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Roth M, Seitz O. A Self-immolative Molecular Beacon for Amplified Nucleic Acid Detection*. Chemistry 2021; 27:14189-14194. [PMID: 34516006 PMCID: PMC8597011 DOI: 10.1002/chem.202102600] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Indexed: 01/18/2023]
Abstract
Fluorogenic hybridization probes allow the detection of RNA and DNA sequences in homogeneous solution. Typically, one target molecule activates the fluorescence of a single probe molecule. This limits the sensitivity of nucleic acid detection. Herein, we report a self‐immolative molecular beacon (iMB) that escapes the one‐target/one‐probe paradigm. The iMB probe includes a photoreductively cleavable N‐alkyl‐picolinium (NAP) linkage within the loop region. A fluorophore at the 5’‐end serves, on the one hand, as a reporter group and, on the other hand, as a photosensitizer of a NAP‐linker cleavage reaction. In the absence of target, the iMB adopts a hairpin shape. Quencher groups prevent photo‐induced cleavage. The iMB opens upon hybridization with a target, and both fluorescent emission as well as photo‐reductive cleavage of the NAP linker can occur. In contrast to previous chemical amplification reactions, iMBs are unimolecular probes that undergo cleavage leading to products that have lower target affinity than the probes before reaction. Aided by catalysis, the method allowed the detection of 5 pm RNA target within 100 min.
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Affiliation(s)
- Magdalena Roth
- Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
| | - Oliver Seitz
- Institute of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Str. 2, 12489, Berlin, Germany
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2
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Abstract
Nucleic acid directed bioorthogonal reactions offer the fascinating opportunity to unveil and redirect a plethora of intracellular mechanisms. Nano- to picomolar amounts of specific RNA molecules serve as templates and catalyze the selective formation of molecules that 1) exert biological effects, or 2) provide measurable signals for RNA detection. Turnover of reactants on the template is a valuable asset when concentrations of RNA templates are low. The idea is to use RNA-templated reactions to fully control the biodistribution of drugs and to push the detection limits of DNA or RNA analytes to extraordinary sensitivities. Herein we review recent and instructive examples of conditional synthesis or release of compounds for in cellulo protein interference and intracellular nucleic acid imaging.
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Affiliation(s)
- Margherita Di Pisa
- Department of ChemistryHumboldt University BerlinBrook-Taylor Strasse 212489BerlinGermany
| | - Oliver Seitz
- Department of ChemistryHumboldt University BerlinBrook-Taylor Strasse 212489BerlinGermany
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Di Pisa M, Hauser A, Seitz O. Maximizing Output in RNA-Programmed Peptidyl-Transfer Reactions. Chembiochem 2017; 18:872-879. [PMID: 28106939 DOI: 10.1002/cbic.201600687] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Indexed: 01/10/2023]
Abstract
A chemical reaction that is triggered by a specific RNA molecule might provide opportunities for the design of artificial feedback loops. We envision a peptidyl transfer reaction in which mRNA encoding an antiapoptotic protein would instruct the synthesis of apoptosis-inducing peptides. In this study, we used the RNA-programmed synthesis of a 16-mer peptide derived from the BH3 domain of the protein Bak, which inhibits the antiapoptotic protein Bcl-xL . The reaction involves the transfer of a thioester-linked donor peptide fragment from one PNA conjugate to an acceptor peptide-PNA conjugate. We asked two key questions. What are the chemical requirements that allow RNA-templated synthesis of a 16-mer peptide to proceed at lower (nanomolar) concentrations of RNA, that is, the concentration range found in cancer cells? Will such reactions provide sufficient amounts of peptide product and sufficient affinity to interfere with the targeted protein-protein interaction? Perhaps surprisingly, the lengths of the peptides involved in peptidyl transfer chemistry have little effect on the achievable rate enhancements. However, the nature of the thioester C terminus, the distance between the targeted template annealing sites, and template affinity play important roles. The investigation revealed guidelines for the reaction design for peptidyl transfer with low amounts (1-10 nm) of RNA, yet still provide sufficient product to antagonize a protein-protein interaction.
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Affiliation(s)
- Margherita Di Pisa
- Department of Chemistry, Humboldt Universität zu Berlin, Brook Taylor Strasse 2, 12849, Berlin, Germany
| | - Anett Hauser
- Department of Chemistry, Humboldt Universität zu Berlin, Brook Taylor Strasse 2, 12849, Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt Universität zu Berlin, Brook Taylor Strasse 2, 12849, Berlin, Germany
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Roloff A, Ficht S, Dose C, Seitz O. DNA-templated native chemical ligation of functionalized peptide nucleic acids: a versatile tool for single base-specific detection of nucleic acids. Methods Mol Biol 2014; 1050:131-41. [PMID: 24297356 DOI: 10.1007/978-1-62703-553-8_11] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Single base-specific detection of DNA/RNA sequences is of importance in the diagnosis of disease-associated genetic disorders or early stage cancer. This chapter introduces DNA-templated native chemical PNA ligation as a potentially useful tool for the sequence specific detection of nucleic acids. The template-induced alignment of PNA-thioesters and 1,2-aminothiol-PNAs in close proximity leads to an increase in their effective molarities. This facilitates PNA ligation to proceed at concentrations where no reaction would be possible in absence of the template. Moreover, hybridization of the rather short PNA conjugates with non-complementary DNA/RNA is disfavored, which prevents PNA ligation to occur on single base-mismatched templates. Different readout strategies of the ligation reaction such as HPLC, MALDI-TOF-MS and fluorecence monitoring are discussed, and examples for the detection of a point mutation within single stranded and PCR-amplified double stranded DNA are provided.
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Affiliation(s)
- Alexander Roloff
- Department of Organic and Bioorganic Chemistry, Humboldt-Universität zu Berlin, Berlin, Germany
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Patzke V, McCaskill JS, von Kiedrowski G. DNA mit 3′-5′-Disulfid-Verknüpfung - schnelle chemische Ligation durch isosteren Ersatz. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201310644] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Patzke V, McCaskill JS, von Kiedrowski G. DNA with 3'-5'-disulfide links--rapid chemical ligation through isosteric replacement. Angew Chem Int Ed Engl 2014; 53:4222-6. [PMID: 24623660 DOI: 10.1002/anie.201310644] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 01/28/2014] [Indexed: 11/11/2022]
Abstract
Efforts to chemically ligate oligonucleotides, without resorting to biochemical enzymes, have led to a multitude of synthetic analogues, and have extended oligomer ligation to reactions of novel oligonucleotides, peptides, and hybrids such as PNA.1 Key requirements for potential diagnostic tools not based on PCR include a fast templated chemical DNA ligation method that exhibits high pairing selectivity, and a sensitive detection method. Here we report on a solid-phase synthesis of oligonucleotides containing 5'- or 3'-mercapto-dideoxynucleotides and their chemical ligations, yielding 3'-5'-disulfide bonds as a replacement for 3'-5'-phosphodiester units. Employing a system designed for fluorescence monitoring, we demonstrate one of the fastest ligation reactions with half-lives on the order of seconds. The nontemplated ligation reaction is efficiently suppressed by the choice of DNA modification and the 3'-5' orientation of the activation site. The influence of temperature on the templated reaction is shown.
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Affiliation(s)
- Volker Patzke
- Lehrstuhl für Bioorganische Chemie, Ruhr-Universität Bochum, 44780 Bochum (Germany).
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7
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Roloff A, Seitz O. Reducing product inhibition in nucleic acid-templated ligation reactions: DNA-templated cycligation. Chembiochem 2013; 14:2322-8. [PMID: 24243697 DOI: 10.1002/cbic.201300516] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Indexed: 01/19/2023]
Abstract
Programmable interactions allow nucleic acid molecules to template chemical reactions by increasing the effective molarities of appended reactive groups. DNA/RNA-triggered reactions can proceed, in principle, with turnover in the template. The amplification provided by the formation of many product molecules per template is a valuable asset when the availability of the DNA or RNA target is limited. However, turnover is usually impeded by reaction products that block access to the template. Product inhibition is most severe in ligation reactions, where products after ligation have dramatically increased template affinities. We introduce a potentially generic approach to reduce product inhibition in nucleic acid-programmed ligation reactions. A DNA-triggered ligation-cyclization sequence ("cycligation") of bifunctional peptide nucleic acid (PNA) conjugates affords cyclic ligation products. Melting experiments revealed that product cyclization is accompanied by a pronounced decrease in template affinity compared to linear ligation products. The reaction system relies upon haloacetylated PNA-thioesters and isocysteinyl-PNA-cysteine conjugates, which were ligated on a DNA template according to a native chemical ligation mechanism. Dissociation of the resulting linear product-template duplex (induced by, for example, thermal cycling) enabled product cyclization through sulfur-halide substitution. Both ligation and cyclization are fast reactions (ligation: 86 % yield after 20 min, cyclization: quantitative after 5 min). Under thermocycling conditions, the DNA template was able to trigger the formation of new product molecules when fresh reactants were added. Furthermore, cycligation produced 2-3 times more product than a conventional ligation reaction with substoichiometric template loads (0.25-0.01 equiv). We believe that cyclization of products from DNA-templated reactions could ultimately afford systems that completely overcome product inhibition.
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Affiliation(s)
- Alexander Roloff
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489-Berlin (Germany)
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Gorska K, Winssinger N. Reactions templated by nucleic acids: more ways to translate oligonucleotide-based instructions into emerging function. Angew Chem Int Ed Engl 2013; 52:6820-43. [PMID: 23794204 DOI: 10.1002/anie.201208460] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2012] [Indexed: 12/30/2022]
Abstract
The programmability of oligonucleotide recognition offers an attractive platform to direct the assembly of reactive partners that can engage in chemical reactions. Recently, significant progress has been made in both the breadth of chemical transformations and in the functional output of the reaction. Herein we summarize these recent progresses and illustrate their applications to translate oligonucleotide instructions into functional materials and novel architectures (conductive polymers, nanopatterns, novel oligonucleotide junctions); into fluorescent or bioactive molecule using cellular RNA; to interrogate secondary structures or oligonucelic acids; or a synthetic oligomer.
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Affiliation(s)
- Katarzyna Gorska
- Institut de Science et Ingénierie Supramoléculaires (ISIS-UMR 7006), Universite de Strasbourg-CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France
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Gorska K, Winssinger N. Reaktionen an Nucleinsäuretemplaten: mehr Methoden zur Übersetzung Oligonucleotid-basierter Informationen in neue Funktionen. Angew Chem Int Ed Engl 2013. [DOI: 10.1002/ange.201208460] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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10
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Roloff A, Seitz O. Bioorthogonal reactions challenged: DNA templated native chemical ligation during PCR. Chem Sci 2013. [DOI: 10.1039/c2sc20961f] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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11
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Chen XH, Roloff A, Seitz O. Consecutive Signal Amplification for DNA Detection Based on De Novo Fluorophore Synthesis and Host-Guest Chemistry. Angew Chem Int Ed Engl 2012; 51:4479-83. [DOI: 10.1002/anie.201108845] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Indexed: 01/27/2023]
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12
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Chen XH, Roloff A, Seitz O. Konsekutive Signalverstärkung für die DNA-Detektion basierend auf einer De-novo-Fluorophorsynthese und Wirt-Gast-Chemie. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201108845] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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13
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Kausar A, McKay RD, Lam J, Bhogal RS, Tang AY, Gibbs-Davis JM. Tuning DNA Stability To Achieve Turnover in Template for an Enzymatic Ligation Reaction. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201102579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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14
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Kausar A, McKay RD, Lam J, Bhogal RS, Tang AY, Gibbs-Davis JM. Tuning DNA stability to achieve turnover in template for an enzymatic ligation reaction. Angew Chem Int Ed Engl 2011; 50:8922-6. [PMID: 21905182 DOI: 10.1002/anie.201102579] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Abu Kausar
- Department of Chemistry, University of Alberta, Edmonton, AB, T6G 2G2, Canada
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15
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Martin AR, Barvik I, Luvino D, Smietana M, Vasseur JJ. Dynamic and Programmable DNA-Templated Boronic Ester Formation. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007170] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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16
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Martin AR, Barvik I, Luvino D, Smietana M, Vasseur JJ. Dynamic and programmable DNA-templated boronic ester formation. Angew Chem Int Ed Engl 2011; 50:4193-6. [PMID: 21445950 DOI: 10.1002/anie.201007170] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2010] [Revised: 02/14/2011] [Indexed: 11/08/2022]
Affiliation(s)
- Anthony R Martin
- Institut des Biomolécules Max Mousseron (IBMM), UMR 5247 CNRS-Universités Montpellier 1 et 2, Place Bataillon, 34095 Montpellier, France
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17
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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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18
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Arian D, Cló E, Gothelf K, Mokhir A. A Nucleic Acid Dependent Chemical Photocatalysis in Live Human Cells. Chemistry 2010; 16:288-95. [DOI: 10.1002/chem.200902377] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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19
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Grossmann TN, Seitz O. Nucleic acid templated reactions: consequences of probe reactivity and readout strategy for amplified signaling and sequence selectivity. Chemistry 2009; 15:6723-30. [PMID: 19496097 DOI: 10.1002/chem.200900025] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA- and RNA-templated chemical reactions can serve as a diagnostic means for the detection of nucleic acids. Reaction schemes that allow amplified detection are of high interest for polymerase chain reaction (PCR)-free DNA and RNA diagnosis. These reactions typically draw upon the catalytic activity of the template, which is able to trigger the conversion of many signaling molecules per template molecule. However, the design of reactive probes that allow both sensitive and selective nucleic acid detection is a challenge and requires insight into three major parameters: a) reactivity of functional groups involved, b) affinity of probes for the template, and c) the readout system. In this study we used peptide nucleic acid (PNA)-based probes to investigate in detail the signaling power and the selectivity of a transfer reaction derived from a native chemical ligation. We show that subtle variations of the thioesters involved had a tremendous impact on the sensitivity and selectivity of the reaction system. The results suggest that reactions at turnover conditions require low rates of non-templated reaction pathways to provide high target selectivity and sensitivity. On the other hand, very high rates of templated reactions should be avoided to allow mismatched probe-template complexes to dissociate prior to bond formation. Furthermore, the temperature dependence of the DNA-catalyzed transfer reaction was studied and provided insight into crucial strand-exchange processes. Further improvements of selective signaling were achieved through a new readout based on pyrene-transfer reactions. This method reduces background signals and enables significant increases in the signaling rates compared with previous fluorescence-based methods.
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Affiliation(s)
- Tom N Grossmann
- Institut für Chemie der Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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20
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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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21
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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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Hackenberger C, Schwarzer D. Chemoselektive Ligations- und Modifikationsstrategien für Peptide und Proteine. Angew Chem Int Ed Engl 2008. [DOI: 10.1002/ange.200801313] [Citation(s) in RCA: 204] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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23
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Hackenberger C, Schwarzer D. Chemoselective Ligation and Modification Strategies for Peptides and Proteins. Angew Chem Int Ed Engl 2008; 47:10030-74. [DOI: 10.1002/anie.200801313] [Citation(s) in RCA: 651] [Impact Index Per Article: 40.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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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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25
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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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26
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Obika S, Tomizu M, Negoro Y, Orita A, Nakagawa O, Imanishi T. Double-stranded DNA-templated oligonucleotide digestion triggered by triplex formation. Chembiochem 2008; 8:1924-8. [PMID: 17868159 DOI: 10.1002/cbic.200700430] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan.
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Affiliation(s)
- Zhuo Tang
- Department of Chemistry, University of Konstanz, Universitätsstrasse 10, 78457 Konstanz, Germany
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