1
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Lee ETT, Sato Y, Ujuagu AF, Nishizawa S. Forced intercalation-induced light-up peptides as fluorogenic indicators for the HIV-1 TAR RNA-ligand assay. Analyst 2024; 149:4179-4186. [PMID: 38860915 DOI: 10.1039/d4an00530a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
Fluorescence indicators capable of binding to human immunodeficiency virus-1 (HIV-1) trans-activation responsive (TAR) RNA are powerful tools for the exploratory studies of the identification of anti-HIV drug candidates. This work presents a new design strategy for fluorogenic indicators with a transactivator of transcription (Tat)-derived peptide based on the forced intercalation of thiazole orange (TO) dyes (FIT). The developed 9-mer FIT peptide (RKKRR-TO-RRR: named FiLuP) features the TO unit integrated onto a Dap (2,3-diaminopropionic acid) residue in the middle of the Tat peptide sequence; the Q (glutamic acid) residue in the Tat peptide (RKKRR-Q-RRR) is replaced with TO as if it were an amino acid surrogate. This facilitates a significant light-up response (450-fold at λem = 541 nm, Φfree = 0.0057, and Φbound = 0.61) upon binding to TAR RNA. The response of FiLuP is highly selective to TAR RNA over other non-cognate RNAs, and FiLuP maintains strong binding affinity (Kd = 1.0 ± 0.6 nM). Significantly, in contrast to previously developed Tat peptide-based FRET probes, FiLuP is able to discriminate between "competitive" and "noncompetitive" inhibitors when used in the fluorescence indicator displacement (FID) assay. The FID assay under stringent screening conditions is also possible, enabling super-strong competitive binders toward TAR RNA to be sieved out.
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Affiliation(s)
- En Ting Tabitha Lee
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Akunna F Ujuagu
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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2
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Aristova D, Selin R, Heil HS, Kosach V, Slominsky Y, Yarmoluk S, Pekhnyo V, Kovalska V, Henriques R, Mokhir A, Chernii S. Trimethine Cyanine Dyes as NA-Sensitive Probes for Visualization of Cell Compartments in Fluorescence Microscopy. ACS OMEGA 2022; 7:47734-47746. [PMID: 36591208 PMCID: PMC9798395 DOI: 10.1021/acsomega.2c05231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
We propose symmetrical cationic trimethine cyanine dyes with β-substituents in the polymethine chain based on modified benzothiazole and benzoxazole heterocycles as probes for the detection and visualization of live and fixed cells by fluorescence microscopy. The spectral-luminescent properties of trimethine cyanines have been characterized for free dyes and in the presence of nucleic acids (NA) and globular proteins. The studied cyanines are low to moderate fluorescent when free, but in the presence of NA, they show an increase in emission intensity up to 111 times; the most pronounced emission increase was observed for the dyes T-2 in the presence of dsDNA and T-1 with RNA. Spectral methods showed the binding of all dyes to nucleic acids, and different interaction mechanisms have been proposed. The ability to visualize cell components of the studied dyes has been evaluated using different human cell lines (MCF-7, A2780, HeLa, and Hs27). We have shown that all dyes are cell-permeant staining nucleus components, probably RNA-rich nucleoli with background fluorescence in the cytoplasm, except for the dye T-5. The dye T-5 selectively stains some structures in the cytoplasm of MCF-7 and A2780 cells associated with mitochondria or lysosomes. This effect has also been confirmed for the normal type of cell line-human foreskin fibroblasts (Hs27). The costaining of dye T-5 with MitoTracker CMXRos Red demonstrates specificity to mitochondria at a concentration of 0.1 μM. Colocalization analysis has shown signals overlapping of dye T-5 and MitoTracker CMXRos Red (Pearson's Coefficient value = 0.92 ± 0.04). The photostability study shows benzoxazole dyes to be up to ∼7 times more photostable than benzothiazole ones. Moreover, studied benzoxazoles are less cytotoxic at working concentrations than benzothiazoles (67% of cell viability for T-4, T-5 compared to 12% for T-1, and ∼30% for T-2, T-3 after 24 h). Therefore, the benzoxazole T-4 dye is proposed for nucleic acid detection in vitro and intracellular fluorescence imaging of live and fixed cells. In contrast, the benzoxazole dye T-5 is proposed as a good alternative to commercial dyes for mitochondria staining in the green-yellow region of the spectrum.
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Affiliation(s)
- Daria Aristova
- Institute
of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
- Instituto
Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Roman Selin
- V.I.
Vernadsky Institute of General and Inorganic Chemistry NASU, 32/34 Palladin Ave, 03142 Kyiv, Ukraine
- Organic
Chemistry II, Friedrich-Alexander-University
of Erlangen-Nuremberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Hannah Sophie Heil
- Instituto
Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Viktoriia Kosach
- Institute
of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Yuriy Slominsky
- Institute
of Organic Chemistry NASU, 5 Murmans’ka St., 02094 Kyiv, Ukraine
| | - Sergiy Yarmoluk
- Institute
of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Vasyl Pekhnyo
- V.I.
Vernadsky Institute of General and Inorganic Chemistry NASU, 32/34 Palladin Ave, 03142 Kyiv, Ukraine
| | - Vladyslava Kovalska
- Institute
of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Ricardo Henriques
- Instituto
Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156 Oeiras, Portugal
| | - Andriy Mokhir
- Organic
Chemistry II, Friedrich-Alexander-University
of Erlangen-Nuremberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Svitlana Chernii
- Institute
of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
- V.I.
Vernadsky Institute of General and Inorganic Chemistry NASU, 32/34 Palladin Ave, 03142 Kyiv, Ukraine
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3
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Photonics of Trimethine Cyanine Dyes as Probes for Biomolecules. Molecules 2022; 27:molecules27196367. [PMID: 36234904 PMCID: PMC9573451 DOI: 10.3390/molecules27196367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/16/2022] [Accepted: 09/22/2022] [Indexed: 11/29/2022] Open
Abstract
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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'Lights, squaraines, action!' - the role of squaraine dyes in photodynamic therapy. Future Med Chem 2022; 14:1375-1402. [PMID: 36069190 DOI: 10.4155/fmc-2022-0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Since they were first synthesized in 1965 by Treibs and Jacob, squaraine dyes have revolutionized the polymethine dyes' 'universe' and their potential applications due to their indisputable physical, chemical and biological properties. After 30 years and up to the present, various research teams have dedicated themselves to studying the squaraines' photodynamic therapy application using in vitro and in vivo models. The various structural modifications made to these compounds, as well as the influence they have shown to have in their phototherapeutic activity, are the main focus of the present review. Finally, the most evident limitations of this class of dyes, as well as future perspectives in the sense of hypothetically successfully overcoming them, are suggested by the authors.
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Ma X, Shi L, Zhang B, Liu L, Fu Y, Zhang X. Recent advances in bioprobes and biolabels based on cyanine dyes. Anal Bioanal Chem 2022; 414:4551-4573. [PMID: 35359180 DOI: 10.1007/s00216-022-03995-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Revised: 02/19/2022] [Accepted: 02/28/2022] [Indexed: 11/30/2022]
Abstract
As a functional dye, cyanine dye promotes the widespread application of bioprobes in the fields of medicine, genetics and environment, owing to its advantages of good photophysical properties, excellent biocompatibility and low toxicity to biological systems. Nowadays, it is mainly used in the fields of life sciences such as fluorescent labeling of biological macromolecules, disease diagnosis, immunoassay and DNA detection, all of which lie at the core of this review. First, we briefly introduced the characteristics and principles of the cyanine dye bioprobe. Afterward, we paid attention to the recent progress of cyanine dye bioprobes widely used in the 10 years from 2010 to 2020. The application of cyanine dyes as bioprobes with different identification elements, including enzymes, organelles, immunity and DNAs, was mainly summarized. Finally, this review gave an outlook on the future development trend of cyanine dye bioprobes. This facilitates the construction of a new type of multifunctional fluorescent probe and promotes its clinical application.
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Affiliation(s)
- Xiaoying Ma
- College of Chemical Engineering, Hebei and Tangshan Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology, 063210, Tangshan, China
| | - Lei Shi
- College of Chemical Engineering, Hebei and Tangshan Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology, 063210, Tangshan, China.
| | - Buyue Zhang
- College of Chemical Engineering, Hebei and Tangshan Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology, 063210, Tangshan, China
| | - Lu Liu
- College of Chemical Engineering, Hebei and Tangshan Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology, 063210, Tangshan, China
| | - Yao Fu
- College of Chemical Engineering, Hebei and Tangshan Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology, 063210, Tangshan, China
| | - Xiufeng Zhang
- College of Chemical Engineering, Hebei and Tangshan Key Laboratory of Medical-Industrial Integration Precision Medicine, North China University of Science and Technology, 063210, Tangshan, China.
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6
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Pronkin PG, Tatikolov AS. Meso-aryl-substituted thiacarbocyanine dyes as spectral-fluorescent probes for DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 269:120744. [PMID: 34929626 DOI: 10.1016/j.saa.2021.120744] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/01/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
The noncovalent interaction of meso-aryl-substituted thiacarbocyanine dyes I and II with dsDNA and ssDNA in aqueous solutions has been studied by spectral-fluorescent methods. Complexation with DNA is accompanied by both aggregation of the dyes and the formation of monomeric strongly fluorescent complexes. Experiments on molecular docking of dyes I and II with dsDNA confirm the previous assumption about the possibility of the formation of complexes of different types: intercalation between base pairs and in the grooves of the double helix of the biopolymer. The possibility of intercalation of the dyes in the complex is confirmed by experiments on thermal dissociation of dsDNA in the presence of dyes I and II, as well as experiments on the interaction of the dyes with ssDNA. An increase in the melting temperatures Tm of dsDNA is obtained in the presence of I and II, similar to that observed for the classical intercalator ethidium bromide. The limits of detection and quantification of DNA, which are important for the use of the dyes as probes for DNA, have been determined. The primary photochemical processes of the dyes in complexes with ssDNA were studied by flash photolysis technique. Complexation with ssDNA hinders photoisomerization and creates favorable conditions for the dye triplet state formation. The decay kinetics of the triplet state of the dyes were monoexponential. The rate constant of quenching of the triplet state by air oxygen was estimated for dye I complexed with ssDNA and was found to be less than the diffusion-controlled limit. This is probably a consequence of the shielding effect of the complex on the triplet quenching process.
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Affiliation(s)
- Pavel G Pronkin
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334 Russia.
| | - Alexander S Tatikolov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334 Russia.
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7
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Pronkin PG, Tatikolov AS. Photonics of meso-substituted carbocyanine dyes in solutions and in complexes with DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 263:120171. [PMID: 34280796 DOI: 10.1016/j.saa.2021.120171] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 06/28/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
Spectral-fluorescent and photochemical properties (photoisomerization and generation of the triplet state) of meso-substituted cationic carbocyanine dyes, 3,3'-di-(β-hydroxyethyl)-5,5'-dimethoxy-9-ethylthiacarbocyanine iodide (K1) and 3,3'-di-(β-hydroxyethyl)-9-methylthiacarbocyanine iodide (K2), have been studied in solutions and in the presence of DNA. In solutions, on passing from acetonitrile to dioxane, a growth of fluorescence of the dyes is observed due to a shift of the equilibrium of cis/trans isomers toward the fluorescent trans-isomer. Upon flash photolysis of dye solutions in dioxane, the formation and subsequent decay of the cis-photoisomers of the dyes are observed. In aqueous solutions, the interaction with DNA leads to the formation of noncovalent complexes of K1 and K2 with DNA, which is accompanied by a significant increase in the fluorescence intensity. The results of the molecular docking experiments showed the possibility of several types of binding, which was confirmed by the data obtained from other experiments. The effects of temperature and additions of NaCl on the stability of the dye-DNA complexes were studied. The spectral-fluorescent data were used to estimate the binding constants of the dyes with DNA and other characteristics of the dyes that are important for their use as probes. Upon flash photolysis of the dyes in complexes with DNA, photoisomerization is not observed, but the quantum yield of intersystem crossing to the triplet state increases. The decay of the triplet states occurs by a two-exponential law. The rate constants for quenching of the triplet states of the dyes complexed with DNA by oxygen were found to be lower than the expected values for diffusion-controlled quenching (taking into account the spin statistical factor 1/9), which is explained by the steric factor of complexation.
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Affiliation(s)
- Pavel G Pronkin
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334, Russia.
| | - Alexander S Tatikolov
- N.M. Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin St. 4, Moscow 119334, Russia.
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8
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Sorour MI, Kistler KA, Marcus AH, Matsika S. Accurate Modeling of Excitonic Coupling in Cyanine Dye Cy3. J Phys Chem A 2021; 125:7852-7866. [PMID: 34494437 DOI: 10.1021/acs.jpca.1c05556] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Accurate modeling of excitonic coupling in molecules is of great importance for inferring the structures and dynamics of coupled systems. Cy3 is a cyanine dye that is widely used in molecular spectroscopy. Its well-separated excitation bands, high sensitivity to the surroundings, and the high energy transfer efficiency make it a perfect choice for excitonic coupling experiments. Many methods have been used to model the excitonic coupling in molecules with varying degrees of accuracy. The atomic transition charge model offers a high-accuracy and cost-effective way to calculating the excitonic coupling. The main focus of this work is to generate high-quality atomic transition charges that can accurately model the Cy3 dye's transition density. The transition density of the excitation of the ground to first excited state is calculated using configuration-interaction singles and time-dependent density functional theory and is benchmarked against the algebraic diagrammatic construction method. Using the transition density we derived the atomic transition charges using two approaches: Mulliken population analysis and charges fitted to the transition electrostatic potential. The quality of the charges is examined, and their ability to accurately calculate the excitonic coupling is assessed via comparison to experimental data of an artificial biscyanine construct. Theoretical comparisons to the supermolecule ab initio couplings and the widely used point-dipole approximation are also made. Results show that using the transition electrostatic potential is a reliable approach for generating the transition atomic charges. A high-quality set of charges, that can be used to model the Cy3 dye dimer excitonic coupling with high-accuracy and a reasonable computational cost, is obtained.
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Affiliation(s)
- Mohammed I Sorour
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
| | - Kurt A Kistler
- Department of Chemistry, Brandywine Campus, The Pennsylvania State University, Media, Pennsylvania 19063, United States
| | - Andrew H Marcus
- Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon 97403, United States
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, Pennsylvania 19122, United States
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9
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Sato Y, Takahashi Y, Tanabe T, Nishizawa S. Conjugating pyrene onto PNA-based fluorescent probes for improved detection selectivity toward double-stranded siRNA. Org Biomol Chem 2021; 18:4009-4013. [PMID: 32420569 DOI: 10.1039/d0ob00794c] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We report on the design of new siRNA-binding fluorescent probes with the improved detection selectivity toward intact double-stranded siRNAs over single-stranded forms by the conjugation of pyrene unit into thiazole orange base surrogate-carrying peptide nucleic acid (PNA) that can simultaneously recognize the 3'-overhang and double-stranded sequences of target siRNAs.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Japan, Sendai 980-8578, Japan.
| | - Yuki Takahashi
- Department of Chemistry, Graduate School of Science, Tohoku University, Japan, Sendai 980-8578, Japan.
| | - Takaaki Tanabe
- Department of Chemistry, Graduate School of Science, Tohoku University, Japan, Sendai 980-8578, Japan.
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Japan, Sendai 980-8578, Japan.
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10
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Aristova D, Kosach V, Chernii S, Slominsky Y, Balanda A, Filonenko V, Yarmoluk S, Rotaru A, Özkan HG, Mokhir A, Kovalska V. Monomethine cyanine probes for visualization of cellular RNA by fluorescence microscopy. Methods Appl Fluoresc 2021; 9. [PMID: 34198271 DOI: 10.1088/2050-6120/ac10ad] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/01/2021] [Indexed: 11/12/2022]
Abstract
We have studied spectral-luminescent properties of the monomethine cyanine dyes both in their free states and in the presence of either double-stranded deoxyribonucleic acids (dsDNAs) or single-stranded ribonucleic acids (RNAs). The dyes possess low fluorescence intensity in an unbound state, which is increased up to 479 times in the presence of the nucleic acids. In the presence of RNAs, the fluorescence intensity increase was stronger than that observed in the presence of dsDNA. Next, we have performed staining of live and fixed cells by all prepared dyes. The dyes proved to be cell and nuclear membrane permeant. They are photostable and brightly stain RNA-containing organelles in both live and fixed cells. The colocalization confirmed the specific nucleoli staining with anti-Ki-67 antibodies. The RNA digestion experiment has confirmed the selectivity of the dyes toward intracellular RNA. Based on the obtained results, we can conclude that the investigated monomethine cyanine dyes are useful fluorescent probes for the visualization of intracellular RNA and RNA-containing organelles such as nucleoli by using fluorescence microscopy.
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Affiliation(s)
- Daria Aristova
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine.,Scientific Services Company Otava Ltd, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Viktoriia Kosach
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Svitlana Chernii
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine.,Scientific Services Company Otava Ltd, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Yuriy Slominsky
- Institute of Organic Chemistry NASU, 5 Murmans'ka St., 02094 Kyiv, Ukraine
| | - Anatoliy Balanda
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine.,Scientific Services Company Otava Ltd, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Valeriy Filonenko
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Sergiy Yarmoluk
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine.,Scientific Services Company Otava Ltd, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
| | - Alexandru Rotaru
- 'Petru Poni' Institute of Macromolecular Chemistry, Romanian Academy, Grigore Ghica Voda Alley 41A, 700487 Iasi, Romania
| | - Hülya Gizem Özkan
- Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nuremberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Andriy Mokhir
- Organic Chemistry II, Friedrich-Alexander-University of Erlangen-Nuremberg, Nikolaus-Fiebiger-Str. 10, 91058 Erlangen, Germany
| | - Vladyslava Kovalska
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine.,Scientific Services Company Otava Ltd, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
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11
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Ganguly S, Murugan NA, Ghosh D, Narayanaswamy N, Govindaraju T, Basu G. DNA Minor Groove-Induced cis- trans Isomerization of a Near-Infrared Fluorescent Probe. Biochemistry 2021; 60:2084-2097. [PMID: 34142803 DOI: 10.1021/acs.biochem.1c00281] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The discovery of small molecules that exhibit turn-on far-red or near-infrared (NIR) fluorescence upon DNA binding and understanding how they bind DNA are important for imaging and bioanalytical applications. Here we report the DNA-bound structure and the DNA binding mechanism of quinone cyanine dithiazole (QCy-DT), a recently reported AT-specific turn-on NIR fluorescent probe for double-stranded DNA. The nuclear magnetic resonance (NMR)-derived structure showed minor groove binding but no specific ligand-DNA interactions, consistent with an endothermic and entropy-driven binding mechanism deduced from isothermal titration calorimetry. Minor groove binding is typically fast because it minimally perturbs the DNA structure. However, QCy-DT exhibited unusually slow DNA binding. The cyanine-based probe is capable of cis-trans isomerization due to overlapping methine bridges, with 16 possible slowly interconverting cis/trans isomers. Using NMR, density functional theory, and free energy calculations, we show that the DNA-free and DNA-bound environments of QCy-DT prefer distinctly different isomers, indicating that the origin of the slow kinetics is a cis-trans isomerization and that the minor groove preferentially selects an otherwise unstable cis/trans isomer of QCy-DT. Flux analysis showed the conformational selection pathway to be the dominating DNA binding mechanism at low DNA concentrations, which switches to the induced fit pathway at high DNA concentrations. This report of cis/trans isomerization of a ligand, upon binding the DNA minor groove, expands the prevailing understanding of unique discriminatory powers of the minor groove and has an important bearing on using polymethine cyanine dyes to probe the kinetics of molecular interactions.
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Affiliation(s)
- Sudakshina Ganguly
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, West Bengal, India
| | - N Arul Murugan
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology, S-106 91 Stockholm, Sweden
| | - Debasis Ghosh
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Nagarjun Narayanaswamy
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Thimmaiah Govindaraju
- Bioorganic Chemistry Laboratory, New Chemistry Unit, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bengaluru 560064, Karnataka, India
| | - Gautam Basu
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VIIM, Kolkata 700054, West Bengal, India
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12
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Ryckelynck M. Development and Applications of Fluorogen/Light-Up RNA Aptamer Pairs for RNA Detection and More. Methods Mol Biol 2021; 2166:73-102. [PMID: 32710404 DOI: 10.1007/978-1-0716-0712-1_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The central role of RNA in living systems made it highly desirable to have noninvasive and sensitive technologies allowing for imaging the synthesis and the location of these molecules in living cells. This need motivated the development of small pro-fluorescent molecules called "fluorogens" that become fluorescent upon binding to genetically encodable RNAs called "light-up aptamers." Yet, the development of these fluorogen/light-up RNA pairs is a long and thorough process starting with the careful design of the fluorogen and pursued by the selection of a specific and efficient synthetic aptamer. This chapter summarizes the main design and the selection strategies used up to now prior to introducing the main pairs. Then, the vast application potential of these molecules for live-cell RNA imaging and other applications is presented and discussed.
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Affiliation(s)
- Michael Ryckelynck
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, Strasbourg, France.
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13
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Pronkin PG, Shvedova LA, Tatikolov AS. Hydrophilic meso-substituted cyanine dyes in solution and in complexes with serum albumins: spectral properties and molecular docking study. J CHEM SCI 2020. [DOI: 10.1007/s12039-020-01858-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Sato Y. Design of Fluorescent Peptide Nucleic Acid Probes Carrying Cyanine Dyes for Targeting Double-Stranded RNAs for Analytical Applications. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20190361] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai, Miyagi 980-8578, Japan
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15
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Sajid H, Ayub K, Arshad M, Mahmood T. Highly selective acridinium based cyanine dyes for the detection of DNA base pairs (adenine, cytosine, guanine and thymine). COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2019.112509] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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16
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Wicks SL, Hargrove AE. Fluorescent indicator displacement assays to identify and characterize small molecule interactions with RNA. Methods 2019; 167:3-14. [PMID: 31051253 DOI: 10.1016/j.ymeth.2019.04.018] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/25/2019] [Accepted: 04/26/2019] [Indexed: 01/15/2023] Open
Abstract
Fluorescent indicator displacement (FID) assays are an advantageous approach to convert receptors into optical sensors that can detect binding of various ligands. In particular, the identification of ligands that bind to RNA receptors has become of increasing interest as the roles of RNA in cellular processes and disease pathogenesis continue to be discovered. Small molecules have been validated as tools to elucidate unknown RNA functions, underscoring the critical need to rapidly identify and quantitatively characterize RNA:small molecule interactions for the development of chemical probes. The successful application of FID assays to evaluate interactions between diverse RNA receptors and small molecules has been facilitated by the characterization of distinct fluorescent indicators that reversibly bind RNA and modulate the fluorescence signal. The utility of RNA-based FID assays to both academia and industry has been demonstrated through numerous uses in high-throughput screening efforts, structure-activity relationship studies, and in vitro target engagement studies. Furthermore, the development, optimization, and validation of a variety of RNA-based FID assays has led to general guidelines that can be utilized for facile implementation of the method with new or underexplored RNA receptors. Altogether, the use of RNA-based FID assays as a general analysis tool has provided valuable insights into small molecule affinity and selectivity, furthering the fundamental understanding of RNA:small molecule recognition. In this review, we will summarize efforts to employ FID assays using RNA receptors and describe the significant contributions of the method towards the development of chemical probes to reveal unknown RNA functions.
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Affiliation(s)
- Sarah L Wicks
- Duke University, Department of Chemistry, Durham, NC 27705, United States
| | - Amanda E Hargrove
- Duke University, Department of Chemistry, Durham, NC 27705, United States.
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17
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Abstract
One of the important features of polymethine (cyanine) dyes is isomerization about one of C–C bonds of the polymethine chain. In this review, spectral properties of the isomers, photoisomer-ization and thermal back isomerization of carbocyanine dyes, mostly meso-substituted carbocy-anine dyes, are considered. meso-Alkyl-substituted thiacarbocyanine dyes are present in polar solvents mainly as cis isomers and, hence, exhibit no photoisomerization, whereas in nonpolar solvents, in which the dyes are in the trans form, photoisomerization takes place. In contrast, the meso-substituted dyes 3,3′-dimethyl-9-phenylthiacarbocyanine and 3,3′-diethyl-9-(2-hydroxy-4-methoxyphenyl)thiacarbocyanine occur as trans isomers and exhibit photoisomerization in both polar and nonpolar solvents. The behavior of these dyes may be ex-plained by the fact that the phenyl ring of the substituent in their molecules can be twisted at some angle, removing the substituent from the plane of the molecule and reducing its steric ef-fect on the conformation of the trans isomer. In some cases, photoisomerization of cis isomers of meso-substituted carbocyanine dyes is also observed (for some meso-alkyl-substituted dyes com-plexed with DNA and chondroitin-4-sulfate; for 3,3′-diethyl-9-methoxythiacarbocyanine in moderate polarity solvents). The cycle photoisomerization–thermal back isomerization of cya-nine dyes can be used in various systems of information storage and deserves further investiga-tion using modern research methods.
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18
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Tikhomirova AA, Tcyrulnikov NA, Wilson RM. Aerobic Oxidation of in Situ Generated Cyanine Dyes Leading to DNA Damage. Org Lett 2019; 21:1449-1452. [PMID: 30763104 DOI: 10.1021/acs.orglett.9b00194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
DNA damage induced by noncatalytic aerobic oxidation of pyridinocyanine dyes is described. The dyes are generated in situ during spontaneous oxidations of tetrakis- and bis( N-methylpyridin-4-ium)alkane salts. The mechanism of aerobic oxidation of the latter compound is proposed, and a rare direct catalyst-free transition from saturated alkane to a gem-diol is demonstrated. Thermal DNA oxidation by cyanine dyes has potential in ROS-based cancer treatment and biomedical research.
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Affiliation(s)
- Anastasiia A Tikhomirova
- Center for Photochemical Sciences and Chemistry Department , Bowling Green State University , Bowling Green , Ohio 43403 , United States
| | - Nikolai A Tcyrulnikov
- Center for Photochemical Sciences and Chemistry Department , Bowling Green State University , Bowling Green , Ohio 43403 , United States
| | - R Marshall Wilson
- Center for Photochemical Sciences and Chemistry Department , Bowling Green State University , Bowling Green , Ohio 43403 , United States
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19
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Abstract
One of the important features of polymethine (cyanine) dyes is isomerization around one of C–C bonds of the polymethine chain. In this review, spectral properties of the isomers, photoisomerization and thermal back isomerization of carbocyanine dyes, mostly meso-substituted carbocyanine dyes, are considered. meso-Alkyl-substituted thiacarbocyanine dyes are present in polar solvents mainly as cis isomers and, hence, exhibit no photoisomerization, whereas in nonpolar solvents, in which the dyes are in the trans form, photoisomerization takes place. In contrast, the meso-substituted dyes 3,3′-dimethyl-9-phenylthiacarbocyanine and 3,3′-diethyl-9-(2-hydroxy-4-methoxyphenyl)thiacarbocyanine occur as trans isomers and exhibit photoisomerization in both polar and nonpolar solvents. The behavior of these dyes may be explained by the fact that the phenyl ring of the substituent in their molecules can be twisted at some angle, removing the substituent from the plane of the molecule and reducing its steric effect on the conformation of the trans isomer. In some cases, photoisomerization of cis isomers of meso-substituted carbocyanine dyes is also observed (for some meso-alkyl-substituted dyes complexed with DNA and chondroitin-4-sulfate; for 3,3′-diethyl-9-methoxythiacarbocyanine in moderate polarity solvents). The cycle photoisomerization–thermal back isomerization of cyanine dyes can be used in various systems of information storage and deserves further investigation using modern research methods.
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20
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LUCS (Light-Up Cell System), a universal high throughput assay for homeostasis evaluation in live cells. Sci Rep 2017; 7:18069. [PMID: 29273711 PMCID: PMC5741755 DOI: 10.1038/s41598-017-18211-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 12/06/2017] [Indexed: 01/14/2023] Open
Abstract
Observations of fluorescent cyanine dye behavior under illumination at 500 nm lead to a novel concept in cell biology allowing the development of a new live cell assay called LUCS, for Light-Up Cell System, measuring homeostasis in live cells. Optimization of the LUCS process resulted in a standardized, straightforward and high throughput assay with applications in toxicity assessment. The mechanisms of the LUCS process were investigated. Electron Paramagnetic Resonance experiments showed that the singlet oxygen and hydroxyl radical are involved downstream of the light effect, presumably leading to deleterious oxidative stress that massively opens access of the dye to its intracellular target. Reversible modulation of LUCS by both verapamil and proton availability indicated that plasma membrane proton/cation antiporters, possibly of the MATE drug efflux transport family, are involved. A mechanistic model is presented. Our data show that intracellular oxidation can be controlled by tuning light energy, opening applications in regulatory purposes, anti-oxidant research, chemotherapy efficacy and dynamic phototherapy strategies.
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21
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Ihmels H, Mahmoud MM, Patrick BO. Optical differentiation between quadruplex DNA and duplex DNA with a [2.2.2]heptamethinecyanine dye. J PHYS ORG CHEM 2017. [DOI: 10.1002/poc.3736] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Heiko Ihmels
- Department of Chemistry and Biology; University of Siegen; Siegen Germany
- Center of Micro- and Nanochemistry and Engineering; University of Siegen; Siegen Germany
| | - Mohamed M.A. Mahmoud
- Department of Chemistry and Biology; University of Siegen; Siegen Germany
- Center of Micro- and Nanochemistry and Engineering; University of Siegen; Siegen Germany
| | - Brian O. Patrick
- Department of Chemistry; University of British Columbia; Vancouver Canada
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22
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Sato Y, Saito H, Aoki D, Teramae N, Nishizawa S. Lysine linkage in abasic site-binding ligand-thiazole orange conjugates for improved binding affinity to orphan nucleobases in DNA/RNA hybrids. Chem Commun (Camb) 2016; 52:14446-14449. [PMID: 27901527 DOI: 10.1039/c6cc07236d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Introduction of lysine linkage in the conjugate between abasic site-binding ligands and thiazole orange significantly improved the binding affinity for target orphan adenine or uracil nucleobase in DNA/RNA hybrids.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Hiroki Saito
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Daisuke Aoki
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Norio Teramae
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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23
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Sun W, Guo S, Hu C, Fan J, Peng X. Recent Development of Chemosensors Based on Cyanine Platforms. Chem Rev 2016; 116:7768-817. [DOI: 10.1021/acs.chemrev.6b00001] [Citation(s) in RCA: 657] [Impact Index Per Article: 82.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Wen Sun
- State Key Laboratory of Fine
Chemicals, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Shigang Guo
- State Key Laboratory of Fine
Chemicals, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Chong Hu
- State Key Laboratory of Fine
Chemicals, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Jiangli Fan
- State Key Laboratory of Fine
Chemicals, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
| | - Xiaojun Peng
- State Key Laboratory of Fine
Chemicals, Dalian University of Technology, 2 Linggong Road, 116024 Dalian, China
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24
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Zakharova GV, Konstantinov RR, Odinokov AV, Chibisov AK, Alfimov MV, Kasheverov IE, Utkin YN, Zhmak MN, Tsetlin VI. Effect of a peptide modeling the nicotinic receptor binding site on the spectral and luminescent properties of dye complexes with cucurbit[8]uril. HIGH ENERGY CHEMISTRY 2016. [DOI: 10.1134/s0018143916020090] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Chilka P, Patlolla PR, Datta B. Selective recognition of G-quadruplexes by a dimeric carbocyanine dye. RSC Adv 2016. [DOI: 10.1039/c6ra05474a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
A novel dimeric carbocyanine dye is found to recognise G-quadruplex structures selectively compared to mixed sequence or double-stranded DNA molecules.
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Affiliation(s)
- P. Chilka
- Department of Biological Engineering
- Indian Institute of Technology Gandhinagar
- Ahmedabad 382424
- India
| | - P. R. Patlolla
- Department of Chemistry
- Indian Institute of Technology Gandhinagar
- Ahmedabad 382424
- India
| | - B. Datta
- Department of Biological Engineering
- Indian Institute of Technology Gandhinagar
- Ahmedabad 382424
- India
- Department of Chemistry
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26
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Sato T, Sato Y, Iwai K, Kuge S, Nishizawa S, Teramae N. Synthetic fluorescent probes capable of selective recognition of 3'-overhanging nucleotides for siRNA delivery imaging. Chem Commun (Camb) 2015; 51:1421-4. [PMID: 25483137 DOI: 10.1039/c4cc08800j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Peptide nucleic acid (PNA)-thiazole orange (TO) conjugates are developed as fluorescent probes capable of selective recognition of 3'-overhanging nucleotides of siRNAs for an accurate analysis of the siRNA delivery process.
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Affiliation(s)
- Takaya Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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27
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Mohammed HS, Delos Santos JO, Armitage BA. Noncovalent binding and fluorogenic response of cyanine dyes to DNA homoquadruplex and PNA-DNA heteroquadruplex structures. ARTIFICIAL DNA, PNA & XNA 2014; 2:43-49. [PMID: 21912726 DOI: 10.4161/adna.2.2.16339] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Accepted: 05/10/2011] [Indexed: 12/18/2022]
Abstract
Two symmetrical cyanine dyes based on benzothiazole heterocycles and a trimethine bridge were found to bind to a parallel-stranded DNA guanine quadruplex based on the MYC oncogene promoter sequence with high nanomolar affinity and 1:1 stoichiometry. The dyes exhibited substantial fluorescence enhancements upon binding. In the presence of homologous guanine-rich peptide nucleic acid oligomers, PNA-DNA heteroquadruplexes were formed. The dyes retained their ability to bind to the heteroquadruplexes at low micromolar concentrations and with varying fluorescence enhancements, although indeterminate stoichiometries preclude quantitative comparison of the affinities with the DNA homoquadruplex precursor. The difference in fluorescence enhancement between DNA homoquadruplex and PNA-DNA heteroquadruplex allows the dyes to be used as fluorogenic indicators of hybridization in a facile method for determining PNA-DNA stoichiometry.
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Affiliation(s)
- Halimatu S Mohammed
- Department of Chemistry and Center for Nucleic Acids Science and Technology; Carnegie Mellon University; Pittsburgh, PA USA
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28
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Sato Y, Kudo M, Toriyabe Y, Kuchitsu S, Wang CX, Nishizawa S, Teramae N. Abasic site-binding ligands conjugated with cyanine dyes for “off–on” fluorescence sensing of orphan nucleobases in DNA duplexes and DNA–RNA hybrids. Chem Commun (Camb) 2014; 50:515-7. [DOI: 10.1039/c3cc47717g] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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29
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Heo JH, Cho HH, Lee JH. Surfactant-free nanoparticle–DNA complexes with ultrahigh stability against salt for environmental and biological sensing. Analyst 2014; 139:5936-44. [DOI: 10.1039/c4an01271b] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A AuNP–DNA complex highly stable in extremely high ionic strength media, such as seawater, was obtained by inserting a few thymine bases into the DNA strands.
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Affiliation(s)
- Jun Hyuk Heo
- School of Advanced Materials Science and Engineering
- Sungkyunkwan University (SKKU)
- Suwon 440-476, Republic of Korea
| | - Hui Hun Cho
- SKKU Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University (SKKU)
- Suwon 440-476, Republic of Korea
| | - Jung Heon Lee
- School of Advanced Materials Science and Engineering
- Sungkyunkwan University (SKKU)
- Suwon 440-476, Republic of Korea
- SKKU Advanced Institute of Nanotechnology (SAINT)
- Sungkyunkwan University (SKKU)
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30
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31
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Cao J, Hu C, Sun W, Xu Q, Fan J, Song F, Sun S, Peng X. The mechanism of different sensitivity of meso-substituted and unsubstituted cyanine dyes in rotation-restricted environments for biomedical imaging applications. RSC Adv 2014. [DOI: 10.1039/c3ra46612d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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32
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Cao J, Wu T, Hu C, Liu T, Sun W, Fan J, Peng X. The nature of the different environmental sensitivity of symmetrical and unsymmetrical cyanine dyes: an experimental and theoretical study. Phys Chem Chem Phys 2013; 14:13702-8. [PMID: 22968489 DOI: 10.1039/c2cp42122d] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Symmetrical and unsymmetrical cyanine dyes are used in different applications due to their different fluorogenic behaviors toward bio-macromolecules and micro-environments. In the present paper, computational studies on these dyes reveal that the potential energy of the electronic excited state is controlled by C-C bond rotational motion, which causes mainly nonradiative deactivation, according to the activation energies for the rotation. The rotations of different C-C bonds in the molecules have quite different rotational activation energies. Symmetrical dyes (Cy) possess an obviously higher rotating energy barrier as well as a larger energy gap compared to unsymmetrical dyes (TO). The C-C bond rotation close to the quinoline moiety of unsymmetrical thiazole orange (TO) allows the dye to possess the lowest energy barrier and also the lowest energy gap. This rotation plays a major role in reducing fluorescence quantum yields and providing a low fluorescent background in the free states of the unsymmetrical cyanine dyes. The results might provide a foundation for the interpretation of the behavior of the dyes and are useful for the future design of new cyanine fluorophores.
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Affiliation(s)
- Jianfang Cao
- State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian, PR China
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33
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Shank NI, Pham HH, Waggoner AS, Armitage BA. Twisted cyanines: a non-planar fluorogenic dye with superior photostability and its use in a protein-based fluoromodule. J Am Chem Soc 2012; 135:242-51. [PMID: 23252842 DOI: 10.1021/ja308629w] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The cyanine dye thiazole orange (TO) is a well-known fluorogenic stain for DNA and RNA, but this property precludes its use as an intracellular fluorescent probe for non-nucleic acid biomolecules. Further, as is the case with many cyanines, the dye suffers from low photostability. Here, we report the synthesis of a bridge-substituted version of TO named α-CN-TO, where the central methine hydrogen of TO is replaced by an electron withdrawing cyano group, which was expected to decrease the susceptibility of the dye toward singlet oxygen-mediated degradation. An X-ray crystal structure shows that α-CN-TO is twisted drastically out of plane, in contrast to TO, which crystallizes in the planar conformation. α-CN-TO retains the fluorogenic behavior of the parent dye TO in viscous glycerol/water solvent, but direct irradiation and indirect bleaching studies showed that α-CN-TO is essentially inert to visible light and singlet oxygen. In addition, the twisted conformation of α-CN-TO mitigates nonspecific binding and fluorescence activation by DNA and a previously selected TO-binding protein and exhibits low background fluorescence in HeLa cell culture. α-CN-TO was then used to select a new protein that binds and activates fluorescence from the dye. The new α-CN-TO/protein fluoromodule exhibits superior photostability to an analogous TO/protein fluoromodule. These properties indicate that α-CN-TO will be a useful fluorogenic dye in combination with specific RNA and protein binding partners for both in vitro and cell-based applications. More broadly, structural features that promote nonplanar conformations can provide an effective method for reducing nonspecific binding of cationic dyes to nucleic acids and other biomolecules.
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Affiliation(s)
- Nathaniel I Shank
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, United States
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34
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Maj M, Jeon J, Góra RW, Cho M. Induced Optical Activity of DNA-Templated Cyanine Dye Aggregates: Exciton Coupling Theory and TD-DFT Studies. J Phys Chem A 2012; 117:5909-18. [DOI: 10.1021/jp309807y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michał Maj
- Department
of Chemistry, Korea University, Seoul 136-701,
Korea
| | - Jonggu Jeon
- Department
of Chemistry, Korea University, Seoul 136-701,
Korea
| | - Robert W. Góra
- Theoretical Chemistry
Group, Institute of Physical and Theoretical Chemistry, Wrocław University of Technology, Wybrzeże
Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Minhaeng Cho
- Department
of Chemistry, Korea University, Seoul 136-701,
Korea
- Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute, Seoul 136-713, Korea
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35
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Abstract
The interactions of a triangle-shaped [2.2.2]heptamethinecyanine dye 1, namely 1,5,7-tris-[3-methylbenzothiazol-2-yl]-[2.2.2]heptamethindiium, with quadruplex DNA were studied with photometric and fluorimetric titrations, thermal DNA denaturation, CD and (1)H-NMR spectroscopy. The ligand binds to the quadruplex DNA with moderate affinity (K = 8 × 10(5) M(-1)), mainly by terminal π stacking. Remarkably, the ligand 1 exhibits a selectivity for quadruplex DNA relative to duplex DNA. Whereas the cyanine dye is very weakly fluorescent in aqueous solution, the emission intensity increases by a factor of >100 upon association with quadruplex DNA. Thus, it is shown that trinuclear cyanine derivatives may be employed as selective probes for the fluorimetric detection of quadruplex DNA.
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Affiliation(s)
- Heiko Ihmels
- University of Siegen, Organic Chemistry II, Adolf-Reichwein-Str. 2, D-57068, Siegen, Germany.
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36
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Near infrared active heptacyanine dyes with unique cancer-imaging and cytotoxic properties. Bioorg Med Chem Lett 2011; 22:1242-6. [PMID: 22177785 DOI: 10.1016/j.bmcl.2011.11.070] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 11/15/2011] [Accepted: 11/18/2011] [Indexed: 12/22/2022]
Abstract
Three near-infrared fluorescent heptacarbocyanine dyes have been synthesized using a facile one-pot synthetic approach. The reaction methodology afforded a mixture of three symmetric and unsymmetric heptacyanines containing various N-indolenine substituents, a dicarbocyclic acid (DA), a monoester (ME), and a diester (DE). These compounds were isolated, purified, characterized and biologically investigated for tumor cell cytotoxicity and uptake selectivity. Using cell viability and in vitro proliferation assays, we found that the esterified dyes (monoester, ME and diester, DE) were selectively cytotoxic to cancer cells and spared normal fibroblast cells. Additionally, confocal fluorescence imaging confirmed selective uptake of these dyes in cancer cells, thus suggesting tumor cell targeting.
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37
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Akimkin TM, Tatikolov AS, Yarmoluk SM. Spectral and fluorescent study of the interaction of cyanine dyes Cyan 2 and Cyan 45 with DNA. HIGH ENERGY CHEMISTRY 2011. [DOI: 10.1134/s0018143911030027] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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38
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Lau V, Heyne B. Calix[4]arene sulfonate as a template for forming fluorescent thiazole orange H-aggregates. Chem Commun (Camb) 2010; 46:3595-7. [PMID: 20372742 DOI: 10.1039/c002128h] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The unexpected interaction between thiazole orange (TO) and calix[4]arene sulfonate is reported herein. H-Aggregates of TO switching on their fluorescence in solution are observed. Surprisingly, fluorescence enhancement is not linked to host-guest inclusion, but rather to calix[4]arene sulfonate serving as a template for several TO molecules.
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Affiliation(s)
- Vivian Lau
- Chemistry Department, University of Calgary, 2500 University drive N.W., T2N 1N4, Calgary, Canada
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39
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Bříza T, Kejík Z, Králová J, Martásek P, Král V. Synthesis of unsymmetric cyanine dye via merocyanine and their interaction with DNA. ACTA ACUST UNITED AC 2009. [DOI: 10.1135/cccc2009034] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
An effective method has been developed for synthesis of neutral merocyanine dye 4 from (4-nitrophenyl)malondialdehyde. Merocyanine 4 was used as a basic building block for preparation of unsymmetric cyanine dyes 9 and 10, both derived from the same aromatic malondialdehyde. With the cyanine 10, pH-dependent affinity to DNA has been studied. Unsymmetric cyanine dye 10 has been compared with symmetric dye 8. The corresponding binding constants (K) have been calculated for various pH.
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