Cycling Probe Technology with RNase H Attached to an Oligonucleotide

Bekkaoui, Faouzi; Poisson, I.; Crosby, William L.; Cloney, Lynn P.; Duck, P.

doi:10.2144/96202rr01

Cited by 48 publications

(44 citation statements)

References 12 publications

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“…The cycling probe technology is a unique nucleic acid-based method that detects single nucleic acid polymorphisms (SNPs) in a target DNA sequence by using a probe-adapted real-time PCR (3,10) (Fig. 1).…”

Section: Methodsmentioning

confidence: 99%

Rapid and Specific Detection of Amantadine-Resistant Influenza A Viruses with a Ser31Asn Mutation by the Cycling Probe Method

et al. 2010

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Section: Methodsmentioning

confidence: 99%

Rapid and Specific Detection of Amantadine-Resistant Influenza A Viruses with a Ser31Asn Mutation by the Cycling Probe Method

et al. 2010

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“…To determine whether AmAOX1e or -1g is abundantly expressed in the thermogenic appendix, we employed the cycleave PCR method and tested the same sample as assayed in the qRT-PCR analysis. Cycleave PCR is a method that can detect a single nucleotide polymorphism by using chimeric DNA/RNA probes and RNase H (Duck et al, 1990;Bekkaoui et al, 1996). In this assay, three probes that specifically hybridize to AmAOX1a, -1b, -1c, -1d, and -1f (ENV type), AmAOX1e and -1g (QNT+QDT type), or AmAOX1g (QDT type) were used.…”

Section: Tissue-specific Expression Of the Amaoxsmentioning

confidence: 99%

“…To detect the transcript levels for ENV-, QNT-, or QDT-type AOX genes, we used the cycleave PCR technique, as described previously (Duck et al, 1990;Bekkaoui et al, 1996). Each chimeric DNA-RNA-DNA probe listed in Supplemental Table S6 was labeled with a fluorescent dye and quencher at each end that targeted the ENV, QNT+QDT, or QDT type of AOX.…”

Section: Cycleave Pcr Analysismentioning

confidence: 99%

Identification of a Gene for Pyruvate-Insensitive Mitochondrial Alternative Oxidase Expressed in the Thermogenic Appendices in Arum maculatum

Ito

Ogata²,

Kakizaki³

et al. 2011

Plant Physiology

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Heat production in thermogenic plants has been attributed to a large increase in the expression of the alternative oxidase (AOX). AOX acts as an alternative terminal oxidase in the mitochondrial respiratory chain, where it reduces molecular oxygen to water. In contrast to the mitochondrial terminal oxidase, cytochrome c oxidase, AOX is nonprotonmotive and thus allows the dramatic drop in free energy between ubiquinol and oxygen to be dissipated as heat. Using reverse transcription-polymerase chain reaction-based cloning, we reveal that, although at least seven cDNAs for AOX exist (AmAOX1a, -1b, -1c, -1d, -1e, -1f, and -1g) in Arum maculatum, the organ and developmental regulation for each is distinct. In particular, the expression of AmAOX1e transcripts appears to predominate in thermogenic appendices among the seven AmAOXs. Interestingly, the amino acid sequence of AmAOX1e indicates that the ENV element found in almost all other AOX sequences, including AmAOX1a, -1b, -1c, -1d, and -1f, is substituted by QNT. The existence of a QNT motif in AmAOX1e was confirmed by nano-liquid chromatography-tandem mass spectrometry analysis of mitochondrial proteins from thermogenic appendices. Further functional analyses with mitochondria prepared using a yeast heterologous expression system demonstrated that AmAOX1e is insensitive to stimulation by pyruvate. These data suggest that a QNT type of pyruvate-insensitive AOX, AmAOX1e, plays a crucial role in stage-and organ-specific heat production in the appendices of A. maculatum.

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“…Cycling probe assay for SNP typing Identification of isolates showing the same genotype as the clinical isolates of L. monocytogenes was performed by using real-time PCR and Cycling Probe Technology (Bekkaoui et al, 1996) SNP typing. Primers and cycling probes were designed to detect SNP in the hlyA, clpC, and inlA genes ( annealing at 50℃ for 15 sec, and elongation at 72℃ for 20 sec.…”

Section: Preparation Of Genomic Dnamentioning

confidence: 99%

“…By multiple alignment analysis of the DNA sequence of the respective genes, DNA polymorphisms were found, and SNP typing and MLST were performed. A novel, rapid SNP typing method was developed by using real-time PCR combined with Cycling Probe Technology (Bekkaoui et al, 1996) to identify L. monocytogenes of the same genotype as the clinical isolates. …”

mentioning

confidence: 99%

Subtyping of Listeria monocytogenes Based on Nucleotide Polymorphism in the clpC, inlA, hlyA, and plcA Genes and Rapid Identification of L. monocytogenes Genetically Similar to Clinical Isolates

Honjoh

Fujihara

Haraguchi

et al. 2008

FSTR

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To develop a new method for identification of Listeria monocytogenes genetically similar to clinical isolates, single-nucleotide polymorphism (SNP) typing and multi-locus sequence typing (MLST) of 126isolates of L. monocytogenes from clinical and environmental samples were performed based on sequence analysis of parts of four genes (hlyA, clpC, inlA, and plcA). Based on the sequences of the isolates in this study, SNP typing showed that hlyA, clpC, inlA, and plcA genes were categorized into 9, 14, 17, and 21 types, respectively. MLST showed that the isolates were grouped into 35 types including 12 types of clinical isolates. Out of those, four MLST types were found in food or environmental and clinical isolates. In particular, all clinical isolates with serotype 1/2a were grouped into the same hlyA SNP A5 type. A method using real-time PCR combined with Cycling Probe Technology was developed for rapid identification of SNP type of L. monocytogenes genetically similar to the clinical isolates. By using this method, the 1/2a clinical isolates showing MLST-2 were successfully identified with a specific primer set and a cycling probe designed on the basis of sequence of hlyA. Furthermore, clinical isolates of serotype 4b showing MLST-4 or -35 were successfully identified by a method using cycling probes based on sequences of clpC and inlA.Keywords: cycling probe technology, Listeria monocytogenes, real-time PCR, SNP typing *To whom correspondence should be addressed. Email: tmiyamot@agr.kyushu-u.ac.jp IntroductionListeria species are widely distributed in the environment. As they are found in soil and in mammals, they are often contaminants in various types of food, mainly meats and dairy products . Listeria monocytogenes is a significant food-borne pathogen and causes an infectious disease known as listeriosis. In the food industry, contamination of food by this bacterium may lead to serious problems since it can grow even at low temperatures and high salt concentrations during storage of readyto-eat foods such as unsterilized dairy products and raw vegetables.In Japan, although sporadic cases of listeriosis have been reported, no serious epidemic has occurred. However, L. monocytogenes is often detected in foodstuffs, which may lead to a potential outbreak of listeriosis (Okutani et al., 2004). Listeriosis may result in mortality for pregnant women, infants, immunocompromised individuals, and elderly individuals .For identification and subtyping of L. monocytogenes, several techniques, such as phenotypic typing (serological typing, phage typing, and multilocus enzyme electrophoresis) and molecular typing techniques (ribotyping, restriction enzyme analysis, PCR-based typing, and DNA sequencing) have been used in epidemiology (Gasanov et al., 2005). Furthermore, multilocus sequence typing (MLST) based on DNA sequences has extremely high and accurate discriminatory power (Gasanov et al., 2005). MLST has been applied to subtyping of L. monocytogenes (Cai et al., 2002;Salcedo et al., 2003). However, because it includes...

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Cycling Probe Technology with RNase H Attached to an Oligonucleotide

Cited by 48 publications

References 12 publications

Rapid and Specific Detection of Amantadine-Resistant Influenza A Viruses with a Ser31Asn Mutation by the Cycling Probe Method

Rapid and Specific Detection of Amantadine-Resistant Influenza A Viruses with a Ser31Asn Mutation by the Cycling Probe Method

Identification of a Gene for Pyruvate-Insensitive Mitochondrial Alternative Oxidase Expressed in the Thermogenic Appendices in Arum maculatum

Subtyping of Listeria monocytogenes Based on Nucleotide Polymorphism in the clpC, inlA, hlyA, and plcA Genes and Rapid Identification of L. monocytogenes Genetically Similar to Clinical Isolates

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