for red and near-infrared fluorophores, and to improve methods for the delivery of probes into cells. A cyanine-dye labeled oligonucleotide probe containing the new quencher-release linker showed unprecedentedly low background signal and high fluorescence turn-on ratios. The combination of a fluorescein-containing and a near-IR emitting probe discriminated E. coli from S. enterica despite nearly identical ribosomal target sequences. Two-color analysis by microscopy and the first successful discrimination of bacteria by two-color flow cytometry with templated reactive probes are described.
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Affiliation(s)
- Raphael M Franzini
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, United States
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53
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Kummer S, Knoll A, Socher E, Bethge L, Herrmann A, Seitz O. Fluoreszenzbildgebung der mRNA von Influenza-H1N1 in lebenden infizierten Zellen durch FIT-PNA mit einem einzigen Chromophor. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201005902] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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54
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Kummer S, Knoll A, Socher E, Bethge L, Herrmann A, Seitz O. Fluorescence imaging of influenza H1N1 mRNA in living infected cells using single-chromophore FIT-PNA. Angew Chem Int Ed Engl 2011; 50:1931-4. [PMID: 21328673 DOI: 10.1002/anie.201005902] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2010] [Revised: 10/22/2010] [Indexed: 01/13/2023]
Affiliation(s)
- Susann Kummer
- Department of Biology, Humboldt University Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
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55
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Franzini RM, Kool ET. Two successive reactions on a DNA template: a strategy for improving background fluorescence and specificity in nucleic acid detection. Chemistry 2011; 17:2168-75. [PMID: 21294182 DOI: 10.1002/chem.201002426] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Indexed: 12/24/2022]
Abstract
We report a new strategy for template-mediated fluorogenic chemistry that results in enhanced performance for the fluorescence detection of nucleic acids. In this approach, two successive templated reactions are required to induce a fluorescence signal, rather than only one. These novel fluorescein-labeled oligonucleotide probes, termed 2-STAR (STAR = Staudinger-triggered α-azidoether release) probes, contain two quencher groups tethered by separate reductively cleavable linkers. When a 2-STAR quenched probe successively binds adjacent to two mono-triphenylphosphine-(TPP)-DNAs or one dual-TPP-DNA, the two quenchers are released, resulting in a fluorescence signal. Because of the requirement for two consecutive reactions, 2-STAR probes display an unprecedented level of sequence specificity for template-mediated probe designs. At the same time, background emission generated by off-template reactions or incomplete quenching is among the lowest of any fluorogenic reactive probes for the detection of DNA or RNA.
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Affiliation(s)
- Raphael M Franzini
- Department of Chemistry, Stanford University, Stanford, CA-94305-5080, USA
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56
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Gorska K, Manicardi A, Barluenga S, Winssinger N. DNA-templated release of functional molecules with an azide-reduction-triggered immolative linker. Chem Commun (Camb) 2011; 47:4364-6. [DOI: 10.1039/c1cc10222b] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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57
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Gorska K, Keklikoglou I, Tschulena U, Winssinger N. Rapid fluorescence imaging of miRNAs in human cells using templated Staudinger reaction. Chem Sci 2011. [DOI: 10.1039/c1sc00216c] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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58
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Dutta S, Mokhir A. An autocatalytic chromogenic and fluorogenic photochemical reaction controlled by nucleic acids. Chem Commun (Camb) 2010; 47:1243-5. [PMID: 21103531 DOI: 10.1039/c0cc02508a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The autocatalytic photochemical reaction, which is potentially controlled by any selected nucleic acid, is highly sequence specific and not inhibited by its products, was developed. This reaction generates colored and fluorescent products, which can be monitored by the naked eye.
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Affiliation(s)
- Subrata Dutta
- Institute of Inorganic Chemistry, University of Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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59
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Kleinbaum DJ, Miller GP, Kool ET. Double displacement: An improved bioorthogonal reaction strategy for templated nucleic acid detection. Bioconjug Chem 2010; 21:1115-20. [PMID: 20509625 DOI: 10.1021/bc100165h] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Quenched autoligation probes have been employed previously in a target-templated nonenzymatic ligation strategy for detecting nucleic acids in cells by fluorescence. A common source of background signal in such probes is the undesired reaction with water and other cellular nucleophiles. Here, we describe a new class of self-ligating probes, double displacement (DD) probes, that rely on two displacement reactions to fully unquench a nearby fluorophore. Three potential double displacement architectures, all possessing two fluorescence quencher/leaving groups (dabsylate groups), were synthesized and evaluated for templated reaction with nucleophile (phosphorothioate) probes both in vitro and in intact bacterial cells. All three DD probe designs provided substantially better initial quenching than a single-Dabsyl control. In isothermal templated reactions in vitro, double displacement probes yielded considerably lower background signal than previous single displacement probes; investigation into the mechanism revealed that one dabsylate acts as a sacrificial leaving group, reacting nonspecifically with water, but yielding little signal because another quencher group remains. Templated reaction with the specific nucleophile probe is required to activate a signal. The double displacement probes provided a ca. 80-fold turn-on signal and yielded a 2-4-fold improvement in signal/background over single Dabsyl probes. The best-performing probe architecture was demonstrated in a two-color, FRET-based two-allele discrimination system in vitro and was shown to be capable of discriminating between two closely related species of bacteria differing by a single nucleotide at an rRNA target site.
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Affiliation(s)
- Daniel J Kleinbaum
- Department of Chemistry, Stanford University, California 94305-5080, USA
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60
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Li H, Franzini RM, Bruner C, Kool ET. Templated chemistry for sequence-specific fluorogenic detection of duplex DNA. Chembiochem 2010; 11:2132-7. [PMID: 20859985 PMCID: PMC4418650 DOI: 10.1002/cbic.201000329] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2010] [Indexed: 12/25/2022]
Abstract
We describe the development of templated fluorogenic chemistry for detection of specific sequences of duplex DNA in solution. In this approach, two modified homopyrimidine oligodeoxynucleotide probes are designed to bind by triple-helix formation at adjacent positions on a specific purine-rich target sequence of duplex DNA. One fluorescein-labeled probe contains an α-azidoether linker to a fluorescence quencher; the second (trigger) probe carries a triarylphosphine group that is designed to reduce the azide and cleave the linker. The data showed that at pH 5.6 these probes yielded a strong fluorescence signal within minutes on addition to a complementary homopurine duplex DNA target. The signal increased by a factor of about 60, and was completely dependent on the presence of the target DNA. Replacement of cytosine in the probes with pseudoisocytosine allowed the templated chemistry to proceed readily at pH 7. Single nucleotide mismatches in the target oligonucleotide slowed the templated reaction considerably; this demonstrated high sequence selectivity. The use of templated fluorogenic chemistry for detection of duplex DNAs has not been previously reported and could allow detection of double-stranded DNA, at least for homopurine-homopyrimidine target sites, under native and nondenaturing conditions.
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Affiliation(s)
| | | | | | - Eric T. Kool
- Prof. Dr. E. T. Kool, H. Li, R.M. Franzini, C. Bruner, Department of Chemistry, Stanford University, Stanford, CA 94305-5080 (USA), Fax: (+1)650-725-0259,
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61
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Kleinbaum DJ, Kool ET. Sandwich probes: two simultaneous reactions for templated nucleic acid detection. Chem Commun (Camb) 2010; 46:8154-6. [PMID: 20927470 DOI: 10.1039/c0cc01968b] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Fluorescence-quenched nucleic acid probes with reactive moieties at both the 5' and 3' ends are synthesized and tested for reaction with two adjacent nucleophile-containing DNAs. These probes improve signal to background over singly reactive probes and can discriminate single nucleotide polymorphisms in the target DNA or RNA.
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62
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Koripelly G, Meguellati K, Ladame S. Dual sensing of hairpin and quadruplex DNA structures using multicolored peptide nucleic acid fluorescent probes. Bioconjug Chem 2010; 21:2103-9. [PMID: 20923172 DOI: 10.1021/bc100335f] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Synthesis of water-soluble 5-mer peptide nucleic acids (PNAs) functionalized at their 5'- and 3'-ends with two original precursors of pentamethine cyanine dye synthesis is reported. The successful use of these PNA probes for sensing DNA hairpin structures in vitro was also demonstrated where specific hairpin formation was associated with the appearance of a characteristic fluorescence signal at 660 nm. A comparative study between three different strategies where PNAs were targeting either the stem or the loop of the hairpin was carried out. Best sensitivity was obtained using PNA sequences complementary to the loop sequence and directing both functional moieties toward the base of loop. Unprecedented proof-of-concept for the simultaneous sensing of hairpin and quadruplex DNAs with a nonoverlapping two-color system (C3 and C5) is also demonstrated.
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Affiliation(s)
- Girish Koripelly
- Institut de Science et d'Ingénierie Supramoléculaires, CNRS UMR, Université de Strasbourg, France
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63
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Prusty DK, Herrmann A. A Fluorogenic Reaction Based on Heavy-Atom Removal for Ultrasensitive DNA Detection. J Am Chem Soc 2010; 132:12197-9. [DOI: 10.1021/ja105181v] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Deepak K. Prusty
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Andreas Herrmann
- Department of Polymer Chemistry, Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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64
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Fülöp A, Peng X, Greenberg MM, Mokhir A. A nucleic acid-directed, red light-induced chemical reaction. Chem Commun (Camb) 2010; 46:5659-61. [PMID: 20574574 DOI: 10.1039/c0cc00744g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first nucleic acid-directed catalytic photochemical reaction that is induced by nontoxic red light was developed. This reaction is fast, high yielding, sequence specific, and enables one to functionalize an oligonucleotide.
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Affiliation(s)
- Annabelle Fülöp
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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65
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Meguellati K, Koripelly G, Ladame S. DNA-templated synthesis of trimethine cyanine dyes: a versatile fluorogenic reaction for sensing G-quadruplex formation. Angew Chem Int Ed Engl 2010; 49:2738-42. [PMID: 20229556 DOI: 10.1002/anie.201000291] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kamel Meguellati
- ISIS Université de Strasbourg, 8, Allée Gaspard Monge, BP 70028, 67083 Strasbourg, France
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66
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Furukawa K, Abe H, Tsuneda S, Ito Y. Photoactivatable fluorescein derivatives with azidomethyl caging groups for tracing oligonucleotides in living human cells. Org Biomol Chem 2010; 8:2309-11. [PMID: 20448888 DOI: 10.1039/b926100a] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new photocaged fluorescent compound, azidomethyl fluorescein, was successfully utilized to monitor the dynamics of oligonucleotides in living human cells.
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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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67
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Meguellati K, Koripelly G, Ladame S. DNA-Templated Synthesis of Trimethine Cyanine Dyes: A Versatile Fluorogenic Reaction for Sensing G-Quadruplex Formation. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201000291] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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68
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Shibata A, Abe H, Furukawa K, Tsuneda S, Ito Y. Reduction-triggered fluorescence probe for peptide-templated reactions. Chem Pharm Bull (Tokyo) 2010; 57:1223-6. [PMID: 19881271 DOI: 10.1248/cpb.57.1223] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We developed a new nucleic acid-based fluorescence probe for protein detection. The method is based on the scission of an aptamer into two probes, which are then attached with a chemically reactive fluorogenic compound. The protein-dependent association of the two probes accelerates a reduction-triggered fluorogenic reaction and indicates the presence of the target protein, which is detected using a fluorescence readout. The fluorescence signal is generated via the deprotection of the azidomethyl group of fluorescein. The arginine-rich motif peptide of the human immunodeficiency virus-1 Rev protein was targeted by this type of probe. Emission was detected at 522 nm and was enhanced by about 19.4-fold in the presence of the target peptide. An oligonucleotide-based reduction-triggered fluorescence probe was successfully applied to the detection of the Rev peptide in solution.
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Affiliation(s)
- Aya Shibata
- Nano Medical Engineering Laboratory, RIKEN Advanced Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
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69
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Franzini RM, Kool ET. Efficient nucleic acid detection by templated reductive quencher release. J Am Chem Soc 2010; 131:16021-3. [PMID: 19886694 DOI: 10.1021/ja904138v] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
RNA-templated fluorescence activation is a nucleic acid detection strategy that offers the possibility of direct visual detection of genetic information in living cells. Here we describe a new reaction strategy for fluorescence activation in which a phosphine on one DNA probe reduces an azide group in a linker on a second probe, resulting in linker cleavage and release of a fluorescence quenching group. These "Q-STAR" probes are shown to yield a strong fluorescence turn-on signal in approximately 20 min, with very low background and substantial amplification by turnover on the template. A green/red pair of such probes allowed the discrimination of two bacterial species by a single nucleotide difference in their 16S rRNA. The beneficial properties of the reductive quencher release design make these probes promising candidates for widespread application in the detection of nucleic acids in vitro and in cells.
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Affiliation(s)
- Raphael M Franzini
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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70
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Arian D, Cló E, Gothelf K, Mokhir A. A Nucleic Acid Dependent Chemical Photocatalysis in Live Human Cells. Chemistry 2010; 16:288-95. [DOI: 10.1002/chem.200902377] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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71
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Shibata A, Abe H, Ito M, Kondo Y, Shimizu S, Aikawa K, Ito Y. DNA templated nucleophilic aromatic substitution reactions for fluorogenic sensing of oligonucleotides. Chem Commun (Camb) 2009:6586-8. [PMID: 19865658 DOI: 10.1039/b912896d] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed an S(N)Ar reaction-triggered fluorescence probe using a new fluorogenic compound derivatized from 7-aminocoumarin for oligonucleotides detection.
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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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