The effect of overhanging nucleotides on fluorescence properties of hybridising oligonucleotides labelled with Alexa-488 and FAM fluorophores

Noble, James; Wang, Lili; Cole, Kenneth D.; Gaigalas, Adolfas K.

doi:10.1016/j.bpc.2004.09.012

Cited by 43 publications

(33 citation statements)

References 23 publications

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“…One cannot, however, exclude other factors: for example, an increase in molar absorptivity of FAM (Table 2), or in the fluorescence quantum yield of this fluorophore, as well as the avoidance from quenching of FAM by adjacent G-bases. [24][25][26] Upon addition of K + , all probes exhibited significant quenching of a donor band (FAM), which was accompanied by the enhanced fluorescence of the acceptor (TAMRA; Figure 3 B). …”

Section: Spectra Of Fat-nmentioning

confidence: 99%

G Quadruplex‐Based FRET Probes with the Thrombin‐Binding Aptamer (TBA) Sequence Designed for the Efficient Fluorometric Detection of the Potassium Ion

et al. 2006

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The dual-labeled oligonucleotide derivative, FAT-0, carrying 6- carboxyfluorescein (FAM) and 6-carboxytetramethylrhodamine (TAMRA) labels at the 5' and 3' termini of the thrombin-binding aptamer (TBA) sequence 5'-GGT TGG TGT GGT TGG-3', and its derivatives, FAT-n (n=3, 5, and 7) with a spacer at the 5'-end of a TBA sequence of T(m)A (m=2, 4, and 6) have been designed and synthesized. These fluorescent probes were developed for monitoring K(+) concentrations in living organisms. Circular dichroism, UV-visible absorption, and fluorescence studies revealed that all FAT-n probes could form intramolecular tetraplex structures after binding K(+). Fluorescence resonance energy transfer and quenching results are discussed taking into account dye-dye contact interactions. The relationship between the fluorescence behavior of the probes and the spacer length in FAT-n was studied in detail and is discussed.

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Section: Spectra Of Fat-nmentioning

confidence: 99%

G Quadruplex‐Based FRET Probes with the Thrombin‐Binding Aptamer (TBA) Sequence Designed for the Efficient Fluorometric Detection of the Potassium Ion

et al. 2006

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“…A large difference in intensity for the dsDNA peaks exists between the simulation and experiment because the fluorescence emission of AF 488 varies because its quantum efficiency is sensitive to its local environment. 21,22 This leads to a difference in emission intensity between ssDNA and dsDNA. Table 2 shows the K D values extracted from our simulations compared with those from online simulation calculators DINAMelt (http://mfold.rna.albany.edu/?q=DINAMelt/Twostate-melting) and IDTDNA Biophysics Tool (http:// biophysics.idtdna.com/) at all conditions.…”

Section: ■ Results and Discussionmentioning

confidence: 99%

Hybridization Thermodynamics of DNA Oligonucleotides during Microchip Capillary Electrophoresis

et al. 2015

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Capillary electrophoresis (CE) is a powerful analytical tool for performing separations and characterizing properties of charged species. For reacting species during a CE separation, local concentrations change leading to nonequilibrium conditions. Interpreting experimental data with such nonequilibrium reactive species is nontrivial due to the large number of variables involved in the system. In this work we develop a COMSOL multiphysics-based numerical model to simulate the electrokinetic mass transport of short interacting ssDNAs in microchip capillary electrophoresis. We probe the importance of the dissociation constant, K(D), and the concentration of DNA on the resulting observed mobility of the dsDNA peak, μ(w), by using a full sweep of parametric simulations. We find that the observed mobility is strongly dependent on the DNA concentration and K(D), as well as ssDNA concentration, and develop a relation with which to understand this dependence. Furthermore, we present experimental microchip capillary electrophoresis measurements of interacting 10 base ssDNA and its complement with changes in buffer ionic strength, DNA concentration, and DNA sequence to vary the system equilibria. We then compare our results to thermodynamically calculated K(D) values.

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“…In the hairpin design, the detection limit can be optimized by varying stem length and modifications. However, the influences of modification site and stem composition on the stability of hairpin structure, the quenching efficiency of guanine [41,42], and the binding ability of aptamer to thrombin [43] are difficult to predict. While in the duplex design, the detection limit can be optimized simply by changing the length of complementary sequences.…”

Section: Detection Limitmentioning

confidence: 99%

Aptamer biosensor for protein detection based on guanine-quenching

Wang

Chen

Qian

et al. 2008

Sensors and Actuators B: Chemical

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The effect of overhanging nucleotides on fluorescence properties of hybridising oligonucleotides labelled with Alexa-488 and FAM fluorophores

Cited by 43 publications

References 23 publications

G Quadruplex‐Based FRET Probes with the Thrombin‐Binding Aptamer (TBA) Sequence Designed for the Efficient Fluorometric Detection of the Potassium Ion

G Quadruplex‐Based FRET Probes with the Thrombin‐Binding Aptamer (TBA) Sequence Designed for the Efficient Fluorometric Detection of the Potassium Ion

Hybridization Thermodynamics of DNA Oligonucleotides during Microchip Capillary Electrophoresis

Aptamer biosensor for protein detection based on guanine-quenching

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