Formation of triplex rA/dA-containing nucleic acid helices induced by new thiazole orange analogues and their biological evaluation. H-aggregate formation conditioned by rA sequence

Zonjić, Iva; Kurutos, Atanas; Mihovilović, Petra; Crnolatac, Ivo; Tumir, Lidija-Marija; Paić, Ana Tomašić; Kralj, Juran; Horvat, Lucija; Brozović, Anamaria; Stojković, Ranko; Stojković, Marijana Radić

doi:10.1016/j.dyepig.2022.110715

Cited by 2 publications

(5 citation statements)

References 68 publications

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“…ICD signals were of different intensity, shape and sign for DNA (B-type helix) and RNA (A-type helix). Similar differentiation of B-and A-helical structures were recently reported with cyanine monomethine dyes and Cl-TOTO/YOYO [11,14]. Moreover, cyanines 3-6 induced different ICD profiles with AT-and GC-DNA.…”

Section: Study Of Interactions Of 1-6 Withsupporting

confidence: 85%

“…Alternating AT and GC polynucleotides were chosen as models for B-helix DNA and AU homopolynucleotide as a model for A-helical structure (RNA) [3,31,32]. As noted for most cyanine dyes [4,12,14], the addition of ds-DNA (AT-DNA, GC-DNA) or ds-RNA (AU-RNA) to solutions of compounds 1-6 led to an increase in their emission (see Figures S9-S26 in SI). Similarly, to recently reported styryl cyanine dyes [13], hypsochromic shifts (6-20 nm) were noticed in all titrations of 1-6 after adding aliquots of ds-DNA and ds-RNA.…”

Section: Study Of Interactions Of 1-6 Withmentioning

confidence: 99%

“…Recently, we reported on dicationic monomethine cyanine dyes (with halogen and halogen free) that induced the triplex formation of consecutive rA/dA-containing nucleic acid helices. Chlorination of cyanine dye resulted in selective stabilization of triplex helices vs. ds-nucleic acid structures and a strong tendency for H-aggregate formation in the presence of rA chain in single-stranded, double-stranded, or triple-stranded polynucleotides [14].…”

Section: Introductionmentioning

confidence: 99%

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Selenium-Substituted Monomethine Cyanine Dyes as Selective G-Quadruplex Spectroscopic Probes with Theranostic Potential

Fabijanić

Kurutos²,

Paić³

et al. 2023

Biomolecules

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The binding interactions of six ligands, neutral and monocationic asymmetric monomethine cyanine dyes comprising benzoselenazolyl moiety with duplex DNA and RNA and G-quadruplex structures were evaluated using fluorescence, UV/Vis (thermal melting) and circular dichroism (CD) spectroscopy. The main objective was to assess the impact of different substituents (methyl vs. sulfopropyl vs. thiopropyl/thioethyl) on the nitrogen atom of the benzothiazolyl chromophore on various nucleic acid structures. The monomethine cyanine dyes with methyl substituents showed a 100-fold selectivity for G-quadruplex versus duplex DNA. Study results indicate that cyanines bind with G-quadruplex via end π-π stacking interactions and possible additional interactions with nucleobases/phosphate backbone of grooves or loop bases. Cyanine with thioethyl substituent distinguishes duplex DNA and RNA and G-quadruplex structures by distinctly varying ICD signals. Furthermore, cell viability assay reveals the submicromolar activity of cyanines with methyl substituents against all tested human cancer cell lines. Confocal microscopy analysis shows preferential accumulation of cyanines with sulfopropyl and thioethyl substituents in mitochondria and indicates localization of cyanines with methyl in nucleus, particularly nucleolus. This confirms the potential of examined cyanines as theranostic agents, possessing both fluorescent properties and cell viability inhibitory effect.

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Section: Study Of Interactions Of 1-6 Withsupporting

confidence: 85%

Section: Study Of Interactions Of 1-6 Withmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Selenium-Substituted Monomethine Cyanine Dyes as Selective G-Quadruplex Spectroscopic Probes with Theranostic Potential

Fabijanić

Kurutos²,

Paić³

et al. 2023

Biomolecules

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“…The subsequent transition, T m2→1 , signifies the dissociation of the Watson-Crick base pairs of the double-stranded poly dA-poly dT [38,39]. The T m values acquired for complexes of 23 with the duplex, under pH 5.0 and ionic strength, I = 0.1 mol dm −3 , are consistent with the T m values observed for the ATT triplex [40]. The promotion of triplex formation was not observed with compound 23 at pH 7.0 and higher ionic strength (I = 0.1 mol dm −3 ), although this effect was noticeable at a lower ionic strength of I = 0.05 mol dm −3 .…”

Section: Thermal Melting Experimentssupporting

confidence: 80%

“…The ATT triplex formation involved mixing the three constituent strands in sodium cacodylate buffer (I = 0.05 mol dm −3 , pH 7.0), supplemented with NaCl (0.05 M) and 1 mM EDTA (≥99.0%). The mixture was then heated to 90 • C for 15 min and gradually cooled to 10 • C [38,40].…”

Section: Spectrophotometric Measurementsmentioning

confidence: 99%

Distinctive Nucleic Acid Recognition by Lysine-Embedded Phenanthridine Peptides

Matić,

Piotrowski,

Vrban

et al. 2024

IJMS

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Three new phenanthridine peptide derivatives (19, 22, and 23) were synthesized to explore their potential as spectrophotometric probes for DNA and RNA. UV/Vis and circular dichroism (CD) spectra, mass spectroscopy, and computational analysis confirmed the presence of intramolecular interactions in all three compounds. Computational analysis revealed that compounds alternate between bent and open conformations, highlighting the latter’s crucial influence on successful polynucleotide recognition. Substituting one glycine with lysine in two regioisomers (22, 23) resulted in stronger binding interactions with DNA and RNA than for a compound containing two glycines (19), thus emphasizing the importance of lysine. The regioisomer with lysine closer to the phenanthridine ring (23) exhibited a dual and selective fluorimetric response with non-alternating AT and ATT polynucleotides and induction of triplex formation from the AT duplex. The best binding constant (K) with a value of 2.5 × 107 M−1 was obtained for the interaction with AT and ATT polynucleotides. Furthermore, apart from distinguishing between different types of ds-DNA and ds-RNA, the same compound could recognize GC-rich DNA through distinct induced CD signals.

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Formation of triplex rA/dA-containing nucleic acid helices induced by new thiazole orange analogues and their biological evaluation. H-aggregate formation conditioned by rA sequence

Cited by 2 publications

References 68 publications

Selenium-Substituted Monomethine Cyanine Dyes as Selective G-Quadruplex Spectroscopic Probes with Theranostic Potential

Selenium-Substituted Monomethine Cyanine Dyes as Selective G-Quadruplex Spectroscopic Probes with Theranostic Potential

Distinctive Nucleic Acid Recognition by Lysine-Embedded Phenanthridine Peptides

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