Spectroscopic studies upon chimeric molecular beacons with i-motif forming sequence in the loop

Dembska, Anna; Masternak, Julia; Prochota, Martina

doi:10.1016/j.molstruc.2020.128436

Cited by 3 publications

(3 citation statements)

References 25 publications

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“…For example, we developed fluorescent molecular beacons, which exploited (a) pyrene excimer emission, (b) FRET pair labelling, (c) 5-(1-pyrenylethynyl)-2′deoxyuridine emission or (d) the 1,3-diazo-2-oxo-phenothiazine (analogue tC) emission as the measurable analytical signal corresponding to the proton-binding event by the pH-sensitive loop of molecular beacons 15 . In our studies upon the dual-pyrene labeled molecular beacons (MBs) with i-motif in the loop, we found that such MBs can be not only easily manipulated leading to sensors with a narrow working range and specific midpoint [16][17][18] ; but also successfully transfected into living cells, where they accumulate in lysosomes and are able to react effectively to intracellular pH changes 16,17 . Recently, we are focused on studies upon MBs integrated with the i-motif, labeled with fluorescent cytosine analogue, tC and another fluorophore, which could act as an energy acceptor from tC 19 .…”

Section: Development Of Fluorescence Oligonucleotide Probes Based On mentioning

confidence: 99%

Development of fluorescence oligonucleotide probes based on cytosine- and guanine-rich sequences

Dembska

Świtalska

Fedoruk-Wyszomirska

2020

Sci Rep

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on DNA. Finally, the obtained solution was further stored in the dark at 4 °C for 2 h to prepare stable DNA-AgNCs. The schematic diagram of the preparation of DNA-AgNCs is presented on Scheme 2. Spectroscopy measurements of fluorescent DNA-AgNCs were performed at 25 °C using 2 µM solutions of a ChONC12 oligonucleotide in 10 mM Tris-CH 3 COOH buffer (pH 7.5) as follows. Absorption spectra of fluorescent DNA-AgNCs. UV-Vis spectra of the DNA-AgNCs were recorded in the spectral range of 200-800 nm by means of Jasco V-750 spectrophotometer (Jasco, Tokyo, Japan). CD spectra of fluorescent DNA-AgNCs. CD measurements were carried out on a Jasco J-820 Spectropolarimeter (Jasco, Tokyo, Japan) with connected a temperature controller (PTC-423L). The CD spectra were obtained by taking the average of three scans in the range of 350-200 nm, with a scan rate of 200 nm/min. Fluorescence spectra. Fluorescence measurements were performed on a Jasco spectrofluorimeter FP-8200 (Jasco, Tokyo, Japan) with 10 nm excitation and 10 nm emission slits and were carried out using 0.4 × 1 cm quartz cuvettes containing 1 ml of solution. Excitation and emission spectra of DNA-AgNCs were recorded in the 200-750 nm range with λ ex = 475 nm/λ em = 560 nm, λ ex = 560 nm/λ em = 610 nm. Sample solution containing 2 μM of fluorescent oligonucleotide in 10 mM Tris-CH 3 COOH buffer (pH 7.5) was equilibrated in a quartz cell at 25 °C for 10 min. Measurements of π-A isotherms and fluorescence spectra at the monolayer interface. To obtain the surface pressure-area (π-A) isotherms for the DODAB (dimethyldioctadecylammonium bromide) monolayer and DODAB/ AgNCs complex at the air-water interface we used the computer-contolled balance system (Langmuir trough small, KSV NIMA, Espoo, Finland) as in Ref. 42. The procedure for creating a monolayer using silver nanoclusters consisted of mixing a DODAB surfactant (5 µL, 1 × 10-3 M in CHCl 3) with a ChONC12 oligonucleotide (5 µL, 1 × 10-3 M in water) (1:1 ratio) and AgNO 3 (6 µl, 1 × 10-2 M in water) and such a mixture was applied to the subphase (after 60 min). At a later stage, freshly prepared NaBH 4 (to reduce Ag + ions) was added behind the barriers. The compression as well as fluorescence measurements of monolayer-silver nanoclusters were carried out analogues as in Ref. 42. Fluorescence emission spectra for ChONC12-AgNCs were recorded in the 400-750 nm range, with the excitation wavelength of 460 nm and 550 nm (λ em = 550 nm/λ em = 610 nm).

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Section: Development Of Fluorescence Oligonucleotide Probes Based On mentioning

confidence: 99%

Development of fluorescence oligonucleotide probes based on cytosine- and guanine-rich sequences

Dembska

Świtalska

Fedoruk-Wyszomirska

2020

Sci Rep

Self Cite

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“…(To avoid the nuclear accumulation, 2′-O methylated MBs were associated with a quantum dot (QD) with a dTbiotin linker group at the 3′ end, while the mitochondrial accumulation could be avoided using cyanine dye labels). They decrease the kinetics of the sensing event [21,37,38] PNA MB PNAs are DNA analogs in which the nucleotide bases are connected to a polypeptide mainstay including repeating N-(2-aminoethyl)-glycine parts (Figure 1C, c), (the interaction of PNA-DNA is shown in Figure 1E). Interactions between the stem with other nucleic acids or between MB-MB and L-DNA can take place.…”

Section: Aptamer-mb (Ambs)mentioning

confidence: 99%

Molecular beacon strategies for sensing purpose

Bidar

Amini

Oroojalian

et al. 2021

TrAC Trends in Analytical Chemistry

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“…However, most studies have primarily focused on the effects of pH, DNA self-modification, and ligands on the i-motif structure, utilizing techniques such as circular dichroism (CD), , nuclear magnetic resonance (NMR), ultraviolet–visible spectroscopy (UV–vis), fluorescence resonance energy transfer (FRET), and so on. While these methods have been successful in characterizing the i-motif structure, they also present certain challenges.…”

Section: Introductionmentioning

confidence: 99%

Nanopore-Based Single-Molecule Investigation of Cation Effect on the i-Motif Structure

Wang,

Cui,

Liu

et al. 2024

J. Phys. Chem. B

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The i-motif, a secondary structure of a four-helix formed by cytosine-rich DNA (i-DNA) through C−C + base pairing, is prevalent in human telomeres and promoters. This structure creates steric hindrance, thereby inhibiting both gene expression and protein coding. The conformation of i-DNA is intricately linked to the intracellular ionic environment. Hence, investigating its conformation under various ion conditions holds significant importance. In this study, we explored the impact of cations on the i-motif structure at the single-molecule level using the α-hemolysin (α-HL) nanochannel. Our findings reveal that the ability of i-DNA to fold into the i-motif structure follows the order Cs + > Na + > K + > Li + for monovalent cations. Furthermore, we observed the interconversion of single-stranded DNA (ss-DNA) and the i-motif structure at high and low concentrations of Mg 2+ and Ba 2+ electrolyte solutions. This study not only has the potential to extend the application of i-motifbased sensors in complex solution environments but also provides a new idea for the detection of metal ions.

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Spectroscopic studies upon chimeric molecular beacons with i-motif forming sequence in the loop

Cited by 3 publications

References 25 publications

Development of fluorescence oligonucleotide probes based on cytosine- and guanine-rich sequences

Development of fluorescence oligonucleotide probes based on cytosine- and guanine-rich sequences

Molecular beacon strategies for sensing purpose

Nanopore-Based Single-Molecule Investigation of Cation Effect on the i-Motif Structure

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