A new dark quencher for use in genetic analysis

May, Jonathan P.; Brown, Lynda J.; Rudloff, Ivo; Brown, Tom

doi:10.1039/b300934c

Cited by 17 publications

(12 citation statements)

References 5 publications

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“…Recently we described a new fluorescence quencher based on 1,4-diaminoanthraquinone. 10 It is a non-fluorescent molecule, thus eliminating any possibility of background signals which can arise when fluorophores are used as quenchers. Importantly, it has a broad absorption in the 550-700 nm region of the visible spectrum and is thus able to quench a wide range of fluorophores, especially those that emit at longer wavelengths.…”

Section: Introductionmentioning

confidence: 99%

Synthesis and evaluation of a new non-fluorescent quencher in fluorogenic oligonucleotide probes for real-time PCR

et al. 2005

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A non-fluorescent quencher, based on the diaminoanthraquinone Disperse Blue 3, has been incorporated into oligonucleotides at the 5'-end, the 3'-end and internally as a thymidine derivative. Fluorimetry and fluorogenic real-time PCR experiments demonstrate that the quencher is effective with a wide range of fluorescent dyes. The anthraquinone moiety increases the melting temperature of DNA duplexes, thus allowing shorter, more discriminatory probes to be used. The quencher has been used in Scorpion primers and TaqMan probes for human DNA sequence recognition and mutation detection.

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Section: Introductionmentioning

confidence: 99%

Synthesis and evaluation of a new non-fluorescent quencher in fluorogenic oligonucleotide probes for real-time PCR

et al. 2005

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“…4-((4'-(Dimethyl-amino) phenyl)azo) benzoic acid (dabcyl) (32) optimally quenches fluorescein, but its quenching efficiency decreases with dyes emitting at longer wavelengths such as rhodamine G6, Texas red or Cy5. Other black Qs are also used such as the BHQ (33) [23] and QSY series [74], Methyl Red (34) [107] that has a large absorption range of 350-550 nm, and the 1,4-diaminoanthraquinone chromophore (35) that has an absorption range of 500-700 nm [108]. Another class of quenching compounds consists of metal clusters (gold nanoparticles (36)…) [109][110][111].…”

Section: Quenchers Fig (4)mentioning

confidence: 99%

Development and Applications of Fluorescent Oligonucleotides

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2006

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Fluorescent oligonucleotides (FONs) are used in a wide variety of areas such as molecular and mechanistics biological studies, molecular diagnostics, therapeutic development, biotechnology and nanotechnology. Ever since the post-genome era, there has been an ever-increasing demand for more rapid and accurate nucleic acid detection and quantification methods. Genetic information analyses require highly sensitive and specific detection of certain sequences, single nucleotide changes, specific structures and varied reactions in different formats in vitro, in living cells and, ultimately in animals and in human beings. Ideally, a unique event could be detected and quantified using the genomic information without amplification of the nucleic acids to be analyzed. Recent developments enabling detection at the single-molecule (SM) level have opened new perspectives for applications. This review reports on the development and applications of different families of FON probes. Specific insight is given to those leading to an important fluorescent signal change upon hybridization with their targets. Applications of FON probes include real time polymerase chain reaction (PCR) quantification, detection of single-nucleotide polymorphisms (SNP), fluorescence in situ hybridization (FISH) including detection of specific messenger RNAs in living cells, analysis of gene expression, analysis of nucleic acid structures and reactions, and in nanotechnology, the assessment of molecular machine motion and functioning.

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“…Thus, an MB containing perylene tethered to threoninol is applicable to the ratiometric detection of these polymorphisms (see below). Since reports of efficient quenchers for perylene are scarce, we first investigated three possible chromophores, dabcyl, azobenzene, and anthraquinone 9. We evaluated their efficiency as perylene quenchers by using the model DNA strands F a and Y b (X) (Figure 1 b), which were constructed with surrogate quenchers synthesized from the corresponding phosphoramidite submonomers.…”

Section: Effect Of the Position Of The E–q Pair On Mb Detectionmentioning

confidence: 99%

In‐Stem Molecular Beacon Containing a Pseudo Base Pair of Threoninol Nucleotides for the Removal of Background Emission

et al. 2009

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Aus heißt auch aus: Ein neuartiger molekularer Beacon wurde entwickelt, der in der Stamm‐Region Pseudobasenpaare aus dem Fluorophor (Perylen) und dem Fluoreszenzlöscher (Anthrachinon) enthält, wobei D‐Threoninol‐Einheiten als Verbindungsstück dienen (in‐stem molecular beacon, ISMB). Der ISMB war in der Lage, eine Einzeldeletionsmutante von der Wildtypsequenz zu unterscheiden, ohne dass Hintergrundemission auftrat (siehe Bild).

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A new dark quencher for use in genetic analysis

Abstract: A novel, long-wavelength, non-fluorescent quencher (LQ), based on 1,4-diaminoanthraquinone, has been incorporated at the 3' and 5'-termini of oligonucleotides. The quencher has been used in Molecular beacons, efficiently quenching the long wavelength fluorophore, Cy5.

Cited by 17 publications

References 5 publications

Synthesis and evaluation of a new non-fluorescent quencher in fluorogenic oligonucleotide probes for real-time PCR

Synthesis and evaluation of a new non-fluorescent quencher in fluorogenic oligonucleotide probes for real-time PCR

Development and Applications of Fluorescent Oligonucleotides

In‐Stem Molecular Beacon Containing a Pseudo Base Pair of Threoninol Nucleotides for the Removal of Background Emission

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