Novel sequence-responding fluorescent oligoDNA probe bearing a silylated pyrene molecule

Sekiguchi, Tohru; Ebara, Yumiko; Moriguchi, Tomohisa; Shinozuka, Kazuo

doi:10.1016/j.bmcl.2007.10.012

Bioorganic & Medicinal Chemistry Letters

2007

DOI: 10.1016/j.bmcl.2007.10.012

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Novel sequence-responding fluorescent oligoDNA probe bearing a silylated pyrene molecule

Tohru Sekiguchi¹,

Yumiko Ebara²,

Tomohisa Moriguchi³

et al.

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Cited by 12 publications

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References 24 publications

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“…Furthermore, both the absorption maxima (l abs ) and the fluorescent emission maxima (l em ) of the silylated pyrene derivatives shifted to longer wavelength (more than 10 nm) compared with those of the unmodified pyrene. [2][3][4][5] This is assumed to be a result of a Si-associated s-p interaction. [6][7][8] After appropriate functionalization, the silylated pyrene derivatives were incorporated into either nucleic acids or cholesterol analogues.…”

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Synthesis and Spectroscopic Properties of a Novel Bifunctional Pyrene Derivative and its Incorporation into OligoDNA

et al. 2015

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A new pyrene derivative bearing a modifiable silyl function (electron-donating group) and cyano function (electronwithdrawing group) was synthesized as a labelling agent for biological substances. The modified pyrene exhibited a marked bathochromic shift in both absorption and fluorescence spectra. The fluorescence quantum yield of the modified pyrene was also significantly increased compared with that of the unmodified pyrene. The modified pyrene was successfully incorporated into oligoDNA.

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Synthesis and Spectroscopic Properties of a Novel Bifunctional Pyrene Derivative and its Incorporation into OligoDNA

et al. 2015

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“…68 Recently, we reported novel fluorescently labeled oligonucleotides bearing a silylated pyrene derivative at the 5¤-terminus. 9 The silylated pyrene derivative was functionalized by the introduction of a hydroxy group, and the hydroxy group was phosphitylated to give the standard phosphoramidite derivative. The oligonucleotides containing the silylated pyrene derivative showed characteristic spectroscopic properties.…”

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confidence: 99%

“…The vinyl silane derivative 2a was synthesized from the reaction of 1-bromopyrene with chlorodimethylvinylsilane using the procedure reported previously. 9 The allylsilane derivative 2b was also prepared by the same procedure. The alcohol derivatives 3a and 3b were successfully prepared by using 9-BBN for hydroboration.…”

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Synthesis and Properties of Novel Fluorescently Labeled Oligonucleotides Possessing Silylated Pyrene at the 5′-Terminus

et al. 2014

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Previously, we reported a novel fluorescence dye, a silylated pyrene derivative, as a DNA labeling agent. In this study, new silylated pyrene derivatives with different linker lengths and different substituents on the silicon atom have been prepared and introduced into oligonucleotides. In particular, when the diphenylsilylpyrene derivative was introduced as a fluorescence dye, the fluorescence intensity of the duplex was enhanced about 20 times compared to the signal in the absence of the target DNA.Fluorescently labeled oligonucleotides have been widely used in the analysis of genetic information.1 Such oligonucleotide probes should exhibit fluorescence emission only in the presence of the fully matched complementary strand, whereas an obvious fluorescent signal will be observed in the presence of the fully matched complementary strand. Various probe DNA and detection systems satisfying this requirement have been developed.2,3 The fluorescence dyes commonly used for fluorescent DNA probes show strong fluorescence intensity and high quantum yield in highly sensitive detection systems that are required for single molecule measurement 4 and in vivo imaging. 5It was reported that the introduction of silyl groups to polyaromatic compounds, such as anthracene and pyrene, induced red shift of the absorption and emission wavelengths, and increased the fluorescence quantum yield. 68 Recently, we reported novel fluorescently labeled oligonucleotides bearing a silylated pyrene derivative at the 5¤-terminus. 9 The silylated pyrene derivative was functionalized by the introduction of a hydroxy group, and the hydroxy group was phosphitylated to give the standard phosphoramidite derivative. The oligonucleotides containing the silylated pyrene derivative showed characteristic spectroscopic properties. While the modified oligonucleotides showed weak emission on the single strand, the presence of the complementary strand induced enhancement of the fluorescent emission. However, the reason for the distinctive spectroscopic behavior is unclear. In this study, in order to elucidate the effect on the fluorescent behavior of the structure, we prepared novel silylated pyrene derivatives, which have different linker lengths to the oligonucleotides and different substituents on the silicon atom instead of the methyl group.First, for elucidation of the relationship between the fluorescent behavior and linker length, we designed various silylated pyrene derivatives having different alkyl linker lengths and different substituents on the silicon atom. Preparation of the silylated pyrene derivatives having different alkyl linker lengths was carried out by the following steps (Scheme 1). The vinyl silane derivative 2a was synthesized from the reaction of 1-bromopyrene with chlorodimethylvinylsilane using the procedure reported previously. 9 The allylsilane derivative 2b was also prepared by the same procedure. The alcohol derivatives 3a and 3b were successfully prepared by using 9-BBN for hydroboration.10

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“…It is worth noting that the fluorescent quantum yield of silylated pyrene 5 increased to 0.64 from 0.32 of unmodified pyrene, as it was reported previously. 3 This can be attributed to the Si-associated ·³ interaction. 5,6 Meanwhile, 3¤,5¤-O-(tetraisopropyldisiloxane-1,3-diyl)uridine (6) was treated with CDI in CH 2 Cl 2 and resulting 2¤-O-(imidazol-1-ylcarbonyl)-3¤,5¤-O-(tetraisopropyldisiloxane-1,3-diyl)uridine (7) was further reacted with compound 5 without isolation.…”

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“…2 On the other hand, silylated pyrene bearing a modifiable functional group is a recently developed new derivative of pyrene capable of introduction into biological molecules such as nucleic acids and lipids. 3,4 The compound exhibits enhanced fluorescent quantum yield along with a bathochromic shift in absorption and emission, due to the specific ·³ interaction. 5,6 Thus, the compound is more advantageous as a fluorescent labeling agent compared to original pyrene.…”

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confidence: 99%

Modified OligoDNA Having Two Consecutive Silylated-pyrene Moieties in Minor Groove Exhibiting an Excimer Fluorescent Signal upon Binding to Fully Complementary DNA Strand

Mogi¹,

Uddin²,

Ichimura³

et al. 2010

Chemistry Letters

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OligoDNA possessing consecutive modified nucleotide residues bearing silylated pyrene at C-2¤ position was synthesized. The fluorescent oligoDNA exhibited marked excimer fluorescent signal upon binding to a fully matched complementary DNA strand, however, the signal was effectively quenched in the single-stranded form as well as in the mismatched base pair duplex.Sensitive and sequence specific detection of certain gene fragments are key technology for diagnostics and genetic studies. Fluorescent oligonucleotide probes have been intensively studied for the past decades as a tool to meet these demands and substituting conventional radio-labeled probes.1 As a feasible gene-detecting tool, however, it is highly desirable that the probe exhibits a specific fluorescent signal only when it binds to the target oligonucleotide. To avoid false results, the probe should also have the capability of recognizing uncomplementary dissimilarities of the target, including single-nucleotide mismatches (SNPs). A probe possessing such ability would greatly simplify the detection process because of the abridgment of tedious separation and washing steps after the binding of the probe to the sample to be examined. Meanwhile, a common fluorescent material pyrene is known to form a characteristic excimer in an appropriate condition to emit bright fluorescence at around 460 nm. Several modified oligonucleotide probes utilizing pyrene to exhibit excimer fluorescence upon hybridization to their complementary oligonucleotides have been reported.2 On the other hand, silylated pyrene bearing a modifiable functional group is a recently developed new derivative of pyrene capable of introduction into biological molecules such as nucleic acids and lipids.3,4 The compound exhibits enhanced fluorescent quantum yield along with a bathochromic shift in absorption and emission, due to the specific ·³ interaction. 5,6 Thus, the compound is more advantageous as a fluorescent labeling agent compared to original pyrene. During the course of our study to investigate the utilities of silylated pyrene derivatives, we have found that a modified oligonucleotide having silylated pyrene moieties at the C-2¤ position of neighboring uridine residues exhibits bright excimer-based fluorescent signal in the presence of fully complementary oligoDNA strand. 7 The signal was, however, strongly quenched in the single-stranded form and in the duplexes having mismatched base pairs.To synthesize a modified oligonucleotide, we have applied C2¤-functionalization via a carbamate function 8 utilizing 1,1¤-carbonyldiimidazole (CDI) and a silylated pyrene derivative bearing primary amine function. The outline of the synthesis of the key compound, a modified uridine phosphoramidite bearing silylated pyrene at 2¤-position through carbamate function (9), is summarized in Scheme 1.1-Bromopyrene (1) was treated with n-BuLi in dry THF (¹78°C) under argon atmosphere followed by the addition of vinyldimethylsilyl chloride. The mixture was allowed to reach room temperature to give the cor...

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Novel sequence-responding fluorescent oligoDNA probe bearing a silylated pyrene molecule

Cited by 12 publications

References 24 publications

Synthesis and Spectroscopic Properties of a Novel Bifunctional Pyrene Derivative and its Incorporation into OligoDNA

Synthesis and Spectroscopic Properties of a Novel Bifunctional Pyrene Derivative and its Incorporation into OligoDNA

Synthesis and Properties of Novel Fluorescently Labeled Oligonucleotides Possessing Silylated Pyrene at the 5′-Terminus

Modified OligoDNA Having Two Consecutive Silylated-pyrene Moieties in Minor Groove Exhibiting an Excimer Fluorescent Signal upon Binding to Fully Complementary DNA Strand

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