Stem–loop probe with universal reporter for sensing unlabeled nucleic acids

Tam-Chang, Suk-Wah; Carson, Travis D.; Huang, Liming; Publicover, Nelson G.; Hunter, Kenneth W.

doi:10.1016/j.ab.2007.03.006

Cited by 9 publications

(5 citation statements)

References 25 publications

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“…Lee et al [70] used the intercalator ruthenium bipyridine (Ru(bpy) 3 2+ ) and suitable detection of hybridization by electrochemiluminescence, with Ru complexes exhibiting excellent chemical stability and a relatively prolonged excited state. Instead of the common methods that use an oligonucleotide probe with a covalently linked fluorophore, a new strategy employs a fluorescently labeled universal reporter strand, which binds a reporter-binding region in the hairpin [73]. A DNA beacon is a single-stranded oligonucleotide labeled with a fluorophore in one extremity and a quencher in the other; the close proximity between them, due to the stem-and-loop (hairpin) format, prevents emission of fluorescence.…”

Section: Other Systemsmentioning

confidence: 99%

Trends in DNA biosensors

Teles

Fonseca

2008

Talanta

368

206

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a b s t r a c tBiosensors have witnessed an escalating interest nowadays, both in the research and commercial fields. Deoxyribonucleic acid (DNA) biosensors (genosensors) have been exploited for their inherent physicochemical stability and suitability to discriminate different organism strains. The main principle of detection among genosensors relies on specific DNA hybridization, directly on the surface of a physical transducer. This review covers the main DNA immobilization techniques reported so far, new microand nanotechnological platforms for biosensing and the transduction mechanisms in genosensors. Clinical applications, in particular, demand large-scale and decentralized DNA testing. New schemes for DNA diagnosis include DNA chips and microfluidics, which couples DNA detection with sample pretreatment under in vivo-like hybridization conditions. Higher sensitivity and specificity may arise from nanoengineered structures, like carbon nanotubes (CNTs) and DNA/protein conjugates. A new platform for universal DNA biosensing is also presented, and its implications for the future of molecular diagnosis are argued.

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Section: Other Systemsmentioning

confidence: 99%

Trends in DNA biosensors

Teles

Fonseca

2008

Talanta

368

206

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“…S4, † the fluorescence intensity of UR decreases as temperature increases due to the fluorescence quenching effect by solvent relaxation and this is a similar result to a previous study. 31 The fluorescence intensity of UR-SP2 increased as temperature increased from 20 to 48 °C due to the reduced quenching effect from G-bases when the closed SP2 undergoes a gradual opening process. The intensity decreased as temperature increased from 48 to 76 °C due to the fluorescence quenching effect of solvent relaxation after SP2 completely changed to the open form.…”

Section: Resultsmentioning

confidence: 99%

Self-assembled biosensor with universal reporter and dual-quenchers for detection of unlabelled nucleic acids

Huang

Aryal

Tam-Chang

et al. 2016

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A novel biosensor with universal reporter and dual quenchers was developed for rapid, sensitive, selective, and inexpensive detection of unlabelled nucleic acids. The biosensor is based on a single-strand DNA stem-loop motif with an extended universal reporter-binding region, a G-base rich stem region, and a universal address-binding region. The self-assembly of these stem-loop probes with fluorescence labeled universal reporter and a universal address region conjugated to gold nanoparticles forms the basis of a biosensor for DNA or microRNA targets in solution. The introduction of dual quenchers (G-base quenching and gold surface plasmon resonance-induced quenching) significantly reduces the fluorescence background to as low as 12% of its original fluorescence intensity and hence enhances the detection limit to 0.01 picomoles without signal ampilication.

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“…(a) All of the presented USD NAT methods employ target-independent reporter molecules that respond to target amplification through a linkage by a bipartite primer or probe. (b) Assays that use doubly modified probes with dedicated quencher moieties (8 ) are capable of multiplexing (9, 11, 16 -18, 29, 36, 37, 43, 50 ), whereas multiplex applications were not demonstrated to use guanine-mediated quenching principles (38,51,52 ). (c) All of the USD NAT methods use common fluorophore and quencher combinations, providing platform-independent reaction chemistry.…”

Section: Comparison Of Methodsmentioning

confidence: 99%

“…In cases in which the coupling of detection to amplification is not required, such as for high initial target concentrations or preamplified sample materials, the target sequence can be directly detected by signal amplification (50 ) or hybridization to NA sensors (51,52 ).…”

Section: Amplification-independent Assays (Preamplification Optional)mentioning

confidence: 99%

Current Methods for Fluorescence-Based Universal Sequence-Dependent Detection of Nucleic Acids in Homogenous Assays and Clinical Applications

2013

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BACKGROUND Specific and sensitive nucleic acid (NA) testing in research and clinical diagnostics is usually performed by use of labeled oligonucleotide probes. However, the use of target-specific fluorogenic probes increases the cost of analysis. Therefore, universal sequence-dependent (USD) NA detection methods have been developed to facilitate cost-effective target detection using standardized reagents. CONTENT We provide a comprehensive review of the current methods for fluorescence-based USD NA detection. Initially, we focus on the emergence of these methods as a means to overcome the shortcomings of common NA detection methods, such as hydrolysis probes and molecular beacons. Thereafter, we provide a critical evaluation of the individual detection methods. These methods include (a) target amplification with bipartite primers introducing a universal detection tag to the amplicon (UniPrimer PCR, universal fluorescence energy transfer probe PCR, attached universal duplex probe PCR, and universal strand displacement amplification) or combined with bipartite probes comprising a universal detection region (mediator probe PCR, universal strand displacement amplification, universal quenching probe PCR) and (b) amplification-independent assays employing either a universal variant of the invader assay or universal NA hybridization sensors. We discuss differences between the methods and review clinical applications. SUMMARY The current methods for USD NA testing are cost-effective and flexible and have concordant analytical performance in comparison with common probe-based techniques. They can detect any target sequence by the simple use of a label-free, low-cost primer or probe combined with a universal fluorogenic reporter. The methods differ in the number of target specificities, capability of multiplexing, and incubation requirements (isothermal/thermocycling). Extensive clinical applications comprise detection of single-nucleotide polymorphisms, study of gene expression, in situ PCR, and quantification of pathogen load.

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Stem–loop probe with universal reporter for sensing unlabeled nucleic acids

Cited by 9 publications

References 25 publications

Trends in DNA biosensors

Trends in DNA biosensors

Self-assembled biosensor with universal reporter and dual-quenchers for detection of unlabelled nucleic acids

Current Methods for Fluorescence-Based Universal Sequence-Dependent Detection of Nucleic Acids in Homogenous Assays and Clinical Applications

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