Monitoring of pH Using an i-Motif-Forming Sequence Containing a Fluorescent Cytosine Analogue, tC

Bielecka, Patrycja; Dembska, Anna

doi:10.3390/molecules24050952

Cited by 23 publications

(27 citation statements)

References 41 publications

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“…Previously, we have indicated that emission of molecular beacon containing tC analogue incorporated in cytosine-rich loop underwent gradual quenching upon changing pH from 8.0 to 5.5 15 . This efficiently quenched fluorescence of tC was ascribed to the protonated tC-H + fluorophore that was generated upon i-motif formation 48,51 . Thus, we expected that tC-MB-520 fluorescence signal would rather decrease upon pH lowering instead of increasing as shown in Fig.…”

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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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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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“…The DNA template used for the synthesis of silver nanoclusters (AgNCs) was cytosine-rich (Crich) oligonucleotide related to the RET sequence: 5′-CCCCGCCCCGCCCCGCCCCA-3′ (RET20) [18]. In this work, we also report fluorescent AgNCs synthesized on tC-modified oligonucleotides that contain the same RET-related sequence: 5′-CCCCGCCCCGCCCCGCCCtCA-3′ (RET19tC) and 5′-CCCCGCCCCGCCCtCGCCCCA-3′ (RET14tC) [20]. 1,3-diaz-2-oxophenoxazine, tC is a tricyclic cytosine analog, which is a highly fluorescent marker with an absorption maximum at 385 nm and an emission maximum at 500 nm [21].…”

Section: Resultsmentioning

confidence: 96%

“…In the presented work, we compare the absorption and emission properties of the obtained systems with silver nanoclusters synthesized on the unmodified oligonucleotide with the RET-related sequence. The oligonucleotides of choice are able to form four-stranded DNA structures called imotifs [18][19][20]. The implications coming from fact using the folded i-motif structure as a template for the synthesis of silver nanoclusters will be also presented and discussed.…”

Section: Introductionmentioning

confidence: 99%

Spectroscopic Studies upon Silver Nanoclusters Formed on Oligonucleotides Containing a Tricyclic Cytosine Analogue, tC

Borysowiec

Świtalska

Dembska

2020

The 1st International Electronic Conference on Biosensors

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Silver nanoclusters (AgNCs) generated on DNA templates belong to a new class of fluorescent tags showing excellent brightness, photostability and biocompatibility. Thus, AgNCs-DNA has been applied in various applications, from the detection of DNA/RNA and environmental monitoring to bioimaging and cancer therapy. In this work, we report fluorescent AgNCs synthesized using two 1,3-diaza-2-oxophenothiazine (tC)-modified oligonucleotides that contain RET-related sequence CCCCGCCCCGCCCCGCCCCA. The communication compares the absorption and emission properties of the obtained systems with silver nanoclusters synthesized on the unmodified oligonucleotide. First, we showed the optimal conditions for AgNCs-DNA synthesis on three DNA templates: (1) RET20 with the sequence 5′-CCC CGC CCC GCC CCG CCC CA-3′; (2) RET19tC with the sequence 5′-CCC CGC CCC GCC CCG CCC tCA-3′; and (3) RET14tC with the sequence 5′-CCC CGC CCC GCC CtCG CCC CA-3′. Next, the silver nanoclusters were characterized by UV/Vis absorption, fluorescence and circular dichroism spectroscopy. Silver nanoclusters RET19tC-AgNCs and RET14tC-AgNCs indicated several times higher fluorescence intensities in the long-wave emission spectra as compared to RET20-AgNCs. Moreover, silver nanoclusters on tC-modified oligonucleotides showed higher stability over time. The possibility of using the silver nanoclusters RET19tC-AgNCs for monitoring pH changes will be also tested.

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“…UV‐Vis and circular dichroism (CD) spectroscopy have also been applied in studies of the hTel iM structure [1a] . Fluorescence spectroscopy has been the most widely used technique for investigating the conformational changes of iM structures because of its low cost and high sensitivity [5–8] …”

Section: Figurementioning

confidence: 99%

“…Fluorescent nucleobases have often been used to modify iM DNA sequences, allowing tracking of, for example, their fluorescence, [5] excimer emission, [6] anisotropy, [7] and photoinduced electron transfer [8] . In most examples of iM structures containing these fluorescent nucleobases, variation of the pH has not led to an increase in fluorescence intensity, but rather a quenching of the emission.…”

Section: Figurementioning

confidence: 99%

2‐Dimethylaminofluorene‐Labeled 2'‐Deoxyuridine as a Turn‐On Fluorescent Probe for i‐Motif DNA

Hong

Hwang

2021

ChemistrySelect

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i‐Motif (iM) DNA, a cytosine‐rich sequence having a four‐stranded structure, is believed to play an important role in regulating gene expression. In this study, we replaced each of the four thymidine units of the human telomeric iM sequence individually with a 2‐dimethylaminofluorene–substituted 2'‐deoxyuridine derivative (UDAF), then evaluated the formation of the iM structures with respect to pH through melting temperature measurements and circular dichroism, fluorescence, and UV‐Vis spectra. Introduction of the UDAF residue did not adversely affect the formation or stability of the iM structure; one of these strands functioned as an efficient fluorescent probe for iM formation.

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Monitoring of pH Using an i-Motif-Forming Sequence Containing a Fluorescent Cytosine Analogue, tC

Cited by 23 publications

References 41 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

Spectroscopic Studies upon Silver Nanoclusters Formed on Oligonucleotides Containing a Tricyclic Cytosine Analogue, tC

2‐Dimethylaminofluorene‐Labeled 2'‐Deoxyuridine as a Turn‐On Fluorescent Probe for i‐Motif DNA

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