Single nucleotide polymorphism analysis using different colored dye dimer probes

Marmé, Nicole; Friedrich, Achim; Denapaite, Dalia; Hakenbeck, Regine; Knemeyer, Jens-Peter

doi:10.1016/j.cplett.2006.07.064

Cited by 10 publications

(8 citation statements)

References 22 publications

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“…Free TMRDex molecules displayed two prominent absorption maxima at 517 and 554 nm attributed to dimeric and monomeric species, respectively. The presence of dimeric (or multimeric) species in rhodamine and its derivatives at high concentrations has previously been reported by Levy et al 31,32 Silica encapsulation red-shifted the maxima by ∼2 nm and changed the intensity ratio of the two peaks (A 517/554 from ∼1.6 to ∼1.3). Silicaencapsulated TMR-APTES molecules displayed primarily monomeric absorption red-shifted by ∼5 nm with a rather small dimer contribution (A 515/554 ) 0.4).…”

Section: Resultsmentioning

confidence: 96%

Photophysical Properties of Dye-Doped Silica Nanoparticles Bearing Different Types of Dye−Silica Interactions

Kell

Tan

et al. 2009

J. Phys. Chem. C

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Vous avez des questions? Nous pouvons vous aider. Pour communiquer directement avec un auteur, consultez la première page de la revue dans laquelle son article a été publié afin de trouver ses coordonnées. Si vous n'arrivez pas à les repérer, communiquez avec nous à PublicationsArchive-ArchivesPublications@nrc-cnrc.gc.ca. Questions? Contact the NRC Publications Archive team atPublicationsArchive-ArchivesPublications@nrc-cnrc.gc.ca. If you wish to email the authors directly, please see the first page of the publication for their contact information. NRC Publications Archive Archives des publications du CNRCThis publication could be one of several versions: author's original, accepted manuscript or the publisher's version. / La version de cette publication peut être l'une des suivantes : la version prépublication de l'auteur, la version acceptée du manuscrit ou la version de l'éditeur. NRC Publications Record / Notice d'Archives des publications de CNRC:http://nparc.cisti-icist.nrc-cnrc.gc.ca/eng/view/object/?id=17745c67-7bcd-486b-8b14-daecbc43474b http://nparc.cisti-icist.nrc-cnrc.gc.ca/fra/voir/objet/?id=17745c67-7bcd-486b-8b14-daecbc43474b Photophysical properties of three types of dye-doped silica nanoparticles (NPs) with different dye-silica interactions have been investigated. In two cases the dye-silica interactions are noncovalent, where tris(2,2′-bipyridine)ruthenium(II) chloride (Rubpy) is attracted to the silica network electrostatically and tetramethylrhodamine-dextran (TMR-Dex) is trapped inside the silica matrix through spatial/steric hindrance. In the third case, tetramethylrhodamine-5-isothiocyanate (TRITC) modified with 3-aminopropyltriethoxysilane (APTES) to form TMR-APTES is bound to the silica matrix covalently. Although in all three types of architectures absorption, excitation, and emission spectra show only small red-shifts (<5 nm) as compared with free dye in water, excited state emission lifetimes, quantum yields, and anisotropies vary significantly and in quite different ways between the three architectures. All three types of interactions facilitate effective encapsulation of dye within a silica network. However, covalent bonding possesses a notable advantage over the other two types of interactions as it results in a large reduction of a nonradiative relaxation rate of the embedded dye (TMR-APTES) and, thus, a large (∼3.55-fold) increase of its quantum yield.

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Section: Resultsmentioning

confidence: 96%

Photophysical Properties of Dye-Doped Silica Nanoparticles Bearing Different Types of Dye−Silica Interactions

Kell

Tan

et al. 2009

J. Phys. Chem. C

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“…The density of dyes that can be embedded is limited by the dye's tendency to aggregate yielding low-fluorescent imperfect H-type aggregates. [6][7][8][9][10] Often it is also observed that dye interactions lead to broad brightness and fluorescence lifetime distributions especially for nanobeads below 60 nm diameter. 11 Only recently, fluorescent nanoparticles with improved photophysical properties such as conjugated polymer dots 12,13 and fluorescent organic nanoparticles 4,14 were developed.…”

mentioning

confidence: 99%

Interchromophoric Interactions Determine the Maximum Brightness Density in DNA Origami Structures

Schröder

Scheible²,

Steiner

et al. 2019

Nano Lett.

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An ideal point light source is as small and as bright as possible. For fluorescent point light sources, homogeneity of the light sources is important as well as that the fluorescent units inside the light source maintain their photophysical properties which is compromised by dye aggregation. Here we propose DNA origami as a rigid scaffold to arrange dye molecules in a dense pixel array with high control of stoichiometry and dye-dye interactions. In order to find the highest labeling density in a DNA origami structure without influencing dye photophysics we alter the distance of two ATTO647N dyes in single base pair steps and probe the dye-dye interactions on the singlemolecule level. For small distances strong quenching in terms of intensity and fluorescence lifetime is observed. With increasing distance, we observe reduced quenching and molecular 8 1 0

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“…36 The advantage of this class of DNA probes, compared to molecular beacons is the easier synthesis because both end of the oligonucleotide are labeled with the same dye instead of using one dye and a quencher moiety. Therefore, the labeling can be done in a single reaction.…”

Section: Dimer Probesmentioning

confidence: 99%

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

et al. 2007

Self Cite

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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.

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Single nucleotide polymorphism analysis using different colored dye dimer probes

Cited by 10 publications

References 22 publications

Photophysical Properties of Dye-Doped Silica Nanoparticles Bearing Different Types of Dye−Silica Interactions

Photophysical Properties of Dye-Doped Silica Nanoparticles Bearing Different Types of Dye−Silica Interactions

Interchromophoric Interactions Determine the Maximum Brightness Density in DNA Origami Structures

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

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