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Loibl N, Arenz C, Seitz O. Monitoring Dicer-Mediated miRNA-21 Maturation and Ago2 Loading by a Dual-Colour FIT PNA Probe Set. Chembiochem 2020; 21:2527-2532. [PMID: 32270536 PMCID: PMC7496889 DOI: 10.1002/cbic.202000173] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/06/2020] [Indexed: 12/14/2022]
Abstract
The inhibition of micro RNA (miRNA) maturation by Dicer and loading matured miRNAs into the RNA-induced silencing complex (RISC) is envisioned as a modality for treatment of cancer. Existing methods for evaluating maturation either focus on the conversion of modified precursors or detect mature miRNA. Whereas the former is not applicable to native pre-miRNA, the latter approach underestimates maturation when both nonmatured and matured miRNA molecules are subject to cleavage. We present a set of two orthogonally labelled FIT PNA probes that distinguish between cleaved pre-miRNA and the mature miRNA duplex. The probes allow Dicer-mediated miR21 maturation to be monitored and Ago2-mediated unwinding of the miR21 duplex to be assayed. A two-channel fluorescence readout enables measurement in real-time without the need for specialized instrumentation or further enzyme mediated amplification.
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Affiliation(s)
- Natalia Loibl
- Department of ChemistryHumbolt-Universität zu BerlinBrook-Taylor-Strase 212489BerlinGermany
| | - Christoph Arenz
- Department of ChemistryHumbolt-Universität zu BerlinBrook-Taylor-Strase 212489BerlinGermany
| | - Oliver Seitz
- Department of ChemistryHumbolt-Universität zu BerlinBrook-Taylor-Strase 212489BerlinGermany
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2
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Chamiolo J, Fang GM, Hövelmann F, Friedrich D, Knoll A, Loewer A, Seitz O. Comparing Agent-Based Delivery of DNA and PNA Forced Intercalation (FIT) Probes for Multicolor mRNA Imaging. Chembiochem 2018; 20:595-604. [PMID: 30326174 PMCID: PMC6470956 DOI: 10.1002/cbic.201800526] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Indexed: 12/19/2022]
Abstract
Fluorogenic oligonucleotide probes allow mRNA imaging in living cells. A key challenge is the cellular delivery of probes. Most delivery agents, such as cell‐penetrating peptides (CPPs) and pore‐forming proteins, require interactions with the membrane. Charges play an important role. To explore the influence of charge on fluorogenic properties and delivery efficiency, we compared peptide nucleic acid (PNA)‐ with DNA‐based forced intercalation (FIT) probes. Perhaps counterintuitively, fluorescence signaling by charged DNA FIT probes proved tolerant to CPP conjugation, whereas CPP–FIT PNA conjugates were affected. Live‐cell imaging was performed with a genetically engineered HEK293 cell line to allow the inducible expression of a specific mRNA target. Blob‐like features and high background were recurring nuisances of the tested CPP and lipid conjugates. By contrast, delivery by streptolysin‐O provided high enhancements of the fluorescence of the FIT probe upon target induction. Notably, DNA‐based FIT probes were brighter and more responsive than PNA‐based FIT probes. Optimized conditions enabled live‐cell multicolor imaging of three different mRNA target sequences.
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Affiliation(s)
- Jasmine Chamiolo
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany
| | - Ge-Min Fang
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany.,Institute of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, P.R. China
| | - Felix Hövelmann
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany
| | - Dhana Friedrich
- Max Delbrück Centrum für Molekulare Medizin, Robert Rössle Strasse 10, 13125, Berlin, Germany.,Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 13, 64287, Darmstadt, Germany
| | - Andrea Knoll
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany
| | - Alexander Loewer
- Max Delbrück Centrum für Molekulare Medizin, Robert Rössle Strasse 10, 13125, Berlin, Germany.,Department of Biology, Technische Universität Darmstadt, Schnittspahnstrasse 13, 64287, Darmstadt, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12849, Berlin, Germany
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Lugovik KI, Popova AV, Eltyshev AK, Benassi E, Belskaya NP. Synthesis of Thiazoles Bearing Aryl Enamine/Aza-enamine Side Chains: Effect of the π-Conjugated Spacer Structure and Hydrogen Bonding on Photophysical Properties. European J Org Chem 2017. [DOI: 10.1002/ejoc.201700518] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Kseniya I. Lugovik
- Ural Federal University; 19 Mira Str. 620002 Yekaterinburg Russian Federation
| | | | | | - Enrico Benassi
- Scuola Normale Superiore; Piazza dei Cavalieri 7 56126 Pisa Italy
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Fang GM, Seitz O. Bivalent Display of Dicysteine on Peptide Nucleic Acids for Homogenous DNA/RNA Detection through in Situ Fluorescence Labelling. Chembiochem 2016; 18:189-194. [PMID: 27883258 DOI: 10.1002/cbic.201600623] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Indexed: 01/06/2023]
Abstract
Fluorogenic probes that signal the presence of specific DNA or RNA sequences are key enabling tools for molecular disease diagnosis and imaging studies. Usually, at least one fluorophore is attached through covalent bonding to an oligonucleotide probe. However, the additional conjugation step increases costs. Here we introduce a method that avoids the requirement for the preparation of fluorescence-labelled oligonucleotides and provides the opportunity to alter the fluorogenic reporter dye without resynthesis. The method is based on adjacent hybridization of two dicysteine-containing peptide nucleic acid (PNA) probes to form a bipartite tetracysteine motif that binds profluorescent bisarsenical dyes such as FIAsH, ReAsH or CrAsH. Binding is accompanied by strong increases in fluorescence emission (with response factors of up to 80-fold and high brightness up to 50 mL mol-1 cm-1 ). The detection system provides sub-nanomolar limits of detection and allows discrimination of single nucleotide variations through more than 20-fold changes in fluorescence intensity. To demonstrate its usefulness, the FIAsH-based readout of the bivalent CysCys-PNA display was interfaced with a rolling-circle amplification (RCA) assay used to detect disease-associated microRNA let-7a.
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Affiliation(s)
- Ge-Min Fang
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
| | - Oliver Seitz
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489, Berlin, Germany
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5
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Berndl S, Dimitrov SD, Menacher F, Fiebig T, Wagenknecht HA. Thiazole Orange Dimers in DNA: Fluorescent Base Substitutions with Hybridization Readout. Chemistry 2016; 22:2386-95. [DOI: 10.1002/chem.201503849] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Indexed: 01/03/2023]
Affiliation(s)
- Sina Berndl
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
| | - Stoichko D. Dimitrov
- Centre for Plastic Electronics; Department of Chemistry; Imperial College London; Exhibition Road London SW7 2AZ UK
| | - Florian Menacher
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
| | - Torsten Fiebig
- Feinberg School of Medicine; Department of Otolaryngology; Northwestern University; 420 East Superior Street Chicago IL 60611 USA
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
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Das S, Li Y, Bornschein C, Pisiewicz S, Kiersch K, Michalik D, Gallou F, Junge K, Beller M. Selective Rhodium-Catalyzed Reduction of Tertiary Amides in Amino Acid Esters and Peptides. Angew Chem Int Ed Engl 2015; 54:12389-93. [DOI: 10.1002/anie.201503584] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2015] [Revised: 05/28/2015] [Indexed: 11/11/2022]
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7
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Das S, Li Y, Bornschein C, Pisiewicz S, Kiersch K, Michalik D, Gallou F, Junge K, Beller M. Selective Rhodium-Catalyzed Reduction of Tertiary Amides in Amino Acid Esters and Peptides. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201503584] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Kanamori T, Ohzeki H, Masaki Y, Ohkubo A, Takahashi M, Tsuda K, Ito T, Shirouzu M, Kuwasako K, Muto Y, Sekine M, Seio K. Controlling the fluorescence of benzofuran-modified uracil residues in oligonucleotides by triple-helix formation. Chembiochem 2014; 16:167-76. [PMID: 25469677 DOI: 10.1002/cbic.201402346] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Indexed: 12/16/2022]
Abstract
We developed fluorescent turn-on probes containing a fluorescent nucleoside, 5-(benzofuran-2-yl)deoxyuridine (dU(BF)) or 5-(3-methylbenzofuran-2-yl)deoxyuridine (dU(MBF)), for the detection of single-stranded DNA or RNA by utilizing DNA triplex formation. Fluorescence measurements revealed that the probe containing dU(MBF) achieved superior fluorescence enhancement than that containing dU(BF). NMR and fluorescence analyses indicated that the fluorescence intensity increased upon triplex formation partly as a consequence of a conformational change at the bond between the 3-methylbenzofuran and uracil rings. In addition, it is suggested that the microenvironment around the 3-methylbenzofuran ring contributed to the fluorescence enhancement. Further, we developed a method for detecting RNA by rolling circular amplification in combination with triplex-induced fluorescence enhancement of the oligonucleotide probe containing dU(MBF).
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Affiliation(s)
- Takashi Kanamori
- Education Academy of Computational Life Sciences, Tokyo Institute of Technology, 4259 Nagatsuta, Midoriku, Yokohama 226-8501 (Japan)
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Hövelmann F, Gaspar I, Loibl S, Ermilov EA, Röder B, Wengel J, Ephrussi A, Seitz O. Brightness through local constraint--LNA-enhanced FIT hybridization probes for in vivo ribonucleotide particle tracking. Angew Chem Int Ed Engl 2014; 53:11370-5. [PMID: 25167966 DOI: 10.1002/anie.201406022] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Indexed: 11/11/2022]
Abstract
Imaging the dynamics of RNA in living cells is usually performed by means of transgenic approaches that require modification of RNA targets and cells. Fluorogenic hybridization probes would also allow the analysis of wild-type organisms. We developed nuclease-resistant DNA forced intercalation (FIT) probes that combine the high enhancement of fluorescence upon hybridization with the high brightness required to allow tracking of individual ribonucleotide particles (RNPs). In our design, a single thiazole orange (TO) intercalator dye is linked as a nucleobase surrogate and an adjacent locked nucleic acid (LNA) unit serves to introduce a local constraint. This closes fluorescence decay channels and thereby increases the brightness of the probe-target duplexes. As few as two probes were sufficient to enable the tracking of oskar mRNPs in wild-type living Drosophila melanogaster oocytes.
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Affiliation(s)
- Felix Hövelmann
- Department of Chemistry, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin (Germany)
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Hövelmann F, Gaspar I, Loibl S, Ermilov EA, Röder B, Wengel J, Ephrussi A, Seitz O. Helligkeit durch lokale Rigidifizierung - LNA-verstärkte FIT-Sonden zur bildgebenden Darstellung von Ribonukleotidpartikeln in vivo. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201406022] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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11
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Hövelmann F, Bethge L, Seitz O. Single labeled DNA FIT probes for avoiding false-positive signaling in the detection of DNA/RNA in qPCR or cell media. Chembiochem 2012; 13:2072-81. [PMID: 22936610 DOI: 10.1002/cbic.201200397] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Indexed: 12/13/2022]
Abstract
Oligonucleotide hybridization probes that fluoresce upon binding to complementary nucleic acid targets allow the real-time detection of DNA or RNA in homogeneous solution. The most commonly used probes rely on the distance-dependent interaction between a fluorophore and another label. Such dual-labeled oligonucleotides signal the change of the global conformation that accompanies duplex formation. However, undesired nonspecific binding events and/or probe degradation also lead to changes in the label-label distance and, thus, to ambiguities in fluorescence signaling. Herein, we introduce singly labeled DNA probes, "DNA FIT probes", that are designed to avoid false-positive signals. A thiazole orange (TO) intercalator dye serves as an artificial base in the DNA probe. The probes show little background because the attachment mode hinders 1) interactions of the "TO base" in cis with the disordered nucleobases of the single strand, and 2) intercalation of the "TO nucleotide" with double strands in trans. However, formation of the probe-target duplex enforces stacking and increases the fluorescence of the TO base. We explored open-chain and carbocyclic nucleotides. We show that the incorporation of the TO nucleotides has no effect on the thermal stability of the probe-target complexes. DNA and RNA targets provided up to 12-fold enhancements of the TO emission upon hybridization of DNA FIT probes. Experiments in cell media demonstrated that false-positive signaling was prevented when DNA FIT probes were used. Of note, DNA FIT probes tolerate a wide range of hybridization temperature; this enabled their application in quantitative polymerase chain reactions.
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Affiliation(s)
- Felix Hövelmann
- Institut für Chemie der Humboldt-Universität zu Berlin, Brook-Taylor Strasse 2, 12489 Berlin, Germany
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12
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Coherent Quenching of a Fluorophore for the Design of a Highly Sensitive In-Stem Molecular Beacon. Angew Chem Int Ed Engl 2010; 49:5502-6. [DOI: 10.1002/anie.201001459] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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13
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Coherent Quenching of a Fluorophore for the Design of a Highly Sensitive In-Stem Molecular Beacon. Angew Chem Int Ed Engl 2010. [DOI: 10.1002/ange.201001459] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Hainke S, Seitz O. Binaphthyl-DNA: stacking and fluorescence of a nonplanar aromatic base surrogate in DNA. Angew Chem Int Ed Engl 2010; 48:8250-3. [PMID: 19790219 DOI: 10.1002/anie.200903194] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Sven Hainke
- Institut für Chemie der Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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15
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Hainke S, Seitz O. Binaphthyl-DNA: Stapelung und Fluoreszenz eines nichtplanaren aromatischen Basensurrogates in DNA. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200903194] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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16
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Jarikote DV, Krebs N, Tannert S, Röder B, Seitz O. Exploring base-pair-specific optical properties of the DNA stain thiazole orange. Chemistry 2007; 13:300-10. [PMID: 17024704 DOI: 10.1002/chem.200600699] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Double-stranded DNA offers multiple binding sites to DNA stains. Measurements of noncovalently bound dye-nucleic acid complexes are, necessarily, measurements of an ensemble of chromophores. Thus, it is difficult to assign fluorescence properties to base-pair-specific binding modes of cyanine dyes or, vice versa, to obtain information about the local environment of cyanines in nucleic acids by using optical spectroscopy. The feasibility to stain DNA and simultaneously probe local perturbations by optical spectroscopy would be a valuable asset to nucleic acid research. So-called FIT probes (forced intercalation probes) were used to pinpoint the location of the DNA stain thiazole orange (TO) in PNADNA duplexes. A detailed analysis of the base-pair dependence of optical properties is provided and enforced binding of TO is compared with "classical" binding of free TO-PRO1. UV-visible absorbance, circular dichroism (CD) and fluorescence spectroscopy, and melting-curve analyses confirmed site-specific TO intercalation. Thiazole orange exhibited base-specific responses that are not observed in noncovalent dye-nucleic acid complexes, such as an extraordinary dependence of the TO extinction coefficient (+/-60 % variation of the averaged epsilon(max) of 57,000 M(-1) cm(-1)) on nearest-neighbor base pairs. TO signals hybridization, as shown by increases in the steady-state fluorescence emission. Studies of TO fluorescence lifetimes in FIT-PNA and in DNADNA and PNADNA complexes highlighted four different fluorescence-decay processes that may be closed or opened in response to matched or single-mismatched hybridization. A very fast decay process (0.04-0.07 ns) and a slow decay process (2.33-3.95 ns) provide reliable monitors of hybridization, and the opening of a fast decay channel (0.22-0.48 ns) that resulted in an attenuation of the fluorescence emission is observed upon the formation of mismatched base pairs.
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Lartia R, Asseline U. New cyanine-oligonucleotide conjugates: relationships between chemical structures and properties. Chemistry 2006; 12:2270-81. [PMID: 16419140 DOI: 10.1002/chem.200500908] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Because the influence of the chemical structure of monomethine cyanine-oligo-2'-deoxyribonucleotide (ODN) conjugates on their binding and fluorescence properties has remained largely undetermined, we synthesized and studied a wide range of conjugates with various structural patterns. Different cyanine dyes such as thiocyanine, quinocyanine, and thiazole orange isomers were obtained. In the case of unsymmetrical cyanines, the linker was attached to either the quinoline or the benzothiazole nucleus. The influence of the ODN counterpart was evaluated by linking the cyanines to the 5'-end or to an internucleotidic phosphate. In the first case, the influence of neighboring nucleic bases was studied, whereas in the second, the stereochemical configuration at the phosphorus atom bearing the cyanine was investigated. We report here on relationships between the structures of the dyes and conjugates and some of their properties, such as the stability and fluorescence changes observed on their hybridization with the target sequence. This study provides useful information towards the design of ODN-cyanine conjugates.
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Affiliation(s)
- Rémy Lartia
- Centre de Biophysique Moléculaire, CNRS UPR 4301 affiliated with the University of Orléans and with INSERM, Rue Charles Sadron, 45071 Orleans Cedex 02, France
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Köhler O, Jarikote DV, Seitz O. Forced intercalation probes (FIT Probes): thiazole orange as a fluorescent base in peptide nucleic acids for homogeneous single-nucleotide-polymorphism detection. Chembiochem 2005; 6:69-77. [PMID: 15584015 DOI: 10.1002/cbic.200400260] [Citation(s) in RCA: 193] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Fluorescent base analogues in DNA are versatile probes of nucleic acid-nucleic acid and nucleic acid-protein interactions. New peptide nucleic acid (PNA) based probes are described in which the intercalator dye thiazole orange (TO) serves as a base surrogate. The investigation of six TO derivatives revealed that the linker length and the conjugation site decided whether a base surrogate conveys sequence-selective DNA binding and whether fluorescence is increased or decreased upon single-mismatched hybridization. One TO derivative conferred universal PNA-DNA base pairing while maintaining duplex stability and hybridization selectivity. TO fluorescence increased up to 26-fold upon hybridization. In contrast to most other probes, in which fluorescence is invariant once hybridization had occurred, the emission of TO-containing PNA probes is attenuated when forced to intercalate next to a mismatched base pair. The specificity of DNA detection is therefore not limited by the selectivity of probe-target binding and a DNA target can be distinguished from its single-base mutant under nonstringent hybridization conditions. This property should be of advantage for real-time quantitative PCR and nucleic acid detection within living cells.
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Affiliation(s)
- Olaf Köhler
- Institut für Chemie, Humboldt-Universität zu Berlin, Brook-Taylor-Strasse 2, 12489 Berlin, Germany
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Seitz O, Köhler O. Convergent strategies for the attachment of fluorescing reporter groups to peptide nucleic acids in solution and on solid phase. Chemistry 2001; 7:3911-25. [PMID: 11596933 DOI: 10.1002/1521-3765(20010917)7:18<3911::aid-chem3911>3.0.co;2-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The site-selective conjugation of peptide nucleic acids (PNA) with fluorescent reporter groups is essential for the construction of hybridisation probes that can report the presence of a particular DNA sequence. This paper describes convergent methods for the solution- and solid-phase synthesis of multiply labelled PNA oligomers. The solid-phase synthesis of protected PNA enabled the selective attachment of fluorescent labels at the C-terminal end (3' in DNA) which demonstrated that further manipulations on protected PNA fragments are feasible. For the conjugation to internal sites, a method is introduced that allows for the on-resin assembly of modified monomers thereby omitting the need to synthesise an entire monomer in solution. Furthermore, it is shown that the application of a highly orthogonal protecting group strategy in combination with chemoselective conjugation reactions provides access to a rapid and automatable solid-phase synthesis of dual labelled PNA probes. Real-time measurements of nucleic acid hybridisation were possible by taking advantage of the fluorescence resonance energy transfer (FRET) between suitably appended fluorophoric groups. Analogously to DNA-based molecular beacons, the dual labelled PNA probes were only weakly fluorescing in the single-stranded state. Hybridisation to a complementary oligonucleotide, however, induced a structural reorganisation and conferred a vivid fluorescence enhancement.
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Affiliation(s)
- O Seitz
- Department of Chemical Biology and Institut für Organische Chemie, Universität Dortmund, Germany.
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Seitz O. Festphasensynthese doppelt markierter Peptidnucleinsäuren als Sonden für die Echtzeitdetektion der Hybridisierung. Angew Chem Int Ed Engl 2000. [DOI: 10.1002/1521-3757(20000915)112:18<3389::aid-ange3389>3.0.co;2-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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21
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Seitz O. Solid-Phase Synthesis of Doubly Labeled Peptide Nucleic Acids as Probes for the Real-Time Detection of Hybridization This work was supported by the Fonds der Chemischen Industrie. Angew Chem Int Ed Engl 2000; 39:3249-3252. [PMID: 11028066 DOI: 10.1002/1521-3773(20000915)39:18<3249::aid-anie3249>3.0.co;2-m] [Citation(s) in RCA: 87] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- O Seitz
- Max-Planck-Institut für Molekulare Physiologie Abteilung Chemische Biologie Otto-Hahn-Strasse 11, 44227 Dortmund (Germany)
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