Self-quenching DNA probes based on dye dimerization for identification of mycobacteria

Knemeyer, Jens-Peter; Marmé, Nicole; Häfner, Bernhard; Habl, Gregor; Schäfer, Gabriela; Müller, Mat­thias; Nolte, Oliver; Sauer, Markus; Wolfrum, J.

doi:10.1080/03067310500146094

Cited by 12 publications

(11 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…19 We synthesized a hairpin-structured DNA probe (5´-TACCGGGTTTTCTCGTGGTGACGGTA-3´) labeled at both ends with MR121 for the discrimination of different mycobacteria. 20 This DNA probe shows an up to 12-fold increase in fluorescence intensity depending on the salt concentration and is appropriate for single-molecule experiments. Indeed, here the quenching is not exclusively due to the formation of non-fluorescent dye dimers because this dye is also quenched by guanine bases via photo-induced electron transfer.…”

Section: Dimer Probesmentioning

confidence: 99%

See 1 more Smart Citation

New hairpin-structured DNA probes: alternatives to classical molecular beacons

et al. 2007

Self Cite

View full text Add to dashboard Cite

In this article we report on two different classes of self-quenching hairpin-structured DNA probes that can be used as alternatives to Molecular Beacons. Compared to other hairpin-structured DNA probes, the so-called smart probes are labeled with only one extrinsic dye. The fluorescence of this dye is efficiently quenched by intrinsic guanine bases via a photo-induced electron transfer reaction in the closed hairpin. After hybridization to a target DNA, the distance between dye and the guanines is enlarged and the fluorescence is restored. The working mechanism of the second class of hairpin DNA probes is similar, but the probe oligonucleotide is labeled at both ends with an identical chromophore and thus the fluorescence of the closed hairpin is reduced due to formation of non-fluorescent dye dimers. Both types of probes are appropriate for the identification of single nucleotide polymorphisms and in combination with confocal single-molecule spectroscopy sensitivities in the picomolar range can be achieved.

show abstract

Section: Dimer Probesmentioning

confidence: 99%

“…19,20 These probes are based on the formation of non-fluorescent dye dimers. The phenomenon of aggregation and dimerization of fluorescent dyes in aqueous solutions has been shown for a wide variety of fluorescent dyes, e. g. the xanthene 21,22 , phenothiazine 23 , squarine 24 , BODIPY 25,26 and cyanine 27,28 dyes.…”

Section: Dimer Probesmentioning

confidence: 99%

New hairpin-structured DNA probes: alternatives to classical molecular beacons

et al. 2007

Self Cite

View full text Add to dashboard Cite

show abstract

“…Such fluorophores have also been used in the design of QF-MBs. The FRET MB in Figure 8.19d containing two MR121 fluorophores attached at the 5 -and 3 -ends is self-quenched [123]. Similarly in Figure 8.19e, two dicyanomethylene dihydrofuran (DCDHF) dyes have been attached at the 5 -and 3 -ends using an NHS-ester derivative of the dye [124].…”

Section: Quencher-free Molecular Beaconmentioning

confidence: 99%

“…19 Representative examples of FRET MB (a)[118], EMS MBs (b and c)[120,121], and DMS MBs (d and e)[123,124].…”

mentioning

confidence: 99%

Labeling Oligonucleotides toward the Biomedical Probe

Lee

Kim

2011

Medicinal Chemistry of Nucleic Acids

View full text Add to dashboard Cite

“…Under aqueous conditions, the fluorophores form non-or only weakly fluorescent dimers [12][13][14]. The formation of non-fluorescent dye dimers has also been successfully applied in DNA assay systems [15,16].…”

Section: Introductionmentioning

confidence: 99%