1
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Development of a Highly Selective and Sensitive Fluorescent Probe for Imaging RNA Dynamics in Live Cells. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27206927. [PMID: 36296519 PMCID: PMC9607629 DOI: 10.3390/molecules27206927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/09/2022] [Accepted: 10/11/2022] [Indexed: 11/06/2022]
Abstract
RNA imaging is of great importance for understanding its complex spatiotemporal dynamics and cellular functions. Considerable effort has been devoted to the development of small-molecule fluorescent probes for RNA imaging. However, most of the reported studies have mainly focused on improving the photostability, permeability, long emission wavelength, and compatibility with live-cell imaging of RNA probes. Less attention has been paid to the selectivity and detection limit of this class of probes. Highly selective and sensitive RNA probes are still rarely available. In this study, a new set of styryl probes were designed and synthesized, with the aim of upgrading the detection limit and maintaining the selectivity of a lead probe QUID−1 for RNA. Among these newly synthesized compounds, QUID−2 was the most promising candidate. The limit of detection (LOD) value of QUID−2 for the RNA was up to 1.8 ng/mL in solution. This property was significantly improved in comparison with that of QUID−1. Further spectroscopy and cell imaging studies demonstrated the advantages of QUID−2 over a commercially available RNA staining probe, SYTO RNASelect, for highly selective and sensitive RNA imaging. In addition, QUID−2 exhibited excellent photostability and low cytotoxicity. Using QUID−2, the global dynamics of RNA were revealed in live cells. More importantly, QUID−2 was found to be potentially applicable for detecting RNA granules in live cells. Collectively, our work provides an ideal probe for RNA imaging. We anticipate that this powerful tool may create new opportunities to investigate the underlying roles of RNA and RNA granules in live cells.
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2
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Maillard J, Rumble CA, Fürstenberg A. Red-Emitting Fluorophores as Local Water-Sensing Probes. J Phys Chem B 2021; 125:9727-9737. [PMID: 34406003 DOI: 10.1021/acs.jpcb.1c05773] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fluorescent probes are known for their ability to sense changes in their direct environment. We introduce here the idea that common red-emitting fluorophores recommended for biological labeling and typically used for simple visualization of biomolecules can also act as reporters of the water content in their first solvent sphere by a simple measurement of their fluorescence lifetime. Using fluorescence spectroscopy, we investigated the excited-state dynamics of seven commercially available fluorophores emitting between 650 and 800 nm that are efficiently quenched by H2O. The amount of H2O in their direct surrounding was modulated in homogeneous H2O-D2O mixtures or, in heterogeneous systems, by confining them into reverse micelles, by encapsulating them into host-guest complexes with cyclodextrins, or by attaching them to peptides and proteins. We found that their fluorescence properties can be rationalized in terms of the amount of H2O in their direct surroundings, which provides a general mechanism for protein-induced fluorescence enhancements of red-emitting dyes and opens perspectives for directly counting water molecules in key biological environments or in polymers.
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Affiliation(s)
| | - Christopher A Rumble
- Department of Chemistry, The Pennsylvania State University, Altoona College, 3000 Ivyside Park, Altoona, Pennsylvania 16601, United States
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3
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De Schutter E, Cappe B, Wiernicki B, Vandenabeele P, Riquet FB. Plasma membrane permeabilization following cell death: many ways to dye! Cell Death Discov 2021; 7:183. [PMID: 34282124 PMCID: PMC8289853 DOI: 10.1038/s41420-021-00545-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/13/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Elke De Schutter
- VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Center of Medical Genetics, Antwerp University Hospital, University of Antwerp, Antwerp, Edegem, Belgium
| | - Benjamin Cappe
- VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Bartosz Wiernicki
- VIB Center for Inflammation Research, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Peter Vandenabeele
- VIB Center for Inflammation Research, Ghent, Belgium. .,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
| | - Franck B Riquet
- VIB Center for Inflammation Research, Ghent, Belgium. .,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium. .,Université de Lille, Lille, France.
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4
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Zhang Q, Wu Y, Xu Q, Ma F, Zhang CY. Recent advances in biosensors for in vitro detection and in vivo imaging of DNA methylation. Biosens Bioelectron 2020; 171:112712. [PMID: 33045657 DOI: 10.1016/j.bios.2020.112712] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/25/2020] [Accepted: 10/07/2020] [Indexed: 02/08/2023]
Abstract
DNA methylation is the predominant epigenetic modification that participates in many fundamental cellular processes through posttranscriptional regulation of gene expression. Aberrant DNA methylation is closely associated with a variety of human diseases including cancers. Therefore, accurate and sensitive detection of DNA methylation may greatly facilitate the epigenetic biological researches and disease diagnosis. In recent years, a series of novel biosensors have been developed for highly sensitive detection of DNA methylation, but an overview of recent advances in biosensors for in vitro detection and especially live-cell imaging of DNA methylation is absent. In this review, we summarize the emerging biosensors for in vitro and in vivo DNA methylation assays in the past five years (2015-2020). Based on the signal types, the biosensors for in vitro DNA methylation assay are classified into five categories including fluorescent, electrochemical, colorimetric, surface enhanced Raman spectroscopy, mass spectrometry, and surface plasmon resonance biosensors, while the biosensors for in vivo DNA methylation assay mainly rely on fluorescent imaging. We review the strategies, features and applications of these biosensors, and provide a new insight into the challenges and future directions in this area.
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Affiliation(s)
- Qian Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China
| | - Yanxia Wu
- Department of Pathology and Pathological Diagnosis & Research Center, Affiliated Hospital of Guangdong Medical University, Zhanjiang, 524001, China
| | - Qinfeng Xu
- School of Food and Biological Engineering, National R&D Center for Goat Dairy Products Processing Technology, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Fei Ma
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China.
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University, Jinan, 250014, China.
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5
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Pyle JR, Piecco KWES, Vicente JR, Chen J. In Situ Sensing of Reactive Oxygen Species on Dye-Stained Single DNA Molecules under Illumination. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:11308-11314. [PMID: 31394036 PMCID: PMC6813813 DOI: 10.1021/acs.langmuir.9b01822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Reactive oxygen species (ROS) are a necessary evil in many biological systems and have been measured with fluorescent probes at the ensemble levels both in vitro and in vivo. Measuring ROS generated from a single molecule is important for mechanistic studies, yet measuring ROS near a dye-labeled single-molecule under illumination has been challenging. Here, we use CellROX, a group of ROS probes, to sense ROS near dye-stained DNA that has been flow-stretched and immobilized on a surface. ROS is responsible for the photodamage of DNA molecules under this circumstance. In this report, we confirmed the ROS sensing reaction in bulk solutions and optimized the conditions for single-molecule experiments including the selection of substrates, dye concentrations, probes in the CellROX series, excitation lasers, and emission filter-sets. We observed a correlation between ROS and the dye-labeled DNA and localized the ROS-activated CellROX probe molecules at both the ensemble level and the single-molecule level.
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Affiliation(s)
- Joseph R. Pyle
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
- Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, OH 45701, USA
| | - Kurt Waldo E. Sy Piecco
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
- Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, OH 45701, USA
- Department of Chemistry, University of the Philippines Visayas, Miagao, Iloilo 5023, Philippines
| | - Juvinch R. Vicente
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
- Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, OH 45701, USA
- Department of Chemistry, University of the Philippines Visayas, Miagao, Iloilo 5023, Philippines
| | - Jixin Chen
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
- Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, OH 45701, USA
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6
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Wang L, Pyle JR, Cimatu KA, Chen J. Ultrafast Transient Absorption Spectra of Photoexcited YOYO-1 molecules call for additional investigations of their fluorescence quenching mechanism. J Photochem Photobiol A Chem 2018; 367:411-419. [PMID: 30410276 PMCID: PMC6217845 DOI: 10.1016/j.jphotochem.2018.09.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In this report, we observed that YOYO-1 immobilized on a glass surface is much brighter when dried (quantum yield 16±4% in the ambient air) or in hexane than in water (quantum yield ~%).YOYO-1 is a typical cyanine dye that has a photo-isomerization reaction upon light illumination. In order to understand this quenching mechanism, we use femtosecond transient absorption spectroscopy to measure YOYO-1's electron dynamics after excitation directly. By deconvoluting the hot-ground-state absorption and the stimulated emission, the dynamics of electronic relaxation and balance are revealed. The results support the intermolecular charge transfer mechanism better than the intramolecular relaxation mechanism that has been widely believed before. We believe that the first step of the relaxation involves a Dexter charge transfer between the photo-excited YOYO-1 molecule and another guest molecule that is directly bound to the YOYO-1 giving two radicals with opposite signs of charges. The charges are recombined either directly between these two molecules, or both molecules start to rotate and separate from each other. Eventually, the two charges recombined non-radiatively via various pathways. These pathways are reflected on the complicated multi-exponential decay curves of YOYO-1 fluorescence lifetime measurements. This charge transfer mechanism suggests that (1) electrical insulation may help improve the quantum yield of YOYO-1 in polar solutions significantly and (2) a steric hindrance for the intramolecular rotation may have a less significant effect.
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Affiliation(s)
- Lei Wang
- Ohio University, Department of Chemistry and Biochemistry, Athens, Ohio, 45701 USA
| | - Joseph R. Pyle
- Ohio University, Department of Chemistry and Biochemistry, Athens, Ohio, 45701 USA
| | - Katherine A. Cimatu
- Ohio University, Department of Chemistry and Biochemistry, Athens, Ohio, 45701 USA
| | - Jixin Chen
- Ohio University, Department of Chemistry and Biochemistry, Athens, Ohio, 45701 USA
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7
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Pont I, González-García J, Inclán M, Reynolds M, Delgado-Pinar E, Albelda MT, Vilar R, García-España E. Aza-Macrocyclic Triphenylamine Ligands for G-Quadruplex Recognition. Chemistry 2018; 24:10850-10858. [DOI: 10.1002/chem.201802077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/14/2018] [Indexed: 12/15/2022]
Affiliation(s)
- Isabel Pont
- Department of Inorganic Chemistry, Institute of Molecular Science; University of Valencia; Catedrático José Beltran 2 46980 Paterna Spain
- Department of Chemistry; Imperial College London; London SW7 2AZ UK
| | - Jorge González-García
- Department of Inorganic Chemistry, Institute of Molecular Science; University of Valencia; Catedrático José Beltran 2 46980 Paterna Spain
- Department of Chemistry; Imperial College London; London SW7 2AZ UK
| | - Mario Inclán
- Department of Inorganic Chemistry, Institute of Molecular Science; University of Valencia; Catedrático José Beltran 2 46980 Paterna Spain
| | - Matthew Reynolds
- Department of Chemistry; Imperial College London; London SW7 2AZ UK
| | - Estefanía Delgado-Pinar
- Department of Inorganic Chemistry, Institute of Molecular Science; University of Valencia; Catedrático José Beltran 2 46980 Paterna Spain
| | - M. Teresa Albelda
- Department of Inorganic Chemistry, Institute of Molecular Science; University of Valencia; Catedrático José Beltran 2 46980 Paterna Spain
- GIBI2030, Grupo de Investigación Biomédica en Imagen, IIS La Fe; Valencia Spain
| | - Ramon Vilar
- Department of Chemistry; Imperial College London; London SW7 2AZ UK
| | - Enrique García-España
- Department of Inorganic Chemistry, Institute of Molecular Science; University of Valencia; Catedrático José Beltran 2 46980 Paterna Spain
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8
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Park CK, Hong SK, Kim YH, Cho H. Nucleic Acid-Binding Fluorochromes and Nanoparticles: Structural Aspects of Binding Affinity and Fluorescence Intensity. Macromol Res 2018. [DOI: 10.1007/s13233-018-6053-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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9
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Hori Y, Otomura N, Nishida A, Nishiura M, Umeno M, Suetake I, Kikuchi K. Synthetic-Molecule/Protein Hybrid Probe with Fluorogenic Switch for Live-Cell Imaging of DNA Methylation. J Am Chem Soc 2018; 140:1686-1690. [PMID: 29381073 DOI: 10.1021/jacs.7b09713] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Hybrid probes consisting of synthetic molecules and proteins are powerful tools for detecting biological molecules and signals in living cells. To date, most targets of the hybrid probes have been limited to pH and small analytes. Although biomacromolecules are essential to the physiological function of cells, the hybrid-probe-based approach has been scarcely employed for live-cell detection of biomacromolecules. Here, we developed a hybrid probe with a chemical switch for live-cell imaging of methylated DNA, an important macromolecule in the repression of gene expression. Using a protein labeling technique, we created a hybrid probe containing a DNA-binding fluorogen and a methylated-DNA-binding domain. The hybrid probe enhanced fluorescence intensity upon binding to methylated DNA and successfully monitored methylated DNA during mitosis. The hybrid probe offers notable advantages absent from probes based on small molecules or fluorescent proteins and is useful for live-cell analyses of epigenetic phenomena and diseases related to DNA methylation.
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Affiliation(s)
- Yuichiro Hori
- Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan.,Immunology Frontier Research Center, Osaka University , Suita, Osaka 565-0871, Japan
| | - Norimichi Otomura
- Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan
| | - Ayuko Nishida
- Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan
| | - Miyako Nishiura
- Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan
| | - Maho Umeno
- Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan
| | - Isao Suetake
- Laboratory of Epigenetics, Institute for Protein Research, Osaka University , Suita, Osaka 565-0871, Japan.,Center for Twin Research, Graduate School of Medicine, Osaka University , Suita, Osaka 565-0871, Japan.,College of Nutrition, Koshien University , Takaraduka, Hyogo 665-0006, Japan
| | - Kazuya Kikuchi
- Graduate School of Engineering, Osaka University , Suita, Osaka 565-0871, Japan.,Immunology Frontier Research Center, Osaka University , Suita, Osaka 565-0871, Japan
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10
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Patlolla PR, Mallajosyula SS, Datta B. Template-Free Self-Assembly of Dimeric Dicarbocyanine Dyes. ChemistrySelect 2017. [DOI: 10.1002/slct.201702045] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Prathap Reddy Patlolla
- Department of Chemistry; Indian Institute of Technology Gandhinagar; Palaj, Gandhinagar 382355 India, Phone: 079-2395-2073, Fax: 079-2397-2622
| | - Sairam S. Mallajosyula
- Department of Chemistry; Indian Institute of Technology Gandhinagar; Palaj, Gandhinagar 382355 India, Phone: 079-2395-2073, Fax: 079-2397-2622
| | - Bhaskar Datta
- Department of Chemistry; Indian Institute of Technology Gandhinagar; Palaj, Gandhinagar 382355 India, Phone: 079-2395-2073, Fax: 079-2397-2622
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11
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Licari G, Cwiklik L, Jungwirth P, Vauthey E. Exploring Fluorescent Dyes at Biomimetic Interfaces with Second Harmonic Generation and Molecular Dynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:3373-3383. [PMID: 28314372 DOI: 10.1021/acs.langmuir.7b00403] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
The adsorption of a DNA fluorescent probe belonging to the thiazole orange family at the dodecane/water and dodecane/phospholipid/water interfaces has been investigated using a combination of surface second harmonic generation (SSHG) and all-atomistic molecular dynamics (MD) simulations. Both approaches point to a high affinity of the cationic dye for the dodecane/water interface with a Gibbs free energy of adsorption on the order of -45 kJ/mol. Similar affinity was observed with a monolayer of negatively charged DPPG (1,2-dipalmitoyl-sn-glycero-3-phospho-rac-(1-glycerol)) lipids. On the other hand, no significant adsorption could be found with the zwitterionic DPPC (1,2-dipalmitoyl-sn-glycero-3-phosphocholine) lipids. This was rationalized in terms of Coulombic interactions between the monolayer surface and the cationic dye. The similar affinity for the interface with and without DPPG, despite the favorable Coulombic attraction in the latter case, could be explained after investigating the interfacial orientation of the dye. In the absence of a monolayer, the dye adsorbs with its molecular plane almost flat at the interface, whereas in the presence of DPPG it has to intercalate into the monolayer and adopt a significantly different orientation to benefit from the electrostatic stabilization.
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Affiliation(s)
- Giuseppe Licari
- Department of Physical Chemistry, University of Geneva , 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Lukasz Cwiklik
- J. Heyrovský Institute of Physical Chemistry, Czech Academy of Sciences , Dolejškova 2155/3, 182 23 Prague 8, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo nam. 2, 16610 Prague 6, Czech Republic
| | - Eric Vauthey
- Department of Physical Chemistry, University of Geneva , 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
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12
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Gao C, Liu SY, Zhang X, Liu YK, Qiao CD, Liu ZE. Two-photon fluorescence and fluorescence imaging of two styryl heterocyclic dyes combined with DNA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 156:1-8. [PMID: 26629954 DOI: 10.1016/j.saa.2015.11.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Revised: 11/16/2015] [Accepted: 11/18/2015] [Indexed: 06/05/2023]
Abstract
Two new styryl heterocyclic two-photon (TP) materials, 4-[4-(N-methyl)styrene]-imidazo [4,5-f][1,10] phenanthroline-benzene iodated salt (probe-1) and 4,4-[4-(N-methyl)styrene]-benzene iodated salt (probe-2) were successfully synthesized and studied as potential fluorescent probes of DNA detection. The linear and nonlinear photophysical properties of two compounds in different solvents were investigated. The absorption, one- and two-photon fluorescent spectra of the free dye and dye-DNA complex were also examined to evaluate their photophysical properties. The binding constants of dye-DNA were obtained according to Scatchard equation with good values. The results showed that two probes could be used as fluorescent DNA probes by two-photon excitation, and TP fluorescent properties of probe-1 are superior to that of probe-2. The fluorescent method date indicated that the mechanisms of dye-DNA complex interaction may be groove binding for probe-1 and electrostatic interaction for probe-2, respectively. The MTT assay experiments showed two probes are low toxicity. Moreover, the TP fluorescence imaging of DNA detection in living cells at 800 nm indicated that the ability to locate in cell nuclei of probe-1 is better than that of probe-2.
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Affiliation(s)
- Chao Gao
- School of Materials Science and Engineering, Qilu University of Technology, Jinan 250353, China; Shandong Provincial Key Laboratory of Processing and Testing Technology of Glass and Functional Ceramics, Key Laboratory of Amorphous and Polycrystalline Materials, Shandong Provincial Key Laboratory of Fine Chemicals, Qilu University of Technology, Jinan 250353, China
| | - Shu-yao Liu
- School of Materials Science and Engineering, Qilu University of Technology, Jinan 250353, China; Shandong Provincial Key Laboratory of Processing and Testing Technology of Glass and Functional Ceramics, Key Laboratory of Amorphous and Polycrystalline Materials, Shandong Provincial Key Laboratory of Fine Chemicals, Qilu University of Technology, Jinan 250353, China
| | - Xian Zhang
- School of Materials Science and Engineering, Qilu University of Technology, Jinan 250353, China; Shandong Provincial Key Laboratory of Processing and Testing Technology of Glass and Functional Ceramics, Key Laboratory of Amorphous and Polycrystalline Materials, Shandong Provincial Key Laboratory of Fine Chemicals, Qilu University of Technology, Jinan 250353, China.
| | - Ying-kai Liu
- School of Materials Science and Engineering, Qilu University of Technology, Jinan 250353, China; Shandong Provincial Key Laboratory of Processing and Testing Technology of Glass and Functional Ceramics, Key Laboratory of Amorphous and Polycrystalline Materials, Shandong Provincial Key Laboratory of Fine Chemicals, Qilu University of Technology, Jinan 250353, China
| | - Cong-de Qiao
- School of Materials Science and Engineering, Qilu University of Technology, Jinan 250353, China; Shandong Provincial Key Laboratory of Processing and Testing Technology of Glass and Functional Ceramics, Key Laboratory of Amorphous and Polycrystalline Materials, Shandong Provincial Key Laboratory of Fine Chemicals, Qilu University of Technology, Jinan 250353, China
| | - Zhao-e Liu
- Qilu Hospital of Shandong University, Jinan 250012, China
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13
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Changenet-Barret P, Gustavsson T, Markovitsi D, Manet I. Ultrafast Electron Transfer in Complexes of Doxorubicin with Human Telomeric G-Quadruplexes and GC Duplexes Probed by Femtosecond Fluorescence Spectroscopy. Chemphyschem 2016; 17:1264-72. [PMID: 26790038 DOI: 10.1002/cphc.201501091] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 01/23/2023]
Abstract
Doxorubicin (DOX) is a natural anthracycline widely used in chemotherapy; its combined application as a chemotherapeutic and photodynamic agent has been recently proposed. In this context, understanding the photoinduced properties of DOX complexes with nucleic acids is crucial. Herein, the study of photoinduced electron transfer in DOX-DNA complexes by femtosecond fluorescence spectroscopy is reported. The behaviour of complexes with two model DNA structures, a G-quadruplex (G4) formed by the human telomeric sequence (Tel21) and a d(GC) duplex, is compared. The DOX affinity for these two sequences is similar. Although both 1:1 and 2:1 stoichiometries have been reported for DOX-G4 complexes, only 1:1 complexes form with the duplex. The steady-state absorption indicates a strong binding interaction with the duplex due to drug intercalation between the GC base pairs. In contrast, the interaction of DOX with Tel21 is much weaker and arises from drug binding on the G4 external faces at two independent binding sites. As observed for DOX-d(GC) complexes, fluorescence of the drug in the first binding site of Tel21 exhibits decays within a few picoseconds following a biphasic pattern; this is attributed to the existence of two drug conformations. The fluorescence of the drug in the second binding site of Tel21 shows slower decays within 150 ps. These timescales are consistent with electron transfer from the guanines to the excited drug, as favoured by the lower oxidation potential of the stacked guanines of G4 with respect to those in the duplex.
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Affiliation(s)
- Pascale Changenet-Barret
- LIDYL, CEA, CNRS, Université Paris Saclay, F-91191, Gif-sur-Yvette, France. .,LOB, CNRS, INSERM, Université Paris Saclay, 91128, Palaiseau, France.
| | - Thomas Gustavsson
- LIDYL, CEA, CNRS, Université Paris Saclay, F-91191, Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris Saclay, F-91191, Gif-sur-Yvette, France
| | - Ilse Manet
- Istituto per la Sintesi Organica e la Fotoreattività, CNR, via P. Gobetti 101, 40129, Bologna, Italy.
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14
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Hu MH, Chen SB, Guo RJ, Ou TM, Huang ZS, Tan JH. Development of a highly sensitive fluorescent light-up probe for G-quadruplexes. Analyst 2016; 140:4616-25. [PMID: 26027520 DOI: 10.1039/c5an00761e] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
G-quadruplexes are higher-order nucleic acid structures that have attracted extensive attention because of their biological significance and potential applications in supramolecular chemistry. An ever-increasing interest in G-quadruplexes has promoted the development of selective and sensitive fluorescent probes as research tools for these structures. However, most current studies primarily focus on the improved selectivity of probes for G-quadruplexes. Their detection limits or ways to improve their detection limits are rarely described. In this study, a new set of di-substituted triarylimidazole fluorescent probes were designed and synthesized, with the aim of upgrading the detection limit of a lead triarylimidazole IZCM-1 for G-quadruplexes. Among these compounds, IZCM-7 was the most promising candidate. The limit of detection (LOD) value of IZCM-7 for the G-quadruplex was up to 3 nM in solution and up to 5 ng in a gel matrix. These values were significantly improved in comparison with those of IZCM-1. Further biophysical studies revealed that the fluorescence quantum yield and binding affinity of IZCM-7 for G-quadruplexes were markedly increased, and these two factors might be responsible for the significantly improved detection limit of IZCM-7. In addition, the sensitive and selective fluorescence performance of IZCM-7 for G-quadruplexes remained the same even in the presence of large amounts of non-G-quadruplex competitors, suggesting its promising application prospect.
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Affiliation(s)
- Ming-Hao Hu
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, 510006, China.
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15
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Berndl S, Dimitrov SD, Menacher F, Fiebig T, Wagenknecht HA. Thiazole Orange Dimers in DNA: Fluorescent Base Substitutions with Hybridization Readout. Chemistry 2016; 22:2386-95. [DOI: 10.1002/chem.201503849] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Indexed: 01/03/2023]
Affiliation(s)
- Sina Berndl
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
| | - Stoichko D. Dimitrov
- Centre for Plastic Electronics; Department of Chemistry; Imperial College London; Exhibition Road London SW7 2AZ UK
| | - Florian Menacher
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
| | - Torsten Fiebig
- Feinberg School of Medicine; Department of Otolaryngology; Northwestern University; 420 East Superior Street Chicago IL 60611 USA
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry; Karlsruhe Institute of Technology (KIT); Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Institute of Organic Chemistry; University of Regensburg; 93040 Regensburg Germany
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16
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Licari G, Brevet PF, Vauthey E. Fluorescent DNA probes at liquid/liquid interfaces studied by surface second harmonic generation. Phys Chem Chem Phys 2016; 18:2981-92. [DOI: 10.1039/c5cp06151b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The excited-state properties of oxazole yellow DNA probes change substantially when going from bulk water to the dodecane/water interface.
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Affiliation(s)
- Giuseppe Licari
- Department of Physical Chemistry
- University of Geneva
- CH-1211 Geneva 4
- Switzerland
| | - Pierre-François Brevet
- Institut Lumière Matière
- UMR CNRS 5306
- Université Claude Bernard
- Lyon 1
- Campus LyonTech – La Doua
| | - Eric Vauthey
- Department of Physical Chemistry
- University of Geneva
- CH-1211 Geneva 4
- Switzerland
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17
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Fernández-Sierra M, Quiñones E. Assays for the determination of the activity of DNA nucleases based on the fluorometric properties of the YOYO dye. Arch Biochem Biophys 2015; 570:40-6. [PMID: 25711531 DOI: 10.1016/j.abb.2015.02.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 02/10/2015] [Accepted: 02/16/2015] [Indexed: 11/25/2022]
Abstract
Here we characterize the fluorescence of the YOYO dye as a tool for studying DNA-protein interactions in real time and present two continuous YOYO-based assays for sensitively monitoring the kinetics of DNA digestion by λ-exonuclease and the endonuclease EcoRV. The described assays rely on the different fluorescence intensities between single- and double-stranded DNA-YOYO complexes, allowing straightforward determination of nuclease activity and quantitative determination of reaction products. The assays were also employed to assess the effect of single-stranded DNA-binding proteins on the λ-exonuclease reaction kinetics, showing that the extreme thermostable single-stranded DNA-binding protein (ET-SSB) significantly reduced the reaction rate, while the recombination protein A (RecA) displayed no effect.
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Affiliation(s)
- Mónica Fernández-Sierra
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, PR 00936, United States
| | - Edwin Quiñones
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, Río Piedras, PR 00936, United States.
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18
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Singh PK, Murudkar S, Mora AK, Nath S. Ultrafast torsional dynamics of Thioflavin-T in an anionic cyclodextrin cavity. J Photochem Photobiol A Chem 2015. [DOI: 10.1016/j.jphotochem.2014.10.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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19
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Chiaraviglio L, Kirby JE. Evaluation of impermeant, DNA-binding dye fluorescence as a real-time readout of eukaryotic cell toxicity in a high throughput screening format. Assay Drug Dev Technol 2015; 12:219-28. [PMID: 24831788 DOI: 10.1089/adt.2014.577] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Interpretation of high throughput screening (HTS) data in cell-based assays may be confounded by cytotoxic properties of screening compounds. Therefore, assessing cell toxicity in real time during the HTS process itself would be highly advantageous. Here, we investigate the potential of putatively impermeant, fluorescent, DNA-binding dyes to give cell toxicity readout during HTS. Amongst 19 DNA-binding dyes examined, three classes were identified that were (1) permeant, (2) cytotoxic, or (3) neither permeant nor cytotoxic during 3-day incubation with a macrophage cell line. In the last class, four dyes (SYTOX Green, CellTox Green, GelGreen, and EvaGreen) gave highly robust cytotoxicity data in 384-well screening plates. As proof of principle, successful combination with a luminescence-based assay in HTS format was demonstrated. Here, both intracellular growth of Legionella pneumophila (luminescence) and host cell viability (SYTOX Green exclusion) were assayed in the same screening well. Incorporation of membrane-impermeant, DNA-binding, fluorescent dyes in HTS assays should prove useful by allowing evaluation of cytotoxicity in real time, eliminating reagent addition steps and effort associated with endpoint cell viability analysis, and reducing the need for follow-up cytotoxicity screening.
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Affiliation(s)
- Lucius Chiaraviglio
- Department of Pathology, Beth Israel Deaconess Medical Center , Boston, Massachusetts
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20
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Xu X, Yan S, Zhou Y, Huang R, Chen Y, Wang J, Weng X, Zhou X. A novel aggregation-induced emission fluorescent probe for nucleic acid detection and its applications in cell imaging. Bioorg Med Chem Lett 2014; 24:1654-6. [DOI: 10.1016/j.bmcl.2014.02.071] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 02/19/2014] [Accepted: 02/25/2014] [Indexed: 10/25/2022]
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21
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Verma P, Pal H. Unusual H-type aggregation of coumarin-481 dye in polar organic solvents. J Phys Chem A 2013; 117:12409-18. [PMID: 24168239 DOI: 10.1021/jp409405a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Coumarin-481 (C481) dye shows intriguing time-resolved (TR) fluorescence behavior in polar organic solvents of both protic and aprotic nature, namely, ethanol (EtOH) and acetonitrile (ACN), demonstrating the presence of multiple emitting species in the solution. Following concentration-dependent and wavelength-dependent TR fluorescence measurements and the time-resolved emission spectra (TRES) and time-resolved area-normalized emission spectra (TRANES) subsequently constructed using wavelength dependent decay parameters, we convincingly conclude that in the studied solvents a part of the dissolved dye undergoes H-type of aggregation, even at a very low dye concentration. This is quite an unusual finding because the dye C481 apparently shows reasonably good solubility in these organic solvents. As the TR measurements indicate, major contribution in the fluorescence decays is due to monomeric dye, having reasonably short lifetime (∼0.64-0.68 ns), which is in accordance with the conversion of fluorescent intramolecular charge transfer (ICT) state to nonfluorescent twisted intramolecular charge transfer (TICT) state suggested for the dye in high polarity solvents, causing an efficient nonradiative deexcitation. The minor contributions arising from the aggregated dyes show its clear presence in the decays at the blue edge of the emission spectra and have relatively longer lifetimes (∼1.2-5.2 ns) because the steric hindrance caused by the stacked dyes resists the ICT to TICT conversion. Aggregation of C481 dye as observed in the present study in polar organic solvents is an intriguing finding, as the dye is a widely used fluorescent probe for various photochemical studies, where overlooking such aggregation can mislead the observed results.
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Affiliation(s)
- Poonam Verma
- Radioanalytical Chemistry Division, and ‡Radiation & Photochemistry Division, Bhabha Atomic Research Centre , Trombay, Mumbai 400 085, India
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22
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Hong Y, Chen S, Leung CWT, Lam JWY, Tang BZ. Water-Soluble Tetraphenylethene Derivatives as Fluorescent “Light-Up” Probes for Nucleic Acid Detection and Their Applications in Cell Imaging. Chem Asian J 2013; 8:1806-12. [DOI: 10.1002/asia.201300065] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2013] [Revised: 03/13/2013] [Indexed: 11/06/2022]
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23
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Kel O, Fürstenberg A, Mehanna N, Nicolas C, Laleu B, Hammarson M, Albinsson B, Lacour J, Vauthey E. Chiral Selectivity in the Binding of [4]Helicene Derivatives to Double-Stranded DNA. Chemistry 2013; 19:7173-80. [DOI: 10.1002/chem.201203915] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Indexed: 11/11/2022]
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24
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Fürstenberg A, Heilemann M. Single-molecule localization microscopy – near-molecular spatial resolution in light microscopy with photoswitchable fluorophores. Phys Chem Chem Phys 2013; 15:14919-30. [DOI: 10.1039/c3cp52289j] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Olsen S, McKenzie RH. A two-state model of twisted intramolecular charge-transfer in monomethine dyes. J Chem Phys 2012; 137:164319. [DOI: 10.1063/1.4762561] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
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26
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Lopez SG, Ruedas-Rama MJ, Casares S, Alvarez-Pez JM, Orte A. Bulk and Single-Molecule Fluorescence Studies of the Saturation of the DNA Double Helix Using YOYO-3 Intercalator Dye. J Phys Chem B 2012; 116:11561-9. [DOI: 10.1021/jp303438d] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sergio G. Lopez
- Department
of Physical Chemistry,
Faculty of Pharmacy, University of Granada, Cartuja Campus, 18071, Granada, Spain
| | - Maria J. Ruedas-Rama
- Department
of Physical Chemistry,
Faculty of Pharmacy, University of Granada, Cartuja Campus, 18071, Granada, Spain
| | - Salvador Casares
- Department of Physical Chemistry,
Faculty of Sciences, University of Granada, Fuentenueva Campus, 18071, Granada, Spain
| | - Jose M. Alvarez-Pez
- Department
of Physical Chemistry,
Faculty of Pharmacy, University of Granada, Cartuja Campus, 18071, Granada, Spain
| | - Angel Orte
- Department
of Physical Chemistry,
Faculty of Pharmacy, University of Granada, Cartuja Campus, 18071, Granada, Spain
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27
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Polymethine dyes as spectral-fluorescent probes for biomacromolecules. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY C-PHOTOCHEMISTRY REVIEWS 2012. [DOI: 10.1016/j.jphotochemrev.2011.11.001] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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28
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Is photocleavage of DNA by YOYO-1 using a synchrotron radiation light source sequence dependent? EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:1121-9. [PMID: 21931957 DOI: 10.1007/s00249-011-0739-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2011] [Revised: 07/21/2011] [Accepted: 07/26/2011] [Indexed: 10/17/2022]
Abstract
The photocleavage of double-stranded and single-stranded DNA by the fluorescent dye YOYO-1 was investigated in real time by using the synchrotron radiation light source ASTRID (ISA, Denmark) both to initiate the reaction and to monitor its progress using Couette flow linear dichroism (LD) throughout the irradiation period. The dependence of LD signals on DNA sequences and on time in the intense light beam was explored and quantified for single-stranded poly(dA), poly[(dA-dT)(2)], calf thymus DNA (ctDNA) and Micrococcus luteus DNA (mlDNA). The DNA and ligand regions of the spectrum showed different LD kinetic behaviors, and there was significant sequence dependence of the kinetics. However, in contrast to expectations from the literature, we found that poly(dA), mlDNA, low salt ctDNA and low salt poly[(dA-dT)(2)] all had significant populations of groove-bound YOYO. It seems that this mode was predominantly responsible for the catalysis of DNA cleavage. In homopolymeric DNAs, intercalated YOYO was unable to cleave DNA. In mixed-sequence DNAs the data suggest that YOYO in some but not all intercalated binding sites can cause cleavage. It is also likely that cleavage occurs at transient single-stranded regions. The reaction rates for a 100 mA beam current of 0.5-μW power varied from 0.6 h(-1) for single-stranded poly(dA) to essentially zero for low salt poly[(dG-dC)(2)] and high salt poly[(dA-dT)(2)]. At the conclusion of the experiments with each kind of DNA, uncleaved DNA with intercalated YOYO remained.
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29
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Hong Y, Xiong H, Lam J, Häußler M, Liu J, Yu Y, Zhong Y, Sung H, Williams I, Wong K, Tang B. Fluorescent Bioprobes: Structural Matching in the Docking Processes of Aggregation-Induced Emission Fluorogens on DNA Surfaces. Chemistry 2010; 16:1232-45. [DOI: 10.1002/chem.200900778] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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30
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ACHYUTHAN KE, WHITTEN DG, BRANCH DW. Supramolecular Self-Assembling Cyanine as an Alternative to Ethidium Bromide Displacement in DNA-Drug Model Interactions during High Throughput Screening. ANAL SCI 2010; 26:55-61. [DOI: 10.2116/analsci.26.55] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
| | - David G. WHITTEN
- Department of Chemical and Nuclear Engineering, University of New Mexico
| | - Darren W. BRANCH
- Biosensors and Nanomaterials Department, Sandia National Laboratories
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31
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Yang WY, Breiner B, Kovalenko SV, Ben C, Singh M, LeGrand SN, Sang QXA, Strouse GF, Copland JA, Alabugin IV. C-lysine conjugates: pH-controlled light-activated reagents for efficient double-stranded DNA cleavage with implications for cancer therapy. J Am Chem Soc 2009; 131:11458-70. [PMID: 19637922 PMCID: PMC2771568 DOI: 10.1021/ja902140m] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Double-stranded DNA cleavage of light-activated lysine conjugates is strongly enhanced at the slightly acidic pH (<7) suitable for selective targeting of cancer cells. This enhancement stems from the presence of two amino groups of different basicities. The first amino group plays an auxiliary role by enhancing solubility and affinity to DNA, whereas the second amino group, which is positioned next to the light-activated DNA cleaver, undergoes protonation at the desired pH threshold. This protonation results in two synergetic effects which account for the increased DNA-cleaving ability at the lower pH. First, lysine conjugates show tighter binding to DNA at the lower pH, which is consistent with the anticipated higher degree of interaction between two positively charged ammonium groups with the negatively charged phosphate backbone of DNA. Second, the unproductive pathway which quenches the excited state of the photocleaver through intramolecular electron transfer is eliminated once the donor amino group next to the chromophore is protonated. Experiments in the presence of traps for diffusing radicals show that reactive oxygen species do not contribute significantly to the mechanism of DNA cleavage at the lower pH, which is indicative of tighter binding to DNA under these conditions. This feature is valuable not only because many solid tumors are hypoxic but also because cleavage which does not depend on diffusing species is more localized and efficient. Sequence-selectivity experiments suggest combination of PET and base alkylation as the chemical basis for the observed DNA damage. The utility of these molecules for phototherapy of cancer is confirmed by the drastic increase in toxicity of five conjugates against cancer cell lines upon photoactivation.
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Affiliation(s)
- Wang-Yong Yang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
| | - Boris Breiner
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
| | - Serguei V. Kovalenko
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
| | - Chi Ben
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
| | - Mani Singh
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
| | - Shauna N. LeGrand
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224
| | - Qing-Xiang Amy Sang
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
| | - Geoffrey F. Strouse
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
| | - John A. Copland
- Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224
| | - Igor V. Alabugin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL 32306-4390, USA
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32
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Berndl S, Wagenknecht HA. Fluorescent color readout of DNA hybridization with thiazole orange as an artificial DNA base. Angew Chem Int Ed Engl 2009; 48:2418-21. [PMID: 19229903 DOI: 10.1002/anie.200805981] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A fluorescent chameleon: A single thiazole orange (TO) dye, when used as an artificial DNA base shows the typical green emission, whereas the interstrand TO dimer exhibits an orange excimer-type emission inside duplex DNA (see picture).
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Affiliation(s)
- Sina Berndl
- Institute for Organic Chemistry, University of Regensburg, 93040 Regensburg, Germany
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33
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Katsuda Y, Yoshikawa Y, Sato T, Saito Y, Chikuma M, Suzuki M, Yoshikawa K. Cisplatin and its analogues induce a significant change in the higher-order structure of long duplex DNA. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.03.026] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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34
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Fluoreszenz-Farbwechsel bei der DNA-Hybridisierung mit Thiazolorange als artifizieller DNA-Base. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200805981] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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35
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Hranjec M, Piantanida I, Kralj M, Suman L, Pavelić K, Karminski-Zamola G. Novel amidino-substituted thienyl- and furylvinylbenzimidazole: derivatives and their photochemical conversion into corresponding diazacyclopenta[c]fluorenes. synthesis, interactions with DNA and RNA, and antitumor evaluation. 4. J Med Chem 2008; 51:4899-910. [PMID: 18652444 DOI: 10.1021/jm8000423] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Synthesis of novel nonfused amidino-substituted thienyl- and furylvinylbenzimidazole: derivatives and their photochemical cyclization into corresponding diazacyclopenta[ c]fluorenes is described. All studied compounds showed prominent growth inhibitory effect. The fused compounds showed stronger activity than nonfused ones, whereby imidazolyl-substituted compound 11 proved to be the most active one. Besides, it induced strong G2/M arrest of the cell cycle followed by drastic apoptosis, which is in accordance with the DNA intercalative binding mode determined by the spectroscopic studies. Nonfused derivatives induced strong S phase arrest of the cell cycle followed by apoptosis that together with DNA minor groove binding mode pointed to topoisomerase I inhibition. In addition, all nonfused compounds revealed pronounced selectivity toward tumor cells in comparison with nontumor cells. On the basis of the presented results, both nonfused and fused thiophene-containing imidazolyl derivatives should be considered as promising lead compounds for further investigation.
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Affiliation(s)
- Marijana Hranjec
- Department of Organic Chemistry, Faculty of Chemical Engineering and Technology, University of Zagreb, Marulićev trg 20, P.O. Box 177, HR-10000 Zagreb, Croatia
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Hong Y, Häußler M, Lam J, Li Z, Sin K, Dong Y, Tong H, Liu J, Qin A, Renneberg R, Tang B. Label-Free Fluorescent Probing of G-Quadruplex Formation and Real-Time Monitoring of DNA Folding by a Quaternized Tetraphenylethene Salt with Aggregation-Induced Emission Characteristics. Chemistry 2008; 14:6428-37. [DOI: 10.1002/chem.200701723] [Citation(s) in RCA: 253] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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37
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Fürstenberg A, Vauthey E. Ultrafast Excited-State Dynamics of Oxazole Yellow DNA Intercalators. J Phys Chem B 2007; 111:12610-20. [DOI: 10.1021/jp073182t] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexandre Fürstenberg
- Department of Physical Chemistry of the University of Geneva, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
| | - Eric Vauthey
- Department of Physical Chemistry of the University of Geneva, 30 quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland
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38
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