51
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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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52
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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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53
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Erben A, Grossmann TN, Seitz O. DNA-instructed acyl transfer reactions for the synthesis of bioactive peptides. Bioorg Med Chem Lett 2011; 21:4993-7. [PMID: 21664815 DOI: 10.1016/j.bmcl.2011.05.027] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2011] [Revised: 05/06/2011] [Accepted: 05/09/2011] [Indexed: 01/31/2023]
Abstract
We present a method which allows for the translation of nucleic acid information into the output of molecules that interfere with disease-related protein-protein interactions. The method draws upon a nucleic acid-templated reaction, in which adjacent binding of reactive conjugates triggers the transfer of an aminoacyl or peptidyl group from a donating thioester-linked PNA-peptide hybrid to a peptide-PNA acceptor. We evaluated the influence of conjugate structures on reactivity and sequence specificity. The DNA-triggered peptide synthesis proceeded sequence specifically and showed catalytic turnover in template. The affinity of the formed peptide conjugates for the BIR3 domain of the X-linked inhibitor of apoptosis protein (XIAP) is discussed.
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Affiliation(s)
- Anne Erben
- Department of Chemistry, Humboldt-Universität zu Berlin, Berlin 12489, Germany
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54
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Gasser G, Sosniak AM, Metzler-Nolte N. Metal-containing peptide nucleic acid conjugates. Dalton Trans 2011; 40:7061-76. [PMID: 21541385 DOI: 10.1039/c0dt01706j] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Peptide Nucleic Acids (PNAs) are non-natural DNA/RNA analogues with favourable physico-chemical properties and promising applications. Discovered nearly 20 years ago, PNAs have recently re-gained quite a lot of attention. In this Perspective article, we discuss the latest advances on the preparation and utilisation of PNA monomers and oligomers containing metal complexes. These metal- conjugates have found applications in various research fields such as in the sequence-specific detection of nucleic acids, in the hydrolysis of nucleic acids and peptides, as radioactive probes or as modulators of PNA·DNA hybrid stability, and last but not least as probes for molecular and cell biology.
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Affiliation(s)
- Gilles Gasser
- Institute of Inorganic Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland.
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55
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Wang C, Guo Q, Fu Y. Theoretical Analysis of the Detailed Mechanism of Native Chemical Ligation Reactions. Chem Asian J 2011; 6:1241-51. [DOI: 10.1002/asia.201000760] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Indexed: 12/22/2022]
Affiliation(s)
- Chen Wang
- Department of Chemistry, University of Science and Technology of China, Hefei 230026 (China), Fax: (+86) 551‐3606689
| | - Qing‐Xiang Guo
- Department of Chemistry, University of Science and Technology of China, Hefei 230026 (China), Fax: (+86) 551‐3606689
| | - Yao Fu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026 (China), Fax: (+86) 551‐3606689
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56
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Erben A, Grossmann TN, Seitz O. DNA-triggered synthesis and bioactivity of proapoptotic peptides. Angew Chem Int Ed Engl 2011; 50:2828-32. [PMID: 21387498 DOI: 10.1002/anie.201007103] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2010] [Indexed: 11/11/2022]
Affiliation(s)
- Anne Erben
- Institut für Chemie der Humboldt Universität zu Berlin, Germany
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57
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Erben A, Grossmann TN, Seitz O. DNA‐gesteuerte Synthese und Bioaktivität proapoptotischer Peptide. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007103] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Anne Erben
- Institut für Chemie der Humboldt Universität zu Berlin, Brook‐Taylor‐Straße 2, 12489 Berlin (Deutschland), Fax: (+49) 30‐2093‐7266
| | - Tom N. Grossmann
- Institut für Chemie der Humboldt Universität zu Berlin, Brook‐Taylor‐Straße 2, 12489 Berlin (Deutschland), Fax: (+49) 30‐2093‐7266
| | - Oliver Seitz
- Institut für Chemie der Humboldt Universität zu Berlin, Brook‐Taylor‐Straße 2, 12489 Berlin (Deutschland), Fax: (+49) 30‐2093‐7266
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58
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59
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Peng X, Li H, Seidman M. A Template-Mediated Click-Click Reaction: PNA-DNA, PNA-PNA (or Peptide) Ligation, and Single Nucleotide Discrimination. European J Org Chem 2010; 2010:4194-4197. [PMID: 23504541 PMCID: PMC3597112 DOI: 10.1002/ejoc.201000615] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Indexed: 01/29/2023]
Abstract
A highly efficient chemical ligation was developed for quantitative conjugation of PNA with DNA (PNA or peptide) using the copper-catalyzed azide-alkyne cycloaddition reaction. While PNAs with an alkyne at the C-terminus and an azide at the N-terminus have been used, an efficient click-click reaction occurs. The PNA click ligation is sequence-specific and capable of single nucleotide discrimination.
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Affiliation(s)
- Xiaohua Peng
- Department of Chemistry and Biochemistry, University of Wisconsin-Milwaukee, 3210 N. Cramer St., Milwaukee, 53211, U.S.A
| | - Hong Li
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, Maryland 21224
| | - Michael Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, Maryland 21224
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60
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Bowler FR, Diaz-Mochon JJ, Swift MD, Bradley M. DNA analysis by dynamic chemistry. Angew Chem Int Ed Engl 2010; 49:1809-12. [PMID: 20155766 DOI: 10.1002/anie.200905699] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Frank R Bowler
- School of Chemistry, University of Edinburgh, EH9 3JJ, Edinburgh, UK
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61
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Chouikhi D, Barluenga S, Winssinger N. Clickable peptide nucleic acids (cPNA) with tunable affinity. Chem Commun (Camb) 2010; 46:5476-8. [PMID: 20571635 DOI: 10.1039/c0cc01081b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Peptide nucleic acids (PNAs) are functional analogues of natural oligonucleotides. Herein, we report the synthesis of PNAs bearing a triazole in lieu of the amide bond assembled using a "click" cycloaddition, their hybridization properties as well as the DNA-templated coupling of the azide and alkyne PNA fragments.
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Affiliation(s)
- Dalila Chouikhi
- Institut de Science et Ingénierie Supramoléculaires (ISIS-UMR 7006)Université de Strasbourg-CNRS, 8 allée Gaspard Monge, F67000 Strasbourg, France
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62
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Roviello GN, Gröschel S, Pedone C, Diederichsen U. Synthesis of novel MMT/acyl-protected nucleo alanine monomers for the preparation of DNA/alanyl-PNA chimeras. Amino Acids 2010; 38:1301-9. [PMID: 19629638 PMCID: PMC2860553 DOI: 10.1007/s00726-009-0324-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2009] [Accepted: 07/08/2009] [Indexed: 10/25/2022]
Abstract
Alanyl-peptide nucleic acid (alanyl-PNA)/DNA chimeras are oligomers envisaged to be beneficial in efficient DNA diagnostics based on an improved molecular beacon concept. A synthesis of alanyl-PNA/DNA chimera can be based on the solid phase assembly of the oligomer with mixed oligonucleotide/peptide backbone under DNA synthesis conditions, in which the nucleotides are introduced as phosphoramidites, whereas the nucleo amino acids make use of the acid labile monomethoxytrityl (MMT) group for temporary protection of the alpha-amino groups and acyl protecting groups for the exocyclic amino functions of the nucleobases. In this work, we realized for the first time the synthesis of all four MMT/acyl-protected nucleo alanines, achieved by deprotection/reprotection of the newly synthesized Boc/acyl intermediates, useful monomers for the obtainment of (alanyl-PNA)/DNA chimeras by conditions fully compatible with the standard phosphoramidite DNA synthesis strategy.
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Affiliation(s)
- G. N. Roviello
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstr. 2, 37077 Göttingen, Germany
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - S. Gröschel
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstr. 2, 37077 Göttingen, Germany
| | - C. Pedone
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, 80134 Naples, Italy
| | - U. Diederichsen
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstr. 2, 37077 Göttingen, Germany
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63
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Bowler F, Diaz-Mochon J, Swift M, Bradley M. DNA Analysis by Dynamic Chemistry. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.200905699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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64
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Xiao Y, Lou X, Uzawa T, Plakos KJI, Plaxco KW, Soh HT. An electrochemical sensor for single nucleotide polymorphism detection in serum based on a triple-stem DNA probe. J Am Chem Soc 2010; 131:15311-6. [PMID: 19807078 DOI: 10.1021/ja905068s] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We report here an electrochemical approach that offers, for the first time, single-step, room-temperature single nucleotide polymorphism (SNP) detection directly in complex samples (such as blood serum) without the need for target modification, postwashing, or the addition of exogenous reagents. This sensor, which is sensitive, stable, and reusable, is comprised of a single, self-complementary, methylene blue-labeled DNA probe possessing a triple-stem structure. This probe takes advantage of the large thermodynamic changes in enthalpy and entropy that result from major conformational rearrangements that occur upon binding a perfectly matched target, resulting in a large-scale change in the faradaic current. As a result, the discrimination capabilities of this sensor greatly exceed those of earlier single- and double-stem electrochemical sensors and support rapid (minutes), single-step, reagentless, room-temperature detection of single nucleotide substitutions. To elucidate the theoretical basis of the sensor's selectivity, we present a comparative thermodynamic analysis among single-, double-, and triple-stem probes.
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Affiliation(s)
- Yi Xiao
- Materials Department, University of California, Santa Barbara, California 93106, USA.
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65
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Xiao Y, Plakos KJI, Lou X, White RJ, Qian J, Plaxco KW, Soh HT. Fluorescence detection of single-nucleotide polymorphisms with a single, self-complementary, triple-stem DNA probe. Angew Chem Int Ed Engl 2009; 48:4354-8. [PMID: 19431180 DOI: 10.1002/anie.200900369] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Singled out for its singularity: In a single-step, single-component, fluorescence-based method for the detection of single-nucleotide polymorphisms at room temperature, the sensor is comprised of a single, self-complementary DNA strand that forms a triple-stem structure. The large conformational change that occurs upon binding to perfectly matched (PM) targets results in a significant increase in fluorescence (see picture; F = fluorophore, Q = quencher).
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Affiliation(s)
- Yi Xiao
- Materials Department, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
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66
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Xiao Y, Plakos K, Lou X, White R, Qian J, Plaxco K, Soh H. Fluorescence Detection of Single-Nucleotide Polymorphisms with a Single, Self-Complementary, Triple-Stem DNA Probe. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900369] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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67
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Pianowski Z, Gorska K, Oswald L, Merten CA, Winssinger N. Imaging of mRNA in Live Cells Using Nucleic Acid-Templated Reduction of Azidorhodamine Probes. J Am Chem Soc 2009; 131:6492-7. [DOI: 10.1021/ja809656k] [Citation(s) in RCA: 142] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Zbigniew Pianowski
- Institut de Science et Ingénierie Supramoléculaires (ISIS − UMR 7006), Université de Strasbourg – CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Katarzyna Gorska
- Institut de Science et Ingénierie Supramoléculaires (ISIS − UMR 7006), Université de Strasbourg – CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Laurence Oswald
- Institut de Science et Ingénierie Supramoléculaires (ISIS − UMR 7006), Université de Strasbourg – CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Christoph A. Merten
- Institut de Science et Ingénierie Supramoléculaires (ISIS − UMR 7006), Université de Strasbourg – CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
| | - Nicolas Winssinger
- Institut de Science et Ingénierie Supramoléculaires (ISIS − UMR 7006), Université de Strasbourg – CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
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68
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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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69
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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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70
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Mukae M, Ihara T, Tabara M, Jyo A. Anthracene–DNA conjugates as building blocks of designed DNA structures constructed by photochemical reactions. Org Biomol Chem 2009; 7:1349-54. [DOI: 10.1039/b821869b] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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71
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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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72
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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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73
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Boontha B, Nakkuntod J, Hirankarn N, Chaumpluk P, Vilaivan T. Multiplex mass spectrometric genotyping of single nucleotide polymorphisms employing pyrrolidinyl peptide nucleic acid in combination with ion-exchange capture. Anal Chem 2008; 80:8178-86. [PMID: 18821781 DOI: 10.1021/ac801336q] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A new ion-exchange capture technique is introduced for label-free sample preparation in single nucleotide polymorphism (SNP) genotyping. The DNA sample is hybridized with a new pyrrolidinyl peptide nucleic acid (PNA) probe and treated with a strong anion exchanger. The complementary PNA.DNA hybrid is selectively captured by the anion exchanger in the presence of noncomplementary or unhybridized PNA, allowing direct detection of the hybridization event on the anion exchanger by MALDI-TOF mass spectrometry after simple washing. The high specificity of the pyrrolidinyl PNA allows simultaneous multiplex SNP typing to be carried out at room temperature without the need for enzyme treatment or heating. Exemplary applications of this technique, in the identification of meat species in feedstuffs and in multiplex SNP typing of the human IL-10 gene promoter region are demonstrated, clearly suggesting the potential for much broader applications.
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Affiliation(s)
- Boonjira Boontha
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
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74
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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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75
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Liu Y, Sha R, Wang R, Ding L, Canary JW, Seeman NC. 2′,2′-Ligation demonstrates the thermal dependence of DNA-directed positional control. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.05.046] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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76
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Kitamura Y, Ihara T, Tsujimura Y, Osawa Y, Sasahara D, Yamamoto M, Okada K, Tazaki M, Jyo A. Template-directed formation of luminescent lanthanide complexes: versatile tools for colorimetric identification of single nucleotide polymorphism. J Inorg Biochem 2008; 102:1921-31. [PMID: 18707760 DOI: 10.1016/j.jinorgbio.2008.06.016] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2008] [Revised: 06/17/2008] [Accepted: 06/24/2008] [Indexed: 12/21/2022]
Abstract
We present the facile technique of colorimetric SNP (single nucleotide polymorphism) analysis through DNA-templated cooperative complexation between a luminescent lanthanide ion (Ln(III): Tb(III) or Eu(III)) and two ODN (oligodeoxyribonucleotide) conjugates carrying a metal chelator. Families of complexane-type chelators and heterocyclic aromatic ligands were covalently attached to ODNs to form conjugates for application as capture and sensitizer probes. The sequences of the conjugates were designed so as to form a ternary tandem duplex with the target, where their auxiliary units face each other, providing a microenvironment to accommodate Ln(III). Only the combination of EDTA (ethylenediaminetetraacetic acid) conjugates and phen (1,10-phenanthroline) conjugates provided significant emissions with quantum yields of 3.3% and 1.5% for Tb(III) and Eu(III), respectively, in the presence of the target. Biallelic polymorphism in the TPMT (thiopurine S-methyltransferase) gene, wt/wt (G/G), mut/mut (C/C), and wt/mut (G/C), were distinguished as emissions in green, red, and yellow, respectively; the colors were identified even by the naked eye.
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Affiliation(s)
- Yusuke Kitamura
- Department of Applied Chemistry and Biochemistry, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan
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77
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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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78
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Affiliation(s)
- Adam P Silverman
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
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79
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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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80
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Jacobsen MF, Cló E, Mokhir A, Gothelf KV. Model Systems for Activation of Nucleic Acid Encoded Prodrugs. ChemMedChem 2007; 2:793-9. [PMID: 17436260 DOI: 10.1002/cmdc.200700013] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The development of more selective chemotherapeutic agents for benign treatments of malicious diseases is highly desirable. In recent years model systems for the release of small molecule drugs from nucleic acid conjugates by templated chemical or photochemical reactions have been designed. Common for these systems is that the stoichiometric or catalytic drug release is controlled by the highly selective hybridization between complementary strands of nucleic acids. Herein, the concepts of the new field of nucleic acid templated release reactions are outlined.
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Affiliation(s)
- Mikkel F Jacobsen
- Centre for DNA Nanotechnology, Center for Catalysis and Interdisciplinary Nanoscience Center (iNANO), Department of Chemistry, University of Aarhus, Langelandsgade 140, 8000 Aarhus C, Denmark
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81
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Griesang N, Giessler K, Lommel T, Richert C. Four-color, enzyme-free interrogation of DNA sequences with chemically activated, 3'-fluorophore-labeled nucleotides. Angew Chem Int Ed Engl 2007; 45:6144-8. [PMID: 16927357 DOI: 10.1002/anie.200600804] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Niels Griesang
- Institut für Organische Chemie, Universität Karlsruhe TH, 76131 Karlsruhe, Germany
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82
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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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83
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Grossmann TN, Sasaki S, Ritzefeld M, Choi SW, Maruyama A, Seitz O. Inducing the replacement of PNA in DNA.PNA duplexes by DNA. Bioorg Med Chem 2007; 16:34-9. [PMID: 17513114 DOI: 10.1016/j.bmc.2007.04.066] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Revised: 04/05/2007] [Accepted: 04/27/2007] [Indexed: 10/23/2022]
Abstract
The uncharged DNA-analogue peptide nucleic acid (PNA) can invade into dsDNA by displacing the non-complementary DNA strand. The formed strand displacement complexes can create a sterical hindrance to block access of enzymes such as nucleases and polymerases. Due to the high stability of DNA.PNA duplexes it is usually not possible to displace the PNA strand by ssDNA or ssRNA. We herein report that the polycationic, comb-type copolymer alphaPLL-g-Dex can induce such a replacement of PNA in DNA.PNA duplexes by ssDNA. The influence of the copolymer on strand exchange highly depends on the nature of the oligonucleotides. Acceleration has only been observed when both the starting duplex and the single-stranded exchanger strand were negatively charged. The presented approach should allow the withdrawal of PNA induced sterical hindrance of DNA by rehybridisation with ssDNA.
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Affiliation(s)
- Tom N Grossmann
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, D-12489 Berlin, Germany
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84
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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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85
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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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86
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Abstract
Herein we describe a novel DNA-catalyzed transfer of a reporter group from a donating to an accepting oligo-peptide nucleic acid (PNA), generating high catalytic turnover numbers in a DNA-sequence specific manner. The demonstrated transfer of the Dabcyl group was designed to switch on emission of a fluorescein dye while switching off emission of a rhodamine dye. This setup allows the highly sensitive and selective detection of DNA-sequences in real time.
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Affiliation(s)
- Tom N Grossmann
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, D-12489 Berlin, Germany
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87
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Four-Color, Enzyme-Free Interrogation of DNA Sequences with Chemically Activated, 3′-Fluorophore-Labeled Nucleotides. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200600804] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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88
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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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89
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Abstract
[reaction: see text] A convergent strategy for synthesizing long contiguous PNA by a native chemical ligation-like technique of PNA segment couplings is presented. This approach required the synthesis of a new PNA-monomer featuring a 1-amino-2-thiol group. It is shown that the additional mercaptomethyl group leaves the hybridization properties of PNA ligation products unaffected. Furthermore, rapid and efficient fluorescence labeling of the ligation products is demonstrated.
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Affiliation(s)
- Christian Dose
- Humboldt-Universität zu Berlin, Institut für Chemie, Brook-Taylor-Strasse 2, D-12489 Berlin, Germany
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90
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91
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Baumhof P, Griesang N, Bächle M, Richert C. Synthesis of oligonucleotides with 3'-terminal 5-(3-acylamidopropargyl)-3'-amino-2',3'-dideoxyuridine residues and their reactivity in single-nucleotide steps of chemical replication. J Org Chem 2006; 71:1060-7. [PMID: 16438521 DOI: 10.1021/jo052097j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligonucleotides with a 3'-terminal 5-alkynyl-3'-amino-2',3'-dideoxyuridine residue were prepared, starting from 2'-deoxyuridine. The optimized route employs a 2',3'-dideoxy-3'-trifluoroacetamido-5-iodouridine 5'-phosphoramidite as building block for DNA synthesis and involves on-support Sonogashira coupling with N-tritylpropargylamine to generate oligonucleotides. The amino group of the propargylamine side chain was acylated to accelerate primer extension reactions involving the 3'-amino group. Three acyl groups were identified that decrease the half-life for DNA-templated extension steps with 7-azabenzotriazole esters of 2'-deoxynucleotides. The residue of 4-pyrenylbutyric acid was found to accelerate primer extension reactions and to render them more selective than those of the control primer. With this substituent, primer extension is also faster than previously measured for three-strand systems involving template, aminoprimer, and a downstream-binding helper oligonucleotide. Fast-reacting primers might become useful for genotyping single nucleotides.
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Affiliation(s)
- Patrick Baumhof
- Institute for Organic Chemistry, University of Karlsruhe (TH), D-76131 Karlsruhe, Germany
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92
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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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93
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Kersebohm T, Kirin SI, Metzler-Nolte N. Insertion of an internal dipeptide into PNA oligomers: thermal melting studies and further functionalization. Bioorg Med Chem Lett 2006; 16:2964-8. [PMID: 16546386 DOI: 10.1016/j.bmcl.2006.02.071] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2005] [Revised: 02/23/2006] [Accepted: 02/25/2006] [Indexed: 11/24/2022]
Abstract
The solid phase synthesis of PNA oligomers with the internal dipeptide Gly-Phe is presented and the interaction with complementary DNA investigated. UV absorbance melting experiments with different but complementary DNA sequences show that stable PNA x DNA duplexes are only obtained when there is no DNA base opposite the dipeptide unit. Instead, the dipeptide spacer forms a loop-like structure within the duplex. Further functionalization with N-heterocyclic ligands is described. p-Nitro-phenylalanine is introduced in place of Phe during solid phase synthesis and subsequently reduced to p-amino-phenylalanine. Reaction with activated acids provides the ligand conjugates in high yield and purity. This strategy opens a universal route to a large number of internal substitutions in PNA chemistry.
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Affiliation(s)
- Tim Kersebohm
- Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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94
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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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95
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Tang H, Radosz M, Shen Y. Template atom transfer radical polymerization of a diaminopyrimidine-derivatized monomer in the presence of a uracil-containing polymer. ACTA ACUST UNITED AC 2006. [DOI: 10.1002/pola.21732] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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96
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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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97
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Boll I, Krämer R, Brunner J, Mokhir A. Templated metal catalysis for single nucleotide specific DNA sequence detection. J Am Chem Soc 2005; 127:7849-56. [PMID: 15913375 DOI: 10.1021/ja0503332] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A catalytic DNA-templated reaction of hydrolysis of an ester group in an N-modified peptide nucleic acid, which is activated by a Cu2+ complex-PNA, has been discovered and optimized. Both the ester-containing PNA and the metal complex PNA bind neighboring sites on a template DNA. This brings the reacting groups (the ester and the Cu2+ complex) in proximity to each other and accelerates the hydrolysis of the ester approximately 500 times in comparison with its hydrolysis in the absence of the template. The hydrolysis reaction provides >10(2)-fold kinetic discrimination between DNAs that are different from each other at a single nucleotide position. Natural enzyme T4 DNA ligase is slightly less selective. On the basis of this reaction a fully homogeneous and sensitive assay for sequence-specific DNA detection has been developed (10 fmol DNA). Identification of one of four DNAs (variation at one position) can be done in a single experiment. Since the Cu2+ ion is tightly bound in an associate containing the ester PNA, the metal complex PNA, and the template DNA, application of this method in buffers containing other Cu2+-binding ligands, e.g., PCR buffer and physiological buffer, is possible.
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Affiliation(s)
- Iris Boll
- Anorganisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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98
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Boll I, Krämer R, Mokhir A. Hybridization dependent cleavage of internally modified disulfide-peptide nucleic acids. Bioorg Med Chem Lett 2005; 15:505-9. [PMID: 15664802 DOI: 10.1016/j.bmcl.2004.11.066] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2004] [Revised: 10/28/2004] [Accepted: 11/25/2004] [Indexed: 10/26/2022]
Abstract
Selectivity of the cleavage of single stranded over hybridized forms of internally modified disulfide-peptide nucleic acids (PNA) has been optimized using a series of phosphines and thiols, which have different sizes and charges. For the most selective cleaver found (tris-(carboxyethyl)-phosphine), reactivity of single stranded PNA is 33 times higher than that of the PNA-DNA duplex. Selectivity of single stranded disulfide-PNA cleavage has been explained in terms of electrostatic interaction between the substrate and the cleaver.
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Affiliation(s)
- Iris Boll
- Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, D-69120 Heidelberg, Germany
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99
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Abe H, Kool ET. Destabilizing Universal Linkers for Signal Amplification in Self-Ligating Probes for RNA. J Am Chem Soc 2004; 126:13980-6. [PMID: 15506759 DOI: 10.1021/ja046791c] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recent studies have established the utility of oligonucleotide ligation methods in the detection of DNAs and RNAs in solution and in cellular imaging. Notably, the ligated full-length oligonucleotide products commonly bind to the target nucleic acid much more tightly than do the two starting half-probes, which effectively limits the resulting signals to one per target. Here, we report on a molecular strategy for destabilizing ligated products in template-promoted self-ligation reactions, thus yielding multiple signals per target. A new universal linker design is described in which a dabsyl leaving group is placed on a short alkane tether. This allows the placement of an electrophile at the end of any DNA sequence, in contrast to earlier ligation strategies, and it also speeds reaction rates by a factor of 4-5. This new class of molecular linker/activator yields as much as 92-fold amplification of signals in DNA and RNA detection, and proceeds without enzymes, added reagents, or thermal cycling. The linker is shown to destabilize the ligation product without destabilizing the transition state for ligation. This lowers product inhibition, and the target DNA or RNA thus becomes a catalyst for isothermally generating multiple signals for its detection. This enhanced signal generation is demonstrated in solution experiments and in solid supported assays.
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Affiliation(s)
- Hiroshi Abe
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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