Recognizing parallel-stranded G-quadruplex by cyanine dye dimer based on dual-site binding mode

Yu, Lijia; Gai, Wei; Yang, Qianfan; Xiang, Junfeng; Sun, Hongxia; Li, Qian; Wang, Lixia; Guan, Aijiao; Tang, Yalin

doi:10.1016/j.cclet.2015.02.002

Cited by 10 publications

(4 citation statements)

References 29 publications

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“…Selenium-containing cyanine-based dye 106 has also been tested as af luorescent G4 probe. [56] The major structural changes relative to the previous structures is the replacement of the indolenine rings by benzoselenazole units in addition to the removal of the cationic end group from the N-alkyl chains. Dye 106 shows higher affinity to c-MYC over human telomeric G4 or dsDNA and preferential binding to parallel G4 over antiparallel, hybrid,o rm ixed G4, which indicates that only the parallel topology can providet he appropriate groove dimensions for binding of 106.…”

Section: Indole-a Nd Thiazole-based Cyanine Dyesmentioning

confidence: 99%

Design of Modular G‐quadruplex Ligands

et al. 2018

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Guanine-rich nucleic acid sequences able to form four-stranded structures (G-quadruplexes, G4) play key cellular regulatory roles and are considered as promising drug targets for anticancer therapy. On the basis of the organization of their structural elements, G4 ligands can be divided into three major families: one, fused heteroaromatic polycyclic systems; two, macrocycles; three, modular aromatic compounds. The design of modular G4 ligands emerged as the answer to achieve not only more drug-like compounds but also more selective ligands by targeting the diversity of the G4 loops and grooves. The rationale behind the design of a very comprehensive set of ligands, with particular focus on the structural features required for binding to G4, is discussed and combined with the corresponding biochemical/biological data to highlight key structure-G4 interaction relationships. Analysis of the data suggests that the shape of the ligand is the major factor behind the G4 stabilizing effect of the ligands. The information here critically reviewed will certainly contribute to the development of new and better G4 ligands with application either as therapeutics or probes.

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Section: Indole-a Nd Thiazole-based Cyanine Dyesmentioning

confidence: 99%

Design of Modular G‐quadruplex Ligands

et al. 2018

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“…Aggregation–deaggregation effects of other trimethine cyanine dyes, 53 (DEC) and 54 ( Figure 12 ), were used to detect G-quadruplexes of DNA [ 57 , 58 ]. It is known that a significant number of ligands, when interacting with G-quadruplexes, bind to G4 at their ends (end stacking); rare ligands are capable of binding in the grooves.…”

Section: Influence Of Interaction With Dna and Other Nucleic Acids On...mentioning

confidence: 99%

“…It is known that a significant number of ligands, when interacting with G-quadruplexes, bind to G4 at their ends (end stacking); rare ligands are capable of binding in the grooves. The cationic meso -substituted cyanine dye 54 binds to parallel G-quadruplex both by end stacking and in the grooves (as a monomer or dimer) [ 57 ]. In the presence of G-quadruplexes, sharp changes are observed in the absorption and fluorescence spectra of the anionic dye 53 as a result of the decomposition of J-aggregates to form fluorescent monomers (an increase in fluorescence intensity occurs at λ fl = 600 nm by ~70 times), which is not observed in the presence of ds- and ssDNA [ 58 ].…”

Section: Influence Of Interaction With Dna and Other Nucleic Acids On...mentioning

confidence: 99%

Photonics of Trimethine Cyanine Dyes as Probes for Biomolecules

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Татиколов

2022

Molecules

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Cyanine dyes are widely used as fluorescent probes in biophysics and medical biochemistry due to their unique photophysical and photochemical properties (their photonics). This review is focused on a subclass of the most widespread and studied cyanine dyes—trimethine cyanines, which can serve as potential probes for biomolecules. The works devoted to the study of the noncovalent interaction of trimethine cyanine dyes with biomolecules and changing the properties of these dyes upon the interaction are reviewed. In addition to the spectral-fluorescent properties, elementary photochemical properties of trimethine cyanines are considered, including: photoisomerization and back isomerization of the photoisomer, generation and decay of the triplet state, and its quenching by oxygen and other quenchers. The influence of DNA and other nucleic acids, proteins, and other biomolecules on these properties is covered. The interaction of a monomer dye molecule with a biomolecule usually leads to a fluorescence growth, damping of photoisomerization (if any), and an increase in intersystem crossing to the triplet state. Sometimes aggregation of dye molecules on biomolecules is observed. Quenching of the dye triplet state in a complex with biomolecules by molecular oxygen usually occurs with a rate constant much lower than the diffusion limit with allowance for the spin-statistical factor 1/9. The practical application of trimethine cyanines in biophysics and (medical) biochemistry is also considered. In conclusion, the prospects for further studies on the cyanine dye–biomolecule system and the development of new effective dye probes (including probes of a new type) for biomolecules are discussed.

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“…32,33 Thus, fluorescent light-up probes that directly detect the G4s are a good alternative. Many fluorescent probes have been reported; for example, the organic molecules, including cyanine, 34 thiazole, 35,36 triphenylmethane, 37 or carbazole, 38 and metal complexes. 39,40 However, poor selectivity and ligand-induced conformation changes limit their application.…”

Section: Introductionmentioning

confidence: 99%