A Highly Discriminating Quencher-Free Molecular Beacon for Probing DNA

Hwang, Gil Tae; Seo, Young Jun; Kim, Byeang Hyean

doi:10.1021/ja049795q

Cited by 175 publications

(85 citation statements)

References 13 publications

(12 reference statements)

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“…[13,14] Besides the use of fluorescein, [15,16] very recently fluorene has also been incorporated into the loop structure of a hairpin architecture. [17] A single base mismatch was detected by de-quenching upon hybridization with the fully matched target and quenching upon hybridization with a target containing a single base mutation.…”

Section: Introductionmentioning

confidence: 99%

Twin Probes as a Novel Tool for the Detection of Single‐Nucleotide Polymorphisms

Ergen

Weber

Jacob

et al. 2006

Chemistry A European J

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Single‐nucleotide polymorphisms (SNPs) are the most common form of DNA sequence variation. There is a strong interest from both academy and industry to develop rapid, sensitive and cost effective methods for SNP detection. Here we report a novel structural concept for DNA detection based on fluorescence dequenching upon hybridization. The so‐called “twin probe” consists of a central fluorene derivative as fluorophore to which two identical oligonucleotides are covalently attached. This probe architecture is applied in homogeneous hybridization assays with subsequent fluorescence spectroscopic analysis. The bioorganic hybrid structure is well suited for sequence specific DNA detection and even SNPs are identified with high efficiency. Additionally, the photophysical properties of the twin probe were investigated. The covalent attachment of two single stranded oligonucleotides leads to strong quenching of the central fluorescence dye induced by the nucleobases. The twin probe is characterized by supramolecular aggregate formation accompanied by red‐shifted emission and broad fluorescence spectra.

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Section: Introductionmentioning

confidence: 99%

Twin Probes as a Novel Tool for the Detection of Single‐Nucleotide Polymorphisms

Ergen

Weber

Jacob

et al. 2006

Chemistry A European J

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“…A fluorene-labeled phosphoramidite was synthesized as described. 4 ODNs were prepared using the β-cyanoethylphosphoramidite method on controlled pore glass supports (1 µmol) with a POLYGEN Basic 10-Column DNA synthesizer and standard methods.…”

Section: Methodsmentioning

confidence: 99%

“…4 Incorporations of the fluorene-labeled deoxyuridine U FL into the central position of the ODN 1 and of the two U FL units into the positions with one deoxycytosine spacer unit were effected using standard protocols of automated DNA synthesis ( Figure 2). …”

mentioning

confidence: 99%

Quencher-free Linear Beacon Systems with Dual Fluorene-labeled Deoxyuridines

Seo¹,

Hwang

2011

Bulletin of the Korean Chemical Society

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“…6 In addition, in the biochemical field, it has been used as "molecular beacons" for detecting nucleic acid hybridization. 7,8 Despite their advantages, applications for analytical use and signaling purposes using fluorene are rather limited.In this communication, using fluorescence, UV, and NMR spectrometries, we describe the photochemical behaviors A new fluorescent ionophore for alkaline earth metal ions, 4′-(9-fluorenecarboxamido)benzo-15-crown-5 (3), was synthesized; its photochemical behavior was investigated using UV, fluorescence, 1 H NMR, and 13 C NMR spectrometry. In the absence of a metal ion, the fluorene moiety showed weak fluorescence emission (fluorescence "Off" state).…”

mentioning

confidence: 99%

mentioning

confidence: 99%

Anomalous Fluorescent Responses of 9-Fluorenecarboxamide Derivatives Possessing Benzo-15-crown-5

2007

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The importance of electron-transfer reactions has attracted many researchers to investigate the fundamental steps of the processes. Especially, many studies have been devoted to photo-induced electron transfer (PET) in electron donoracceptors linked by a covalent bond system. 1 In that context, we have reported photochemical behavior of a series of donoracceptor systems. Recently, we reported that some aromatic amide derivatives that have fluorescent active groups in the molecules showed quite weak emission. The presence of Nphenyl-amide groups caused the formation of charge separation at the excited state through electron transfer between fluorescence-active groups and a benzene ring via the amide bond. Using results of a previous study, new fluorescent ionophores based on an ethyleneoxy chain containing N-phenyl-9-anthracenecarboxamide 2 and N-phenyl-1-pyrenylcarboxamide 3 were synthesized and characterized. These fluoroionophores showed weak emission corresponding to their monomers in the absence of metal ions, although their alkaline earth metal ion complexes indicated strong emissions. Their photochemical action of complexation suggested that the most likely relaxation pathway was twisted intramolecular charge transfer (TICT). To extend these investigations, we synthesized novel chemosensors based on benzo-crown ether 4 and linear polyether 5 possessing N-phenyl-1-naphthalenelacetamide. These sensors indicated that the binding of alkaline earth metal ions is signaled by a switching "on" of the naphthalene fluorescence. Fluorescence spectroscopic data suggest that their quenching process was intermolecular charge transfer involving a TICT character. These results might be construed to mean that TICT has occurred not only through the amide bond but also over the CH2 group. The concept of TICT usually emphasizes the torsion of a single bond, although the CT action of these cases was obtained over the two bonds (amide and CH2 group). The charge-transfer behavior of N-phenyl-1-naphthaleneacetamide was unique.We used 9-fluorenecarboxamide as a comparison to confirm that this CT action is peculiar to naphthalene. Fluorene has a similar UV absorption band to that of naphthalene, in addition to a unique bridge carbon out of the conjugation constructed by the biphenyl moiety. A similar UV absorption spectrum would probably use the same excited-state. The nine-positioned carbon should provide evidence for considering of the effects of the donor-acceptor distance. Fluorene is also a promising material for organic light-emitting devices because of its good chemical stability and high photoluminescence quantum efficiency, both in solution and in the solid state. 6 In addition, in the biochemical field, it has been used as "molecular beacons" for detecting nucleic acid hybridization. 7,8 Despite their advantages, applications for analytical use and signaling purposes using fluorene are rather limited.In this communication, using fluorescence, UV, and NMR spectrometries, we describe the photochemical behaviors A new fluore...

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A Highly Discriminating Quencher-Free Molecular Beacon for Probing DNA

Cited by 175 publications

References 13 publications

Twin Probes as a Novel Tool for the Detection of Single‐Nucleotide Polymorphisms

Twin Probes as a Novel Tool for the Detection of Single‐Nucleotide Polymorphisms

Quencher-free Linear Beacon Systems with Dual Fluorene-labeled Deoxyuridines

Anomalous Fluorescent Responses of 9-Fluorenecarboxamide Derivatives Possessing Benzo-15-crown-5

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