51
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Franzini RM, Kool ET. 7-Azidomethoxy-coumarins as profluorophores for templated nucleic acid detection. Chembiochem 2009; 9:2981-8. [PMID: 19035374 DOI: 10.1002/cbic.200800507] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Templated nucleic acid detection is an emerging bioanalytical method that makes use of the target DNA or RNA strand to initiate a fluorogenic reaction. The Staudinger reduction holds particular promise for templated sensing of nucleic acids because the involved functional groups are highly chemoselective. Here, the azidomethoxy group, which can be removed under Staudinger conditions, is used to cage 7-hydroxycoumarin fluorophores. Reduction by phosphines and subsequent loss of the azidomethoxy substituent induce a significant bathochromic shift of the major absorbance band in the near UV region. When excited at the appropriate wavelength, this change in the absorbance spectrum translates into a substantial fluorescence turn-on signal. The described profluorophores are readily conjugated to amino-modified DNAs and are rapidly uncaged by a triphenylphosphine-DNA probe under the control of a DNA template. In addition, turnover of the probes on the target strand occurs and yields substantial signal amplification.
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Affiliation(s)
- Raphael M Franzini
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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52
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Grossmann TN, Strohbach A, Seitz O. Achieving turnover in DNA-templated reactions. Chembiochem 2009; 9:2185-92. [PMID: 18752239 DOI: 10.1002/cbic.200800290] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Tom N Grossmann
- Institut für Chemie der Humboldt-Universität zu Berlin, Germany
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53
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Altenbrunn F, Grossmann TN, Haase C, Mende F, Röglin L, Thurley S, Seitz O. Chemical control of biomolecular interaction modules. PURE APPL CHEM 2009. [DOI: 10.1351/pac-con-08-08-07] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The mutual recognition of biomacromolecules often is mediated by dedicated interaction modules. We take two main approaches in order to recognize and control nucleic acid-nucleic acid, protein-protein, and protein-nucleic acid interactions. In one, the rules that govern the formation of nucleic acid structures are used to design molecules that respond to the presence of nucleic acid or protein targets by showing changes of conformation or reactivity. For example, hybrid molecules can transduce changes of nucleic acid structure to changes of peptide structure, and vice versa. The other approach takes advantage of protein domains that once may form the basis of sensor materials and control elements. However, the current chemical synthesis methods have still not reached the level of maturity required to provide routine access to folded protein domains. In this article, we also describe recent progress that may facilitate the chemical synthesis of protein interaction domains.
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Affiliation(s)
- Frank Altenbrunn
- 1Institute for Chemistry, Humboldt University, Brook-Taylor-Str. 2, D-12489 Berlin, Germany
| | - Tom N. Grossmann
- 1Institute for Chemistry, Humboldt University, Brook-Taylor-Str. 2, D-12489 Berlin, Germany
| | - Christian Haase
- 1Institute for Chemistry, Humboldt University, Brook-Taylor-Str. 2, D-12489 Berlin, Germany
| | - Franziska Mende
- 1Institute for Chemistry, Humboldt University, Brook-Taylor-Str. 2, D-12489 Berlin, Germany
| | - Lars Röglin
- 2Laboratory of Chemical Biology, Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, The Netherlands
| | - Stefanie Thurley
- 1Institute for Chemistry, Humboldt University, Brook-Taylor-Str. 2, D-12489 Berlin, Germany
| | - Oliver Seitz
- 1Institute for Chemistry, Humboldt University, Brook-Taylor-Str. 2, D-12489 Berlin, Germany
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54
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Furukawa K, Abe H, Wang J, Uda M, Koshino H, Tsuneda S, Ito Y. Reduction-triggered red fluorescent probes for dual-color detection of oligonucleotide sequences. Org Biomol Chem 2008; 7:671-7. [PMID: 19194582 DOI: 10.1039/b817228e] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We have developed a new red fluorogenic compound derived from naphthorhodamine for a reduction-triggered fluorescence probe to sense oligonucleotides. The fluorogenic reaction between naphthorhodamine azide derivatives and reducing reagents such as triphenylphosphine (TPP) on the DNA target does not use any enzyme or reagent, and fluoresces at 650 nm. The probes were used for dual color detection of a single nucleotide difference on the leukemia-related bcr/abl gene.
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Affiliation(s)
- Kazuhiro Furukawa
- Nano Medical Engineering Laboratory, Advance Science Institute, RIKEN, 2-1, Hirosawa, Wako-Shi, Saitama 351-0198, Japan
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55
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Grossmann TN, Röglin L, Seitz O. Target-catalyzed transfer reactions for the amplified detection of RNA. Angew Chem Int Ed Engl 2008; 47:7119-22. [PMID: 18677727 DOI: 10.1002/anie.200801355] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Tom N Grossmann
- Institut für Chemie der Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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56
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Resonance energy transfer methods of RNA detection. Anal Bioanal Chem 2008; 393:125-35. [DOI: 10.1007/s00216-008-2336-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Revised: 08/01/2008] [Accepted: 08/04/2008] [Indexed: 12/29/2022]
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57
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Grossmann T, Röglin L, Seitz O. Target-katalysierte Transferreaktionen für den signalverstärkten RNA-Nachweis. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801355] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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58
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Nakayama S, Yan L, Sintim HO. Junction Probes − Sequence Specific Detection of Nucleic Acids via Template Enhanced Hybridization Processes. J Am Chem Soc 2008; 130:12560-1. [DOI: 10.1021/ja803146f] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shizuka Nakayama
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Lei Yan
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
| | - Herman O. Sintim
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742
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59
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Franzini RM, Kool ET. Organometallic activation of a fluorogen for templated nucleic acid detection. Org Lett 2008; 10:2935-8. [PMID: 18549220 DOI: 10.1021/ol800878b] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A nucleic acid detection scheme that employs DNA-mediated delivery of an organomercury activator to unmask a fluorophore is described. The approach relies on adjacent hybridization of two oligonucleotide conjugates containing organomercury and caged rhodamine functionalities. Postsynthetic conjugation of amino-modified DNAs enabled efficient preparation of these probes. Complementary DNA templates yielded fluorescence signals arising from metal-assisted rhodamine uncaging.
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Affiliation(s)
- Raphael M Franzini
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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60
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Pianowski ZL, Winssinger N. Nucleic acid encoding to program self-assembly in chemical biology. Chem Soc Rev 2008; 37:1330-6. [PMID: 18568159 DOI: 10.1039/b706610b] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
This tutorial review serves as an introduction to the use of oligonucleotides and in particular peptide nucleic acids (PNAs) to encode function beyond heredity. Applications in chemical biology are reviewed starting with the use of nucleic acid tags to program self-assembled microarrays of small and macromolecules, followed by the use of nucleic acid templated reactions for the purpose of DNA or RNA sensing and finally, the use of nucleic acid templates to display ligands.
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Affiliation(s)
- Zbigniew L Pianowski
- Organic and Bioorganic Chemistry Laboratory, Institut de Science et Ingénierie Supramoléculaires, Université Louis Pasteur, 8 allée Gaspard Monge, Strasbourg, 67000
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61
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Kovács J, Mokhir A. Catalytic Hydrolysis of Esters of 2-Hydroxypyridine Derivatives for Cu2+ Detection. Inorg Chem 2008; 47:1880-2. [DOI: 10.1021/ic7022242] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- János Kovács
- Ruprecht-Karls-Universität Heidelberg, Anorganisch-Chemisches Institut, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
| | - Andriy Mokhir
- Ruprecht-Karls-Universität Heidelberg, Anorganisch-Chemisches Institut, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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62
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Socher E, Jarikote DV, Knoll A, Röglin L, Burmeister J, Seitz O. FIT probes: peptide nucleic acid probes with a fluorescent base surrogate enable real-time DNA quantification and single nucleotide polymorphism discovery. Anal Biochem 2008; 375:318-30. [PMID: 18249184 DOI: 10.1016/j.ab.2008.01.009] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Revised: 01/08/2008] [Accepted: 01/08/2008] [Indexed: 11/19/2022]
Abstract
The ability to accurately quantify specific nucleic acid molecules in complex biomolecule solutions in real time is important in diagnostic and basic research. Here we describe a DNA-PNA (peptide nucleic acid) hybridization assay that allows sensitive quantification of specific nucleic acids in solution and concomitant detection of select single base mutations in resulting DNA-PNA duplexes. The technique employs so-called FIT (forced intercalation) probes in which one base is replaced by a thiazole orange (TO) dye molecule. If a DNA molecule that is complementary to the FIT-PNA molecule (except at the site of the dye) hybridizes to the probe, the TO dye exhibits intense fluorescence because stacking in the duplexes enforces a coplanar arrangement even in the excited state. However, a base mismatch at either position immediately adjacent to the TO dye dramatically decreases fluorescence, presumably because the TO dye has room to undergo torsional motions that lead to rapid depletion of the excited state. Of note, we found that the use of d-ornithine rather than aminoethylglycine as the PNA backbone increases the intensity of fluorescence emitted by matched probe-target duplexes while specificity of fluorescence signaling under nonstringent conditions is also increased. The usefulness of the ornithine-containing FIT probes was demonstrated in the real-time PCR analysis providing a linear measurement range over at least seven orders of magnitude. The analysis of two important single nucleotide polymorphisms (SNPs) in the CFTR gene confirmed the ability of FIT probes to facilitate unambiguous SNP calls for genomic DNA by quantitative PCR.
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Affiliation(s)
- Elke Socher
- Institut für Chemie, Humboldt-Universität zu Berlin, D-12489 Berlin, Germany
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63
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Liu M, Jinmei H, Abe H, Ito Y. Chemical Aminoacylation of RNA by an Intermolecular Adenosine Transfer Reaction. CHEM LETT 2008. [DOI: 10.1246/cl.2008.102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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64
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Narita A, Ogawa K, Sando S, Aoyama Y. Cis-regulatory hairpin-shaped mRNA encoding a reporter protein: catalytic sensing of nucleic acid sequence at single nucleotide resolution. Nat Protoc 2008; 2:1105-16. [PMID: 17546001 DOI: 10.1038/nprot.2007.140] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
DNA sensing at a single nucleotide resolution is achieved using a hairpin-shaped, unmodified (unlabeled) RNA probe or the precursor double-stranded DNA (dsDNA) in a prokaryotic cell-free translation medium. The molecular-beacon-like probe consists of a loop region that is complementary to the target sequence and a stem composed of a ribosome-binding site (RBS) and its docking domain; the RBS is followed by the gene for a reporter protein such as luciferase or beta-galactosidase. Target binding at the loop opens the hairpin to make RBS accessible by the ribosome to start translation of the reporter protein. This sensing system is signal amplifying by virtue of catalytic DNA-to-RNA transcription when using a dsDNA probe, catalytic RNA-to-protein translation, catalytic signal transduction by the enzymatic reaction of the translated reporter protein and, in the presence of RNase H, catalytic or even irreversible translation-activation of the target-probe heteroduplex. Preparation of a probe takes 1-3 d and gene sensing using the probe takes 1-3 h.
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Affiliation(s)
- Atsushi Narita
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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65
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Abstract
Methods are described for preparation and use of quenched autoligation (QUAL) probes. These modified oligonucleotide fluorescent probes can be used to detect DNA and RNA in solution, on solid surfaces, and in fixed and living bacterial and human cells. They are quenched probes, and thus provide a "lighting up" signal in a single step, without removing unbound or unreacted probes from the analyte. QUAL probe signals can be detected by fluorescence spectrometer, fluorescence microscope, or flow cytometry. These probes can distinguish between very small variations, including single nucleotide differences, in nucleic acid targets. The described method includes a description of how to prepare the needed dabsyl quencher linker, how to prepare the QUAL probes by DNA synthesizer, and how to employ them in detecting nucleic acids in solution and in detecting RNAs in bacterial and human cells.
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66
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Yoshimura Y, Taya Y, Matsumura H, Fujimoto K. Photosensitized Cleavage of the Thymine Dimer in DNA via Carbazole Nucleoside. J PHOTOPOLYM SCI TEC 2008. [DOI: 10.2494/photopolymer.21.525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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67
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Abe H, Kondo Y, Jinmei H, Abe N, Furukawa K, Uchiyama A, Tsuneda S, Aikawa K, Matsumoto I, Ito Y. Rapid DNA Chemical Ligation for Amplification of RNA and DNA Signal. Bioconjug Chem 2007; 19:327-33. [DOI: 10.1021/bc700244s] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hiroshi Abe
- Nano Medical Engineering Laboratory, Discovery Research Institute, RIKEN, 2-1, Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Yuko Kondo
- Nano Medical Engineering Laboratory, Discovery Research Institute, RIKEN, 2-1, Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Hiroshi Jinmei
- Nano Medical Engineering Laboratory, Discovery Research Institute, RIKEN, 2-1, Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Naoko Abe
- Nano Medical Engineering Laboratory, Discovery Research Institute, RIKEN, 2-1, Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Kazuhiro Furukawa
- Nano Medical Engineering Laboratory, Discovery Research Institute, RIKEN, 2-1, Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Atsushi Uchiyama
- Nano Medical Engineering Laboratory, Discovery Research Institute, RIKEN, 2-1, Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Satoshi Tsuneda
- Nano Medical Engineering Laboratory, Discovery Research Institute, RIKEN, 2-1, Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Kyoko Aikawa
- Nano Medical Engineering Laboratory, Discovery Research Institute, RIKEN, 2-1, Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Isamu Matsumoto
- Nano Medical Engineering Laboratory, Discovery Research Institute, RIKEN, 2-1, Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory, Discovery Research Institute, RIKEN, 2-1, Hirosawa, Wako-Shi, Saitama, 351-0198 Japan, Department of Chemistry, Faculty of Science, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo 112-8610, Japan, and Department of Life Science and Medical Bio-Science, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan
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68
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Ohkubo A, Tanaka K, Taguchi H, Seio K, Nagasawa H, Tsukahara T, Sekine M. An effective method for the in situ synthesis of DNA-CPG conjugates using chemical ligation technology as tools for SNP analysis. Bioorg Med Chem Lett 2007; 17:5969-73. [PMID: 17845851 DOI: 10.1016/j.bmcl.2007.07.066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2007] [Revised: 07/17/2007] [Accepted: 07/19/2007] [Indexed: 10/22/2022]
Abstract
In this paper, we report a new method for the SNP analysis by using a chemical ligation (CL) technique on CPG plates with high coupling efficiency. This method showed markedly high match/mismatch discrimination ability. Particularly, replacement of thymidine with 2-thiothymidine in DNA probes used in the CL technology resulted in significant improvement of the base discrimination ability of the thymine base in this system.
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Affiliation(s)
- Akihiro Ohkubo
- 4259, Nagatsuta, Department of Life Science, Tokyo Institute of Technology, Yokohama 226-8501, Japan
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69
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Affiliation(s)
- Adam P Silverman
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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70
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Ihara T, Mukae M. Homogeneous DNA-detection based on the non-enzymatic reactions promoted by target DNA. ANAL SCI 2007; 23:625-9. [PMID: 17575342 DOI: 10.2116/analsci.23.625] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Much effort has focused on methods for detecting various genetic differences in individuals, including single nucleotide polymorphisms (SNPs). SNP can be characterized as a substitution, insertion, or deletion at a single base position on a DNA strand. There is expected to be on average one SNP for every 1000 bases of the human genome, and some variations located in genes are suspected to alter both the protein structure and the expression level. Therefore, highly sensitive techniques with a simple procedure would be desirable for a high-throughput screening of millions of SNPs widely dispersed throughout the human genome. In this short review, we consider recently reported unique techniques for genotyping in a homogeneous solution, and organize them in terms of the chemical and physical processes accelerated on DNA.
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Affiliation(s)
- Toshihiro Ihara
- Department of Applied Chemistry and Biochemistry, Graduate School of Science and Technology, Kumamoto University, Japan.
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71
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Dose C, Ficht S, Seitz O. Reducing product inhibition in DNA-template-controlled ligation reactions. Angew Chem Int Ed Engl 2007; 45:5369-73. [PMID: 16847859 DOI: 10.1002/anie.200600464] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Christian Dose
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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72
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Narita A, Ogawa K, Sando S, Aoyama Y. Visible sensing of nucleic acid sequences with a genetically encodable unmodified RNA probe. Angew Chem Int Ed Engl 2007; 45:2879-83. [PMID: 16550617 DOI: 10.1002/anie.200503836] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Atsushi Narita
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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73
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Miller GP, Silverman AP, Kool ET. New, stronger nucleophiles for nucleic acid-templated chemistry: Synthesis and application in fluorescence detection of cellular RNA. Bioorg Med Chem 2007; 16:56-64. [PMID: 17502150 PMCID: PMC2265789 DOI: 10.1016/j.bmc.2007.04.051] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Revised: 09/15/2006] [Accepted: 04/27/2007] [Indexed: 01/14/2023]
Abstract
Nucleic acid-templated chemistry is a promising strategy for imaging genetic sequences in living cells. Here we describe the synthesis of two new nucleophiles for use in templated nucleophilic displacements with DNA probes. The nucleophilic groups are phosphorodithioate and phosphorotrithioate; we report on synthetic methods for introducing these groups at the 3'-terminus of oligonucleotides. Both new nucleophiles are found to be more highly reactive than earlier phosphoromonothioates. This increased nucleophilicity is shown to result in more rapid templated reactions with electrophilic DNA probes. The new probes were demonstrated in detection of specific genetic sequences in solution, with clear signal over background being generated in as little as 20 min. The probes were also tested for imaging ribosomal RNA sequences in live Escherichia coli; useful signal was generated in 20 min to 1h, approximately one quarter to one-half the time of earlier monothioate probes, and the signal-to-noise ratio was increased as well.
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74
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Dose C, Seitz O. Single nucleotide specific detection of DNA by native chemical ligation of fluorescence labeled PNA-probes. Bioorg Med Chem 2007; 16:65-77. [PMID: 17499998 DOI: 10.1016/j.bmc.2007.04.059] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2006] [Revised: 04/05/2007] [Accepted: 04/27/2007] [Indexed: 10/23/2022]
Abstract
DNA-directed chemical ligations provide the opportunity to diagnose DNA sequences with very high sequence specificity. Fluorescent labels have been attached to reactive probes to enable the homogeneous detection of DNA and RNA. However, it has frequently been found that the attachment of fluorescent labels results in decreases of ligation fidelity. Herein we describe the development of a fluorogenic ligation reaction that provides for 10(2)-fold to perfect sequence selectivity. The reaction is based on the isocysteine-mediated native chemical PNA ligation. It is shown that DNA-induced rate accelerations of approximately 43.000-fold can be obtained through subtle variations of the ligation conditions. PNA-thioesters and isocysteine-PNA conjugates were labeled with FAM and TMR fluorophores, respectively. For gaining rapid synthetic access, a convenient on-resin labeling approach was developed. A new PNA monomer featuring an Alloc-protected lysine side chain was synthesized and coupled in solid-phase PNA synthesis. In the event of a ligation reaction the two fluorophores are brought into proximity. It is shown that fluorescence resonance energy transfer provides a positive fluorescence signal which is specific for product formation rather than for loss of starting materials. Single base mutations can be detected within minutes and with very high sequence selectivity at optimized conditions.
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Affiliation(s)
- Christian Dose
- Institut für Chemie der Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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75
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Martí AA, Li X, Jockusch S, Stevens N, Li Z, Raveendra B, Kalachikov S, Morozova I, Russo JJ, Akins DL, Ju J, Turro NJ. Design and characterization of two-dye and three-dye binary fluorescent probes for mRNA detection. Tetrahedron 2007; 63:3591-3600. [PMID: 19907676 PMCID: PMC2775546 DOI: 10.1016/j.tet.2006.08.109] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We report the design, synthesis and characterization of binary oligonucleotide probes for mRNA detection. The probes were designed to avoid common problems found in standard binary probes such as direct excitation of the acceptor fluorophore and overlap between the donor and acceptor emission spectra. Two different probes were constructed that contained an array of either two or three dyes and that were characterized using steady-state fluorescence spectroscopy, time-resolved fluorescence spectroscopy and fluorescence depolarization measurements. The three-dye binary probe (BP-3d) consists of a Fam fluorophore which acts as a donor, collecting light and transferring it as energy to Tamra, which subsequently transfers energy to Cy5 when the two probes are hybridized to mRNA. This design allows the use of 488 nm excitation, which avoids the direct excitation of Cy5 and at the same time provides a good fluorescence resonance energy transfer (FRET) efficiency. The two-dye binary probe system (BP-2d) was constructed of Alexa488 and Cy5 fluorophores. Although the overlap between the fluorescence of Alexa488 and the absorption of Cy5 is relatively low, FRET still occurs due to their close physical proximity when the probes are hybridized to mRNA. This framework also decreases the direct excitation of Cy5 and reduces the fluorescence overlap between the donor and the acceptor. Picosecond time-resolved spectroscopy showed a reduction in the fluorescence lifetime of donor fluorophores after the formation of the hybrid between the probes and target mRNA. Interestingly, BP-2d in the presence of mRNA shows a slow rise in the fluorescence decay of Cy5 due to a relatively low FRET rate, which together with the reduction in the Alexa488 lifetime provides a way to improve the signal to background ratio using time-resolved fluorescence spectra (TRES). In addition, fluorescence depolarization measurements showed complete depolarization of the acceptor dyes (Cy5) for both BP-3d (due to sequential FRET steps) and BP-2d (due to the relatively low FRET rate) in the presence of the mRNA target.
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Affiliation(s)
- Angel A Martí
- Department of Chemistry, Columbia University, New York, NY, 10027
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76
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Bethge L, Jarikote DV, Seitz O. New cyanine dyes as base surrogates in PNA: forced intercalation probes (FIT-probes) for homogeneous SNP detection. Bioorg Med Chem 2007; 16:114-25. [PMID: 17981472 DOI: 10.1016/j.bmc.2006.12.044] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2006] [Accepted: 12/22/2006] [Indexed: 10/23/2022]
Abstract
Forced intercalation probes (FIT-probes) are nucleic acid probes, in which an intercalator cyanine dye such as thiazole orange (TO) serves as a replacement of a canonical nucleobase. These probes signal hybridization by showing strong increases of fluorescence. TO in FIT-probes responds to adjacent base mismatches by attenuation of fluorescence intensities at conditions where both matched and mismatched target DNA are bound. The interesting features of TO labeled FIT-probes posed the question whether the forced intercalation concept can be extended to other cyanine dyes of the thiazole orange family. Herein, we present the synthesis of three asymmetrical cyanine dyes and their incorporation into PNA-conjugates by means of both divergent and linear solid-phase synthesis. Melting analysis revealed that the DNA affinity of PNA probes remained high irrespective of the replacement of a nucleobase by the cyanines YO (oxazole yellow), MO or JO. Of the three new tested dye-PNA-conjugates, the YO-containing PNA has properties useful for homogeneous SNP detection. YO-PNA is demonstrated to signal the presence of fully complementary DNA by up to 20-fold enhancement of fluorescence. In addition, YO emission discriminates against single base mismatches by attenuation of fluorescence. Oxazole yellow (YO) as a base surrogate in PNA may prove useful in the multiplex detection of single base mutations at non-stringent conditions.
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Affiliation(s)
- Lucas Bethge
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Str. 2, 12489 Berlin, Germany
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77
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78
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Silverman AP, Baron EJ, Kool ET. RNA-Templated Chemistry in Cells: Discrimination of Escherichia, Shigella and Salmonella Bacterial Strains With a New Two-Color FRET Strategy. Chembiochem 2006; 7:1890-4. [PMID: 17031884 DOI: 10.1002/cbic.200600278] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Adam P Silverman
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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79
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Dose C, Ficht S, Seitz O. Verringerung der Produkthemmung bei DNA-templatkontrollierten Verknüpfungsreaktionen. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600464] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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80
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Yoshimura Y, Noguchi Y, Sato H, Fujimoto K. Template-directed DNA photoligation in rapid and selective detection of RNA point mutations. Chembiochem 2006; 7:598-601. [PMID: 16502477 DOI: 10.1002/cbic.200500534] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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81
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Narita A, Ogawa K, Sando S, Aoyama Y. Visible Sensing of Nucleic Acid Sequences with a Genetically Encodable Unmodified RNA Probe. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200503836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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82
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Yoshimura Y, Fujimoto K. Catalytic Repair of a Thymine Dimer in DNA via Carbazole Nucleoside. CHEM LETT 2006. [DOI: 10.1246/cl.2006.386] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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83
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Ficht S, Dose C, Seitz O. As fast and selective as enzymatic ligations: unpaired nucleobases increase the selectivity of DNA-controlled native chemical PNA ligation. Chembiochem 2006; 6:2098-103. [PMID: 16208732 DOI: 10.1002/cbic.200500229] [Citation(s) in RCA: 78] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
DNA-controlled reactions offer interesting opportunities in biological, chemical, and nanosciences. In practical applications, such as in DNA sequence analysis, the sequence fidelity of the chemical-ligation reaction is of central importance. We present a ligation reaction that is as fast as and much more selective than enzymatic T4 ligase-mediated oligonucleotide ligations. The selectivity was higher than 3000-fold in discriminating matched from singly mismatched DNA templates. It is demonstrated that this enormous selectivity is the hallmark of the particular ligation architecture, which is distinct from previous ligation architectures designed as "nick ligations". Interestingly, the fidelity of the native chemical ligation of peptide nucleic acids was increased by more than one order of magnitude when performing the ligation in such a way that an abasic-site mimic was formed opposite an unpaired template base. It is shown that the high sequence fidelity of the abasic ligation could facilitate the MALDI-TOF mass-spectrometric analysis of early cancer onset by allowing the detection of as little as 0.2 % of single-base mutant DNA in the presence of 99.8 % wild-type DNA.
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Affiliation(s)
- Simon Ficht
- Institut für Chemie der Humboldt-Universität zu Berlin, Germany
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84
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Abstract
In this article we unify a series of recent studies on bio- and chemosensors under a single signaling strategy: signal amplification by allosteric catalysis (SAAC). The SAAC strategy mimics biological signal transduction processes, where molecular recognition between an external signal and a protein receptor is allosterically transduced into catalytically amplified chemical information (usually second messengers). Several recent biosensing and chemosensing studies apply this nature-inspired strategy by using engineered allosteric enzymes, ribozymes, or regulatable organic catalysts. The factors pertinent to achieving high sensitivity and specificity in SAAC strategies are analyzed. The authors believe that these early studies from a variety of research groups have opened up a new venue for the development of sensing technologies where molecular recognition and catalysis can be coupled for practical purposes.
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Affiliation(s)
- Lei Zhu
- Department of Chemistry and Biochemistry, University of Texas at Austin, Austin, TX 78712, USA
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85
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86
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Abe H, Kool ET. Flow cytometric detection of specific RNAs in native human cells with quenched autoligating FRET probes. Proc Natl Acad Sci U S A 2005; 103:263-8. [PMID: 16384914 PMCID: PMC1326184 DOI: 10.1073/pnas.0509938103] [Citation(s) in RCA: 126] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We describe the use of modified fluorescent-labeled oligonucleotide probes in the sequence-specific detection of messenger RNAs in live human cells. To make this detection possible, we developed a previously undescribed probe design that combines earlier quenched autoligation chemistry with a previously undescribed fluorescence resonance energy transfer (FRET) strategy to lower background signals. The probe pairs consisted of a nucleophilic 3'-phosphorothioate probe carrying a Cy5 FRET acceptor, and an electrophilic probe containing the combination of a 5' end electrophile/quencher and a fluorescein FRET donor. Probes were introduced to HL-60 cells by use of the streptolysin O pore-forming peptide. Signals from three different messenger RNAs, as well as 28S ribosomal RNA, could be detected and quantitated by flow cytometry. Probes targeted to ribosomal sequences and beta-actin mRNA also could be detected over background by confocal fluorescence microscopy. Varying the target site and probe backbone chemistry were found to have large effects on signal. The data suggest that quenched autoligating probes may be of general utility as biological tools in following localization, transcription, and processing of eukaryotic cellular messages and may have applications in diagnostic or prognostic analysis of disease-related RNAs in human tissues.
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Affiliation(s)
- Hiroshi Abe
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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87
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Silverman AP, Kool ET. Quenched autoligation probes allow discrimination of live bacterial species by single nucleotide differences in rRNA. Nucleic Acids Res 2005; 33:4978-86. [PMID: 16284198 PMCID: PMC1199560 DOI: 10.1093/nar/gki814] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Quenched autoligation (QUAL) probes are a class of self-reacting nucleic acid probes that give strong fluorescence signal in the presence of fully complementary RNAs and selectivity against single nucleotide differences in solution. Here, we describe experiments designed to test whether QUAL probes can discriminate between bacterial species by the detection of small differences in their 16S rRNA sequences. Probes were introduced into live cells using small amounts of detergent, thus eliminating the need for fixation, and fluorescence signal was monitored both by microscopy and by flow cytometry without any washing steps. The effects of probe length, modified backbone, probe concentration and growth state of the bacteria were investigated. The data demonstrate specific fluorescence discrimination between three closely related bacteria, Escherichia coli, Salmonella enterica and Pseudomonas putida, based on single nucleotide differences in their 16S rRNA. Discrimination was possible with cells in mid-log phase or in lag phase. These results suggest that QUAL probes may be useful for rapid identification of microorganisms in laboratory and clinical settings.
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Affiliation(s)
| | - Eric T. Kool
- To whom correspondence should be addressed. Tel: +1 650 724 4741; Fax: +1 650 725 0259;
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88
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Abstract
Nucleic acid-based RNA detection is a promising field in molecular biotechnology that is leading to the rapid and accurate identification of microorganisms, diagnosis of infections and imaging of gene expression. The specificity of short synthetic DNA probes raises the hope of distinguishing small differences in sequence, ultimately achieving single nucleotide resolution. Recent work using quenched fluorescently labeled oligonucleotide probes as sensors for RNA in bacterial and human cells has overcome several difficult hurdles on the way to these goals, including delivery of probes to live cells, accessing RNA sites containing a high degree of secondary structure, and eliminating many sources of background. Two new classes of quenched oligonucleotide probes, molecular beacons and quenched auto-ligation probes, have shown the most promise for in situ RNA detection. High-specificity detection, at the single-nucleotide resolution level, is now possible in solution with these classes of probes. However, for applications in intact cells, signal and background issues still need to be addressed before the full potential of these methods is achieved.
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Affiliation(s)
- Adam P Silverman
- Department of Chemistry, Stanford University, Stanford, CA 94305-5080, USA
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89
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Sando S, Narita A, Sasaki T, Aoyama Y. Locked TASC probes for homogeneous sensing of nucleic acids and imaging of fixed E. coli cells. Org Biomol Chem 2005; 3:1002-7. [PMID: 15750642 DOI: 10.1039/b418078j] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We have designed a second-generation TASC (target-assisted self-cleavage) probe. It is based on the switching-on of incorporated cis-acting DNAzyme activity upon the target-induced conformational change of the otherwise inactive off-target probes locked in an intrastrand base-paired hairpin geometry. With E. coli 16S ribosomal RNA-relevant oligonucleotides as targets, the locked TASC probe exhibits an allosteric factor of k(on)/k(off) = 65 and the sequence selectivity is high, in terms of single nucleotide difference, when particular sequence and length of targets are chosen. Preliminary experiments with fixed E. coli cells show that the locked TASC probe with a FRET pair can be used to image fixed E. coli cells.
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Affiliation(s)
- Shinsuke Sando
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, 615-8510, Japan
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