DNA Probes Using Fluorescence Resonance Energy Transfer (FRET): Designs and Applications

Didenko, Vladimir V.

doi:10.2144/01315rv02

Cited by 370 publications

(299 citation statements)

References 93 publications

(136 reference statements)

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“…TaqMan probes consist of a sequence of 25-30 nucleotides in length which is labelled with a donor fluorophore (as reporter) at the 5' end, and an acceptor dye (as quencher) at the 3' end ( Figure 2). Generally, a fluorophore is a molecule that absorbs light energy and is promoted to an excited state, and a quencher is a molecule that can receive energy from a fluorophore and disperse the energy by proximal quenching or by fluorescence resonance energy transfer (FRET) (Didenko 2001). In FRET quenching, as a dynamic quenching mechanism, the fluorophore transfers its energy to the quencher, and the energy is released as light of a longer wavelength (Schena et al 2013).…”

Section: Detection Based On Sequence Specific Methodsmentioning

confidence: 99%

“…So, until the time when the probe is not hydrolysed, the quencher and the fluorophore remain in proximity to each other, separated by the probe length. However, this proximity does not entirely quench the fluorescence of the reporter dye and a background fluorescence is detected (Didenko 2001). During PCR, the probe hybridizes to the single-stranded DNA (ssDNA) template.…”

Section: Detection Based On Sequence Specific Methodsmentioning

confidence: 99%

“…This structure brings the fluorophore in close proximity with the quencher and avoids fluorescence. Scorpion makes the molecular beacon technique more efficient by combining the functions of the probe and the 5' PCR primer (Didenko 2001). In the absence of the target, the quencher nearly absorbs the fluorescence emitted by the fluorophore.…”

Section: Detection Based On Sequence Specific Methodsmentioning

confidence: 99%

See 2 more Smart Citations

Real-time PCR applied to study on plant pathogens: potential applications in diagnosis - a review

Mirmajlessi¹,

Loit²,

Mänd³

et al. 2015

Plant Prot. Sci.

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Mirmajlessi S.M., Loit E., Mänd M., Mansouripour S.M. (2015): Real-time PCR applied to study on plant pathogens: potential applications in diagnosis -a review. Plant Protect Sci., 51: 177-190.Quantitative real-time PCR (qPCR) technique incorporates traditional polymerase chain reaction (PCR) efficiency with the production of a specific fluorescent signal, measuring the kinetics of the reaction in the early PCR phases and providing quantification of specific targets in various environmental samples. There are an increasing number of chemistries to detect PCR products, which are widely used in plant pathology as they cluster into the amplicon sequence non-specific and sequence-specific techniques. In this review, we illustrate a general description of major chemistries and discuss some considerations for assay development as it applies for a wide range of applications in epidemiological studies. The technique has become the gold standard for early detection of pathogens and a fundamental tool in the research laboratory.

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Section: Detection Based On Sequence Specific Methodsmentioning

confidence: 99%

Section: Detection Based On Sequence Specific Methodsmentioning

confidence: 99%

Section: Detection Based On Sequence Specific Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Real-time PCR applied to study on plant pathogens: potential applications in diagnosis - a review

Mirmajlessi¹,

Loit²,

Mänd³

et al. 2015

Plant Prot. Sci.

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show abstract

“…http://dx.doi.org/10.1101/125583 doi: bioRxiv preprint first posted online Apr. 26, 2017; 3 reporters for different purposes, including molecular probes, 24 single-molecule studies, [25][26][27][28] DNA machines 29,30 and DNA walkers. 31 Here, we report a systematic study of PAT molecular rulers using DNA nanostructures to precisely tune the distance between a fluorophore and quencher pair suitable for in vivo imaging in the near-infrared (NIR) optical window.…”

Section: Photoacoustic (Pa) Tomography (Pat) Is Emerging As An In Vivmentioning

confidence: 99%

Photoacoustic molecular rulers based on DNA nanostructures

Joseph

Köehler

Zuehlsdorff

et al. 2017

Preprint

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Molecular rulers that rely on the Förster resonance energy transfer (FRET) mechanism are widely used to investigate dynamic molecular processes that occur on the nanometer scale. However, the capabilities of these fluorescence molecular rulers are fundamentally limited to shallow imaging depths by light scattering in biological samples. Photoacoustic tomography (PAT) has recently emerged as a high resolution modality for in vivo imaging, coupling optical excitation with ultrasound detection. In this paper, we report the capability of PAT to probe distance-dependent FRET at centimeter depths. Using DNA nanotechnology we created several nanostructures with precisely positioned fluorophore-quencher pairs over a range of nanoscale separation distances. PAT of the DNA nanostructures showed distancedependent photoacoustic signal generation and experimentally demonstrated the ability of PAT to reveal the FRET process deep within tissue mimicking phantoms. Further, we experimentally validated these DNA nanostructures as providing a novel and biocompatible strategy to augment the intrinsic photoacoustic signal generation capabilities of small molecule fluorescent dyes.

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“…The energy of the donor fluorophore transfers and excites the acceptor fluorophore. FRET is widely used in biological investigations, including enzyme modification and screening (1,(7)(8)(9)(10), protein-protein interaction (9,(11)(12)(13)(14)(15)(16)(17)(18)(19)(20)(21), single-nucleotide polymorphisms (22)(23)(24), and analysis of regulatory sequences (12,(25)(26)(27)(28)(29).…”

mentioning

confidence: 99%

Flow cytometric measurement of fluorescence (Förster) resonance energy transfer from cyan fluorescent protein to yellow fluorescent protein using single‐laser excitation at 458 nm

Bradrick

Karpova

et al. 2003

Cytometry Pt A

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Background: Use of distinct green fluorescent protein (GFP) variants permits the study of protein-protein interactions and colocalization in viable transfected cells by fluorescence (Förster) resonance energy transfer (FRET). Flow cytometry is a sensitive method to detect FRET. However, the typical dual-laser methods used in flow cytometric FRET assays are not generally applicable because they require a specialized krypton ultraviolet (UV) laser. The purpose of this work was to develop a flow cytometric method to detect FRET between cyan fluorescent protein (CFP; donor) and yellow fluorescent protein (YFP; acceptor) by using the 458-nm excitation from a single tunable argon-ion laser. Methods: FUSE-binding protein (FBP) interacting repressor (FIR) and FBP are c-myc transcription factors and are known to interact physically. To examine their interaction within viable cells, FIR and the binding motif of FBP, the FBP central domain (FBPcd), were fused with CFP and YFP, respectively, and this pair of fluorescently-tagged proteins was used to detect FRET in vivo. Cells transfected with expression plasmids encoding a CFP-FIR fusion protein and YFP as a negative control, a CFP-YFP fusion protein as a positive control, or CFP-FIR and YFP-FBPcd fusion proteins were examined for FRET after excitation with a 458-nm line from a tunable argon-ion laser. FRET was measured as the ratio of YFP:CFP emission or as YFP emission at 564 -606 nm. Conventional FRET using the 413-nm UV line from a krypton laser was examined for comparison. Fluorescence signals were separated with a customized optical filter configuration using 530-nm shortpass, 500-nm longpass, and 560-nm shortpass dichroics in

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DNA Probes Using Fluorescence Resonance Energy Transfer (FRET): Designs and Applications

Cited by 370 publications

References 93 publications

Real-time PCR applied to study on plant pathogens: potential applications in diagnosis - a review

Real-time PCR applied to study on plant pathogens: potential applications in diagnosis - a review

Photoacoustic molecular rulers based on DNA nanostructures

Flow cytometric measurement of fluorescence (Förster) resonance energy transfer from cyan fluorescent protein to yellow fluorescent protein using single‐laser excitation at 458 nm

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