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52
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Astakhova IV, Korshun VA, Jahn K, Kjems J, Wengel J. Perylene attached to 2'-amino-LNA: synthesis, incorporation into oligonucleotides, and remarkable fluorescence properties in vitro and in cell culture. Bioconjug Chem 2008; 19:1995-2007. [PMID: 18771303 DOI: 10.1021/bc800202v] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
During recent years, fluorescently labeled oligonucleotides have been extensively investigated within diagnostic approaches. Among a large variety of available fluorochromes, the polyaromatic hydrocarbon perylene is an object of increasing interest due to its high fluorescence quantum yield, long-wave emission compared to widely used pyrene, and photostability. These properties make perylene an attractive label for fluorescence-based detection in vitro and in vivo. Herein, the synthesis of 2'- N-(perylen-3-yl)carbonyl-2'-amino-LNA monomer X and its incorporation into oligonucleotides is described. Modification X induces high thermal stability of DNA:DNA and DNA:RNA duplexes, high Watson-Crick mismatch selectivity, red-shifted fluorescence emission compared to pyrene, and high fluorescence quantum yields. The thermal denaturation temperatures of duplexes involving two modified strands are remarkably higher than those for double-stranded DNAs containing modification X in only one strand, suggesting interstrand communication between perylene moieties in the studied 'zipper' motifs. Fluorescence of single-stranded oligonucleotides having three monomers X is quenched compared to modified monomer (quantum yields Phi F = 0.03-0.04 and 0.67, respectively). However, hybridization to DNA/RNA complements leads to Phi F increase of up to 0.20-0.25. We explain it by orientation of the fluorochrome attached to the 2'-position of 2'-amino-LNA in the minor groove of the nucleic acid duplexes, thus protecting perylene fluorescence from quenching with nucleobases or from the environment. At the same time, the presence of a single mismatch in DNA or RNA targets results in up to 8-fold decreased fluorescence intensity of the duplex. Thus, distortion of the duplex geometry caused by even one mismatched nucleotide induces remarkable quenching of fluorescence. Additionally, a perylene-LNA probe is successfully applied for detection of mRNA in vivo providing excitation wavelength, which completely eliminates cell autofluorescence.
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Affiliation(s)
- Irina V Astakhova
- Nucleic Acid Center, Department of Physics and Chemistry, University of Southern Denmark, DK-5230 Odense M, Denmark
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53
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Affiliation(s)
- Jens Müller
- Faculty of Chemistry, Dortmund University of Technology, Otto‐Hahn‐Str. 6, 44227 Dortmund, Germany, Fax: +49 231 755 3797
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54
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Sando S, Narita A, Hayami M, Aoyama Y. Transcription monitoring using fused RNA with a dye-binding light-up aptamer as a tag: a blue fluorescent RNA. Chem Commun (Camb) 2008:3858-60. [PMID: 18726014 DOI: 10.1039/b808449a] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The "light-up" RNA aptamer-Hoechst pair can be used as a fluorescent tag to monitor transcription processes.
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Affiliation(s)
- Shinsuke Sando
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto, Japan.
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55
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Sando S, Narita A, Aoyama Y. Light-up Hoechst-DNA aptamer pair: generation of an aptamer-selective fluorophore from a conventional DNA-staining dye. Chembiochem 2008; 8:1795-803. [PMID: 17806095 DOI: 10.1002/cbic.200700325] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We have designed a strategy to generate a light-up fluorophore-aptamer pair based on a down-modification of a conventional DNA-staining dye to suppress its affinity to the original dsDNA targets, followed by reselection of aptamers that would bind to the modified dye. Following this line, we prepared a micropolarity-sensitive Hoechst derivative possessing two tBu groups with low affinity to the usual AT-rich dsDNA targets. DNA aptamers selected in vitro from a random pool worked as triggers to enhance the fluorescence of an otherwise nonfluorescent Hoechst derivative, and the shortened 25-mer sequence showed remarkable enhancement (light-up). The 25-mer sequence was split into binary aptamer probes, thus enabling us to detect a target nucleic acid sequence with a single-nucleotide resolution by use of unmodified DNA as a probe.
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Affiliation(s)
- Shinsuke Sando
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan.
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56
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Saito Y, Mizuno E, Bag SS, Suzuka I, Saito I. Design of a novel G-quenched molecular beacon: a simple and efficient strategy for DNA sequence analysis. Chem Commun (Camb) 2007:4492-4. [PMID: 17971966 DOI: 10.1039/b709715h] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
G-quenched MBs are devised from readily available starting materials and used for sequence specific DNA detection with high efficiency.
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Affiliation(s)
- Yoshio Saito
- Department of Materials Chemistry and Engineering, School of Engineering, Nihon University, Koriyama, Fukushima 963-8642, Japan.
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57
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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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58
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Kiel A, Kovacs J, Mokhir A, Krämer R, Herten DP. Direct monitoring of formation and dissociation of individual metal complexes by single-molecule fluorescence spectroscopy. Angew Chem Int Ed Engl 2007; 46:3363-6. [PMID: 17397126 DOI: 10.1002/anie.200604965] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Alexander Kiel
- Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg, Germany
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59
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Narita A, Ogawa K, Sando S, Aoyama Y. Visible sensing of nucleic acid sequences with a genetically encodable unmodified RNA probe. Angew Chem Int Ed Engl 2007; 45:2879-83. [PMID: 16550617 DOI: 10.1002/anie.200503836] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Atsushi Narita
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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60
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Kiel A, Kovacs J, Mokhir A, Krämer R, Herten DP. Einzelmolekülfluoreszenzspektroskopische Beobachtung der Bildung und des Zerfalls individueller Metallkomplexe. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200604965] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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61
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Wu JS, Wang PF, Zhang XH, Wu SK. Novel fluorescent sensor for detection of Cu(II) in aqueous solution. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2006; 65:749-52. [PMID: 16530467 DOI: 10.1016/j.saa.2006.01.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2005] [Revised: 12/20/2005] [Accepted: 01/06/2006] [Indexed: 05/07/2023]
Abstract
A novel fluorescent chemosensor based on aminonaphthol, which can selectively recognize copper(II) over other metal ions in aqueous solution within a broad pH span, was synthesized.
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Affiliation(s)
- Jia-Sheng Wu
- Nano-Organic Photoelectronic Laboratory, Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Beijing 100101, PR China
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62
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Singhal NK, Ramanujam B, Mariappanadar V, Rao CP. Carbohydrate-Based Switch-On Molecular Sensor for Cu(II) in Buffer: Absorption and Fluorescence Study of the Selective Recognition of Cu(II) Ions by Galactosyl Derivatives in HEPES Buffer. Org Lett 2006; 8:3525-8. [PMID: 16869651 DOI: 10.1021/ol061274f] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[graph: see text] 1-(Beta-D-galactopyranosyl-1'-deoxy-1'-iminomethyl)-2-hydroxynaphthalene (L1), possessing an ONO binding core, was found to be selective for Cu2+ ions in N-[2-hydroxyethyl]piperazine-N'-[2-ethanesulfonic acid] buffer, at concentrations < or = 580 ppb, at physiological pH by eliciting switch-on behavior, whereas the other ions, viz., Mg2+, Ca2+, Mn2+, Fe2+, Co2+, Ni2+, Zn2+, and Cd2+, caused no significant change in the fluorescence. Whereas the binding characteristics were ascertained by absorption spectroscopy, the species formed were shown by Q-TOF ES MS.
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Affiliation(s)
- Nitin Kumar Singhal
- Bioinorganic Laboratory, Department of Chemistry, Indian Institute of Technology Bombay, Mumbai 400 076, India
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63
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Kovbasyuk L, Krämer R. A selective fluorescent sensor for Cu2+ and its immobilization on CPG beads. INORG CHEM COMMUN 2006. [DOI: 10.1016/j.inoche.2006.03.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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64
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Kim SJ, Kool ET. Sensing metal ions with DNA building blocks: fluorescent pyridobenzimidazole nucleosides. J Am Chem Soc 2006; 128:6164-71. [PMID: 16669686 PMCID: PMC2533741 DOI: 10.1021/ja0581806] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We describe novel fluorescent N-deoxyribosides (1 and 2) having 2-pyrido-2-benzimidazole and 2-quino-2-benzimidazole as aglycones. The compounds were prepared from the previously unknown heterocyclic precursors and Hoffer's chlorosugar, yielding alpha anomers as the chief products. X-ray crystal structures confirmed the geometry and showed that the pyridine and benzimidazole ring systems deviated from coplanarity in the solid state by 154 degrees and 140 degrees , respectively. In methanol compounds 1 and 2 had absorption maxima at 360 and 370 nm, respectively, and emission maxima at 494 and 539 nm. Experiments revealed varied fluorescence responses of the nucleosides to a panel of 17 monovalent, divalent, and trivalent metal ions in methanol. One or both of the nucleosides showed significant changes with 10 of the metal ions. The most pronounced spectral changes for ligand-nucleoside 1 included red shifts in fluorescence (Au(+), Au(3+)), strong quenching (Cu(2+), Ni(2+), Pt(2+)), and substantial enhancements in emission intensity coupled with red shifts (Ag(+), Cd(2+), Zn(2+)). The greatest spectral changes for ligand-nucleoside 2 included a red shift in fluorescence (Ag(+)), a blue shift (Cd(2+)), strong quenching (Pd(2+), Pt(2+)), and substantial enhancements in emission intensity coupled with a blue shift (Zn(2+)). The compounds could be readily incorporated into oligodeoxynucleotides, where an initial study revealed that they retained sensitivity to metal ions in aqueous solution and demonstrated possible cooperative sensing behavior with several ions. The two free nucleosides alone can act as differential sensors for multiple metal ions, and they are potentially useful monomers for contributing metal ion sensing capability to DNAs.
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Affiliation(s)
- Su Jeong Kim
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
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65
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Narita A, Ogawa K, Sando S, Aoyama Y. Visible Sensing of Nucleic Acid Sequences with a Genetically Encodable Unmodified RNA Probe. Angew Chem Int Ed Engl 2006. [DOI: 10.1002/ange.200503836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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66
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Kierat RM, Krämer R. A fluorogenic and chromogenic probe that detects the esterase activity of trace copper(II). Bioorg Med Chem Lett 2005; 15:4824-7. [PMID: 16140531 DOI: 10.1016/j.bmcl.2005.07.042] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2005] [Revised: 07/08/2005] [Accepted: 07/14/2005] [Indexed: 11/18/2022]
Abstract
Bis(picolinoyl)fluorescein, a new fluorogenic and chromogenic probe for monitoring the esterase activity of metal ions, has been synthesized. The probe is highly selective for Cu2+ and is applicable both to quantification of the free ion and detection of esterolytic activity of Cu bound to organic ligands or biomolecules, with a detection limit of 100 nM by fluorimetry.
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Affiliation(s)
- Radoslaw M Kierat
- Anorganisch-Chemisches Institut, Universität Heidelberg, Im Neuenheimer Feld 270, 69120 Heidelberg, Germany
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67
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Gao X, Zhang Y, Wang B. A highly fluorescent water-soluble boronic acid reporter for saccharide sensing that shows ratiometric UV changes and significant fluorescence changes. Tetrahedron 2005. [DOI: 10.1016/j.tet.2005.07.035] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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68
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Mokhir A, Kiel A, Herten DP, Kraemer R. Fluorescent Sensor for Cu2+ with a Tunable Emission Wavelength. Inorg Chem 2005; 44:5661-6. [PMID: 16060616 DOI: 10.1021/ic050362d] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A concept of fluorescent metal ion sensing with an easily tunable emission wavelength is presented and its principle demonstrated by detection of Cu(2+). A fluorescein dye was chemically modified with a metal chelating group and then attached to the terminus of ss-DNA. This was combined with a complementary ss-DNA modified with another fluorescent dye (ATTO 590), emitting at a longer wavelength. In the assembled duplex, fluorescence resonance energy transfer (FRET) between the fluorescein donor (excited at 470 nm) and the ATTO 590 acceptor (emitting at 624 nm) is observed. Proper positioning within the rigid DNA double helix prevents intramolecular contact quenching of the two dyes. Coordination of paramagnetic Cu(2+) ions by the chelating unit of the sensor results in direct fluorescence quenching of the fluorescein dye and indirect (by loss of FRET) quenching of the ATTO 590 emission at 624 nm. As a result, emission of the acceptor dye can be used for monitoring of the concentration of Cu(2+), with a 20 nM detection limit. The emission wavelength is readily tuned by replacement of ATTO-DNA by other commercially available DNA-acceptor dye conjugates. Fluorescent metal ion sensors emitting at >600 nm are very rare. The possibility of tuning the emission wavelength is important with respect to the optimization of this sensor type for application to biological samples, which usually show broad autofluorescence at <550 nm.
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Affiliation(s)
- Andriy Mokhir
- Institute of Inorganic Chemistry, Ruprecht-Karls-Universität Heidelberg, Germany.
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69
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Sando S, Narita A, Abe K, Aoyama Y. Doubly Catalytic Sensing of HIV-1-Related CCR5 Sequence in Prokaryotic Cell-Free Translation System using Riboregulator-Controlled Luciferase Activity. J Am Chem Soc 2005; 127:5300-1. [PMID: 15826150 DOI: 10.1021/ja0507057] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A molecular-beacon-type riboregulator (mRNA) was applied to multiply catalytic gene sensing. It consists of a reporter gene for firefly protein luciferase and, upstream thereof, a regulator hairpin domain composed of an RBS/anti-RBS stem (RBS = ribosome binding site) and a loop which is complementary to the target. The hairpin and, hence, the RBS are rendered open upon binding of a target oligonucleotide of the human CC chemokine receptor 5 sequence in a prokaryotic cell-free translation system (10 muL) to ignite ribosomal catalytic translation, or transcription/translation when using a DNA form of the probe, to produce luciferase, which is assayed by a catalytic chemiluminescence reaction. The sensing, using an unmodified RNA or even dsDNA as a probe with a chemiluminescence output, is thus doubly catalytic or amplifiable with a sensitivity at </=50 fmol in respect to the target with 4.5 fmol (1 ng/muL) of probe and a single nucleotide resolution.
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Affiliation(s)
- Shinsuke Sando
- Department of Synthetic Chemistry and Biological Chemistry, Kyoto University, Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
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