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Yamana, Kazushige; Zako, Hirofumi; Asazuma, Kentarou; Iwase, Reiko; Nakano, Hirofumi; Murakami, Akira

doi:10.1002/1521-3757(20010316)113:6<1138::aid-ange11380>3.3.co;2-i

Cited by 21 publications

(42 citation statements)

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“…Continuous development of such oligonucleotide probes has led to several formats of fluorescence nucleic acid assays, e.g. detection by fluorescence polarization 5 or fluorescence resonance energy transfer (FRET) 6 , Taqman probes (also known as 5′-nuclease probes) 7 , sunrise primers 8 , molecular beacons 9 , duplex scorpion primers 10 , and oligonucleotides labeled with a single kind of a hybridization-sensitive substance [11][12][13][14][15][16][17] . Each of these methods and constructs has its own specific strengths and weaknesses, but there is still no universal approach of choice 18 .…”

mentioning

confidence: 99%

Fluorescent oligonucleotides containing a novel perylene 2′-amino-α-L-LNA monomer: Synthesis and analytical potential

Astakhova

Kumar

Wengel

2011

Collect. Czech. Chem. Commun.

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Dedicated to Professor Antonín Holý on the occasion of his 75th birthday in recognition of his outstanding contributions to the area of nucleic acid chemistry.Herein, a novel fluorescent nucleotide analogue, perylene-2′-amino-α-L-LNA, has been prepared and studied within synthetic oligonucleotides of different sequences. The phosphoramidite reagent was synthesized in 85% overall yield starting from 2′-amino-α-L-LNA nucleoside. Incorporation efficiency of the resulting perylene-2′-amino-α-L-LNA monomer (T*) into synthetic oligonucleotides was significantly improved by replacement of the typically used 1H-tetrazole activator with pyridine hydrochloride. Generally, oligonucleotides containing monomer T* showed high binding affinity towards complementary DNA and RNA targets, batochromically shifted excitation/emission wavelengths with respect to the often applied polyaromatic hydrocarbon pyrene, high fluorescent quantum yields and very low target detection limits (5-10 nM). Fluorescence of single stranded LNA/DNA mixmer oligonucleotide having two incorporations of monomers T* was quenched (quantum yield Φ F = 0.21) relative to duplexes of this probe with complementary DNA and RNA (Φ F = 0.42 and 0.35, respectively). On the contrary, a strong fluorescence quenching upon target binding was demonstrated by two short oligonucleotides of analogues sequences containing monomers T* at 5′-and 3′-terminal positions. We explain the hybridization-induced light-up effect observed for double-labeled probe by a reduction of fluorescence quenching due to precise positioning of the fluorophores within the double-stranded complexes. Furthermore, we propose that a covalent link between two T* monomers in the double-labeled probe provides a remarkable degree of rigidity in the double helix which enforces positioning of the bulky perylene moieties in the nonpolar groove resulting in reduced fluorescence quenching.

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confidence: 99%

Fluorescent oligonucleotides containing a novel perylene 2′-amino-α-L-LNA monomer: Synthesis and analytical potential

Astakhova

Kumar

Wengel

2011

Collect. Czech. Chem. Commun.

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“…For more information on the structure of polymers and the polymerization mechanism, we calculated the atomic electron-density population ( Table 1) and proportion of the frontier orbitals (Scheme 2) of the BrP monomers using the B3LYP/6-31G(d,p) level of Gaussian 03 software. In Table 1, the results of the main atomic electron-density populations revealed negative electric charges at the C (3) , C (4) , C (5) , C (6) , C (8) , C (9) , and C (10) positions in aromatic biphenyl, which implied that these atoms may donate electrons during electrochemical polymerization through radical cation intermediates. But the C (3) , C (6) , and C (8) positions have the more negative electric charges than C (4) , C (5) , C (9) , and C (10) positions.…”

Section: Atommentioning

confidence: 90%

“…Electron spin density C (1) 0.230744 C (3) 0.200172 C (5) 0.108189 C (7) −0.103711 C (9) 0.079460 C (11) −0.008778 (4) 0.066499 C (6) 0.238242 C (8) 0.229568 C (10) 0.087606 C (12) 0.003900 C (14) −0.016000 OBrP were both soluble in common organic solvents such as acetone, ACN, DMSO, and CH 2 Cl 2 . Therefore, the UVvis spectra of BrP, the dedoped OBrP dissolved in DMSO, were examined carefully, as shown in Fig.…”

Section: Uv-vis and Fluorescence Spectramentioning

confidence: 99%

“…Oztekin et al used glucose oxidase and poly-1,10-phenanthroline (PPMH) gained via electrochemical deposition to get the PPMH-modified GC electrode [3]. A pyrene label covalently attached to the sugar part of nucleosides has been used for the detection of nucleic acid hybridization [4][5][6][7][8][9]. Moreover, pyrene is a blue-emitting chromophore and has been proposed as a fluorescent temperature indicator.…”

Section: Introductionmentioning

confidence: 99%

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Electrosynthesis of blue-light-emitting oligo(1-bromopyrene) with favorable solubility

Wang

Lai

et al. 2011

J Solid State Electrochem

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Bromo-group-substituted oligopyrene films were electrochemically synthesized by direct anodic oxidation of 1-bromopyrene (BrP) in boron trifluoride diethyl etherate (BFEE). The oxidation potential of BrP was measured to be approximately 0.52 V (vs. Ag/AgCl), which was much lower than that detected in a neutral electrolyte such as acetonitrile (1.2 V vs. Ag/AgCl) and CH 2 Cl 2 (1.25 V vs. Ag/AgCl). Oligo(1-bromopyrene) (OBrP) films showed good redox activity in both BFEE and concentrated sulfuric acid. Fourier transform infrared spectroscopy, 1 H NMR, and theoretical calculations showed that the electropolymerization of the BrP monomer mainly occurred at the C (3) , C (6) , and C (8) positions. As-formed OBrP was a typical blue light emitter with fluorescent quantum yields of 0.27, also emitted strong and bright blue photoluminescence at excitation of 365 nm UV light. Furthermore, the films were readily soluble in dimethyl sulfoxide, CH 2 Cl 2 , acetonitrile, and acetone. All these results indicate that the striking OBrP films have many potential applications in various fields, such as optoelectronic materials, DNA fluorescence probes, and electrochemical sensors.

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“…The other example of solution-based assays is the use of pyrene fluorescence [11,12,17,19,21,22,[42][43][44][45][46][47][48][49]. Both pyrene monomer and excimer fluorescence has been used as indicator for monitoring hybridization.…”

Section: Bis-pyrene Modified Oligonucleotidesmentioning

confidence: 99%

Nucleic Acid Seqeuence Analysis Using Oligonucleotide Probes

Nakamura¹,

Kanaori²,

Yamana³

2005

Frontiers in Organic Chemistry

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We have designed and synthesized oligonucleotides possessing a pyrene or a bis-pyrene at the defined position using phosphoramidite chemistry. The pyrene probes exhibit strongly enhanced fluorescence upon binding to specific sequences of DNA/RNA. The attractive features of our probes are that the pyrene fluorescence is sensitive to local base sequences and structures of probe-nucleic acid complexes around the pyrene modification. The pyrene probes would thus be useful in fluorescence recognition of nucleic acid sequences and structures.

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Cited by 21 publications

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Fluorescent oligonucleotides containing a novel perylene 2′-amino-α-L-LNA monomer: Synthesis and analytical potential

Fluorescent oligonucleotides containing a novel perylene 2′-amino-α-L-LNA monomer: Synthesis and analytical potential

Electrosynthesis of blue-light-emitting oligo(1-bromopyrene) with favorable solubility

Nucleic Acid Seqeuence Analysis Using Oligonucleotide Probes

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