Characterization and applications of CataCleave probe in real-time detection assays

Harvey, John; Lee, S. Paul; Chan, Edward K. L.; Kim, Jung Ho; Hwang, Eung Soo; Chen, Yong; Knutson, Jay R.; Han, Mira

doi:10.1016/j.ab.2004.05.037

Cited by 32 publications

(15 citation statements)

References 29 publications

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“…The CataCleave probe should be compatible with real-time genotyping methods such as PCR, strand displacement amplification (SDA), and nucleic acid sequence-based amplification (NASBA). We have previously used the CataCleave probe for the real-time detection of PCR products of the B. anthracis Cap C gene (26). Realtime SNP detection of PCR-amplified targets is tenable; this capability is clear in Fig.…”

Section: Discussionmentioning

confidence: 99%

“…Oligonucleotides and CataCleave probes were synthesized using a PerSeptive Biosystems Expedite nucleic acid synthesis system (Applied Biosystems, Foster, CA) and purified as previously described (26). Nucleic acid sequences are listed in Table 1.…”

Section: Preparation Of Oligonucleotides and Catacleave Probesmentioning

confidence: 99%

“…We previously observed a significant reduction in cleavage rates when target DNA contained single base mismatches within the RNA/DNA hybridizing region (26). Hence, we prepared a CataCleave probe for a SNP located within intron 2 of IGF-2 ( Table 1).…”

Section: Snp Analysis Of Igf-2 Using Catacleave Probesmentioning

confidence: 99%

“…CataCleave probes for rs734351 wild-type and mutant alleles were designed so that both fluorescein (FRET donor) and tetramethylrhodamine (FRET acceptor) were attached internally to the probe (26). Cleavage of the wild-type probe IGF-2PW was initially tested with its target, IGF-2TW (Table 1).…”

Section: Snp Analysis Of Igf-2 Using Catacleave Probesmentioning

confidence: 99%

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SNP analysis using catacleave probes

Harvey¹,

Brant²,

Knutson³

et al. 2008

Clinical Laboratory Analysis

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CataCleave" probes are catalytically cleavable fluorescence probes having a chimeric deoxyribonucleic acid (DNA)-ribonucleic acid (RNA)-DNA structure that can be used for realtime detection of single nucleotide polymorphisms (SNPs), insertions, and deletions. Fluorescent donor emission is normally quenched by Förster resonance energy transfer (FRET). Upon binding to the target, if the RNA/DNA hybrid is correctly base-paired, ribonuclease (RNase) H will cleave the RNA moiety and the probe fragments will dissociate. FRET is lost and the donor fluorescence signal is recovered. A single-base mismatch within the hybrid region causes probe cleavage to be significantly reduced. We designed CataCleave probes to detect SNPs located in the insulin-like growth factor 2 (IGF-2) gene and at position 702 within the NOD2/CARD15 gene. Probes were also designed to detect a six-basepair deletion in the amelogenin gene and a partially methylated target DNA. Discrimination between wild-type and SNP is demonstrated for both genes in homogeneous reactions under isothermal and temperature cycling conditions. These probes were also able to identify a multibase deletion and methylated DNA. Cleavage rates were proportional to target concentration. Probe length and position of fluorescent labels may also be modified for use in multiplexing high-throughput SNP assays. This represents a novel method for the detection of SNPs.

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Section: Discussionmentioning

confidence: 99%

Section: Preparation Of Oligonucleotides and Catacleave Probesmentioning

confidence: 99%

Section: Snp Analysis Of Igf-2 Using Catacleave Probesmentioning

confidence: 99%

Section: Snp Analysis Of Igf-2 Using Catacleave Probesmentioning

confidence: 99%

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SNP analysis using catacleave probes

Harvey¹,

Brant²,

Knutson³

et al. 2008

Clinical Laboratory Analysis

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“…When cleavage takes place anywhere between the conjugated dyes, the result is a complete and irreversible disruption of FRET. Although a number of ways to achieve the probe cleavage have been explored, [6][7][8] the TaqMan technology was the first developed 9 and it remains widely used for real-time nucleic acid detection in PCR. 10 The method utilizes the 5 ¢ -nuclease activity of Thermus aquaticus (Taq) DNA polymerase.…”

mentioning

confidence: 99%

Use of Base Modifications in Primers and Amplicons to Improve Nucleic Acids Detection in the Real-Time Snake Polymerase Chain Reaction

Kutyavin¹

2011

ASSAY and Drug Development Technologies

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The addition of relatively short flap sequence at the 5 ¢ -end of one of the polymerase chain reaction (PCR) primers considerably improves performance of real-time assays based on 5 ¢ -nuclease activity. This new technology, called Snake, was shown to supersede the conventional methods like TaqMan, Molecular Beacons, and Scorpions in the signal productivity and discrimination of target polymorphic variations as small as single nucleotides. The present article describes a number of reaction conditions and methods that allow further improvement of the assay performance. One of the identified approaches is the use of duplex-destabilizing modifications such as deoxyinosine and deoxyuridine in the design of the Snake primers. This approach was shown to solve the most serious problem associated with the antisense amplicon folding and cleavage. As a result, the method permits the use of relatively long-in this study-14-mer flap sequences. Investigation also revealed that only the 5 ¢ -segment of the flap requires the deoxyinosine/ deoxyuridine destabilization, whereas the 3 ¢ -segment is preferably left unmodified or even stabilized using 2-amino deoxyadenosine d(2-amA) and 5-propynyl deoxyuridine d(5-PrU) modifications. The basemodification technique is especially effective when applied in combination with asymmetric three-step PCR. The most valuable discovery of the present study is the effective application of modified deoxynucleoside 5 ¢ -triphosphates d(2-amA)TP and d(5-PrU)TP in Snake PCR. This method made possible the use of very short 6-8-mer 5 ¢ -flap sequences in Snake primers.

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Visible Sensing of Nucleic Acid Sequences with a Genetically Encodable Unmodified RNA Probe

et al. 2006

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DNA‐Nachweis mit RNA: Ein einfacher und empfindlicher DNA‐Nachweis gelang mit einer RNA‐Sonde aus einer einem „molekularen Leuchtfeuer“ ähnlichen cis‐Repressorsequenz und einem Gen für das Reporterprotein. Das an die RNase‐H‐Aktivität gekoppelte Leuchtfeuer‐mRNA‐System ermöglichte den optischen Nachweis der Ziel‐Nucleotidsequenz in einer zellfreien Translationslösung (siehe Bild).

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Characterization and applications of CataCleave probe in real-time detection assays

Cited by 32 publications

References 29 publications

SNP analysis using catacleave probes

SNP analysis using catacleave probes

Use of Base Modifications in Primers and Amplicons to Improve Nucleic Acids Detection in the Real-Time Snake Polymerase Chain Reaction

Visible Sensing of Nucleic Acid Sequences with a Genetically Encodable Unmodified RNA Probe

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