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Yoshikawa K. Quantitative evaluation of DNA double-strand breaks (DSBs) through single-molecule observation. Enzymes 2022; 51:7-27. [PMID: 36336410 DOI: 10.1016/bs.enz.2022.08.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
By adapting the method of single molecular observation for individual DNAs, it will be shown that reliable analysis of double-strand breaks, DSBs, becomes possible for various kinds of damage sources. Single DNA above the size of several-tens kilo base-pairs exhibits the length scale above several μm, indicating that their whole conformation is visible with fluorescence microscopy by adding suitable fluoresce dye to the solution. Various examples of the quantitative evaluation on DSBs are described, together with the evaluation of the protective effects of anti-oxidants.
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Affiliation(s)
- Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, Japan; Center for Integrative Medicine and Physics, Institute for Advanced Study, Kyoto University, Kyoto, Japan.
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2
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Fu F, Liao K, Liu Z, Hong D, Yang H, Tian Y, Wei W, Liu C, Li S, Ma J, Li W. Controlled Fluorescence Enhancement of DNA-Binding Dye Through Chain Length Match between Oligoguanine and TOTO. J Phys Chem B 2021; 125:518-527. [PMID: 33426891 DOI: 10.1021/acs.jpcb.0c09611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Fluorescent DNA-binding dyes are extensively employed as probe and biosensing in biological detection and imaging. Experiments and theoretical calculations of thiazole orange homodimeric (TOTO) dye binding to a single-strand DNA (ssDNA), poly(dG)n (n = 2, 4, 6, 8), reveal that the n = 6 complex shows about 300-fold stronger fluorescence than n = 2, 4 and a slightly stronger one than n = 8 complexes, which is benefited from the length match between TOTO and poly(dG)6. The machine learning, based on molecular dynamics trajectories, indicates that TOTO is featured by the dihedral angle along its backbone and its end-to-end distance, in which the latter one defines the stretch and hairpin structures of TOTO, respectively. The time-dependent density functional theory calculations on the low-lying excited states show that the stretched TOTO with π-π end-stacking binding mode can bring about strong fluorescence with localized π-π* transitions. For the n = 2, 4, and 8 complexes, the linear scaling quantum mechanics calculations indicate that the dominant hairpin TOTO with intercalative binding modes have relatively larger binding energies, leading to fluorescence quenching by intramolecular charge transfer. Our results may provide an insight for modulating the DNA-dye binding modes to tune the degree of charge transfer and designing fluorescent probes for the recognition of specific DNA sequences.
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Affiliation(s)
- Fangjia Fu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Kang Liao
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Ziteng Liu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Daocheng Hong
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Haitang Yang
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Yuxi Tian
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Wei Wei
- Jiangsu Engineering Laboratory of Smart Carbon-Rich Materials and Device, Jiangsu Province Hi-Tech Key Laboratory for Bio-medical Research, School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Chungen Liu
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Shuhua Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Jing Ma
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Wei Li
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210023, P. R. China
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3
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Detection of phospholipase A 2 in serum based on LRET mechanism between upconversion nanoparticles and SYBR green I. Anal Chim Acta 2020; 1143:37-44. [PMID: 33384128 DOI: 10.1016/j.aca.2020.11.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 11/18/2020] [Accepted: 11/20/2020] [Indexed: 02/01/2023]
Abstract
Phospholipase A2 (PLA2) may be a vital biomarker for the prediction and diagnosis of some diseases. Consequently, it is of great significance to quantitatively detect PLA2 in biologic samples. Herein, on the basis of the principle of luminescence resonance energy transfer (LRET) between upconversion nanoparticles (UCNPs) and SYBR Green I (SG), we proposed a technology for the highly sensitive detection of PLA2 amount. Therein, as an energy receptor, SG will be quantitatively loaded into liposomes firstly. Then, due to the hydrolysis of liposomes under the catalysis of PLA2, SG will be released and inserted into the double-stranded DNA (dsDNA) on the surface of UCNPs, which triggers the LRET because of the shortening of effective spatial distance between UCNPs and SG. Under exciting of NIR light, UCNPs emit luminescence at 476 nm, which makes SG emit fluorescence at 522 nm through LRET. Under optimal conditions, the emission intensity ratio (I522 nm/I476 nm) increased linearly with the PLA2 amount in the range of 20 U/L to 400 U/L, and the limit of detection (LOD) reached 15 U/L. Here, after comparing with the clinical standard method, it is found that the biosensor is expected to provide a convenient and sensitive assay for the detection of PLA2 in actual serum samples. Furthermore, such biosensor can also be used to test the inhibitor of PLA2.
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Ahoulou EO, Drinkard KK, Basnet K, St. Lorenz A, Taratula O, Henary M, Grant KB. DNA Photocleavage in the Near-Infrared Wavelength Range by 2-Quinolinium Dicarbocyanine Dyes. Molecules 2020; 25:molecules25122926. [PMID: 32630496 PMCID: PMC7355653 DOI: 10.3390/molecules25122926] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/19/2020] [Accepted: 06/22/2020] [Indexed: 12/21/2022] Open
Abstract
Here, we report the syntheses of two pentamethine cyanine dyes containing quinolinium rings and substituted with either hydrogen (3) or bromine (4) at the meso carbon. The electron withdrawing bromine atom stabilizes dye 4 in aqueous buffer, allowing complex formation to occur between the dye and double-helical DNA. UV–visible, CD, and fluorescence spectra recorded at low DNA concentrations suggest that dye 4 initially binds to the DNA as a high-order aggregate. As the ratio of DNA to dye is increased, the aggregate is converted to monomeric and other low-order dye forms that interact with DNA in a non-intercalative fashion. The brominated dye 4 is relatively unreactive in the dark, but, under 707–759 nm illumination, generates hydroxyl radicals that cleave DNA in high yield (pH 7.0, 22 °C). Dye 4 is also taken up by ES2 ovarian carcinoma cells, where it is non-toxic under dark conditions. Upon irradiation of the ES2 cells at 694 nm, the brominated cyanine reduces cell viability from 100 ± 10% to 14 ± 1%. Our results suggest that 2-quinolinium-based carbocyanine dyes equipped with stabilizing electron withdrawing groups may have the potential to serve as sensitizing agents in long-wavelength phototherapeutic applications.
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Affiliation(s)
- Effibe O. Ahoulou
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
| | - Kaitlyn K. Drinkard
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
| | - Kanchan Basnet
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
| | - Anna St. Lorenz
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR 97201, USA; (A.S.L.); (O.T.)
| | - Oleh Taratula
- Department of Pharmaceutical Sciences, College of Pharmacy, Oregon State University, Portland, OR 97201, USA; (A.S.L.); (O.T.)
| | - Maged Henary
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
- Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
- Correspondence: (M.H.); (K.B.G.); Tel.: +1-404-413-5566 (M.H.); +1-404-413-5522 (K.B.G.)
| | - Kathryn B. Grant
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; (E.O.A.); (K.K.D.); (K.B.)
- Correspondence: (M.H.); (K.B.G.); Tel.: +1-404-413-5566 (M.H.); +1-404-413-5522 (K.B.G.)
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5
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Shen R, Jia Y, Mak PI, Martins RP. Clip-to-release on amplification (CRoA): a novel DNA amplification enhancer on and off microfluidics. LAB ON A CHIP 2020; 20:1928-1938. [PMID: 32352133 DOI: 10.1039/d0lc00318b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Despite its high sensitivity, low cost, and high efficiency as a DNA amplification indicator with a yes/no answer, dsDNA-binding dye encounters incompatibility when used in microfluidic systems, resulting in problems such as false negative amplification results. Besides, its inhibition of amplification at high concentrations hinders its application both on-chip and off-chip. In this study, we propose a novel DNA amplification enhancer to counteract the drawbacks of dsDNA-binding dyes. It acts as a temporary reservoir for the free-floating dyes in solution and releases them on demand during the amplification process. Through this clip-to-release on amplification mechanism, the enhancer lowered the background fluorescence of sample droplets before amplification, enhanced the signal-to-background ratio of positive samples, and eliminated the false negative signal of on-chip PCR. Moreover, the enhancer increased the off-chip polymerase chain reaction (PCR) efficiency, boosted the fluorescence signal up to 10-fold, and made less nonspecific amplification product. All the factors affecting the enhancer's performance are investigated in detail, including its structure and concentration, and the types of dsDNA-binding dye used in the reaction. Finally, we demonstrated the broad application of the proposed amplification enhancer in various DNA amplification systems, for various genes, and on various amplification platforms. It would reignite the utilization of dsDNA dyes for wider applications in DNA analysis both on-chip and off-chip.
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Affiliation(s)
- Ren Shen
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China. and Faculty of Science and Technology - ECE, University of Macau, Macau, China
| | - Yanwei Jia
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China. and Faculty of Science and Technology - ECE, University of Macau, Macau, China and Faculty of Health Sciences, University of Macau, Macau, China
| | - Pui-In Mak
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China. and Faculty of Science and Technology - ECE, University of Macau, Macau, China
| | - Rui P Martins
- State-Key Laboratory of Analog and Mixed-Signal VLSI, Institute of Microelectronics, University of Macau, Macau, China. and Faculty of Science and Technology - ECE, University of Macau, Macau, China and On Leave from Instituto Superior Técnico, Universidade de Lisboa, Portugal
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6
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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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7
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Park G, Chakkarapani SK, Ju S, Ahn S, Kang SH. Super-resolution morphological dissemination of intercalating dye in single DNA molecules via binding activated localization microscopy. CHINESE CHEM LETT 2018. [DOI: 10.1016/j.cclet.2017.08.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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8
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Zhang S, Li J, Wei J, Yin M. Perylenediimide chromophore as an efficient photothermal agent for cancer therapy. Sci Bull (Beijing) 2018; 63:101-107. [PMID: 36658921 DOI: 10.1016/j.scib.2017.12.015] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Revised: 11/24/2017] [Accepted: 11/24/2017] [Indexed: 01/21/2023]
Abstract
Photothermal agents with improved bioavailabilities can generate heat from near-infrared light, which has been efficiently used for in vivo photothermal therapy (PTT) for cancer, with minimum tissue invasion. Strategies for developing organic near-infrared-absorbing molecules for photothermal cancer therapy have drawn intensive attention among academic investigators. However, conventional organic near-infrared-absorbing molecules may not only have complex synthesis procedures, but also easily suffer from photobleaching under light irradiation. These drawbacks might lead to an increase in the synthesis cost, and elicit a risk of side effects in PTT. Thus, it is essential to devise an organic photothermal agent with stable photothermal capacity, which involves a facile synthesis process. In this study, incorporating a secondary amine group (donor) in the bay regions of perylenediimides (PDIs) could lead to a 150-nm bathochromic shift of the absorption maximum. Next, a modification of poly(ethylene glycol) (PEG) at the periphery of the chromophore renders the targeted macromolecule PDI-PEG highly water-soluble, and capable of intense absorption in the near-infrared region. The self-assembled PDI-based nanoparticles (PDI-NPs) have a size of 55 nm in aqueous solutions. PDI-NPs with excellent photostability possess a high photothermal conversion efficiency of up to 43% ± 2%. Finally, PDI-NPs allow for efficient in vitro and in vivo photothermal cancer therapy. Meanwhile, PDI-NPs exhibit quite low cytotoxicity and no biotoxicity on major organs in vivo. Thus, these easily-manufactured PDI-NPs can serve as extremely stable photothermal agents for efficient photothermal cancer therapy.
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Affiliation(s)
- Shaobo Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jianhao Li
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jie Wei
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China
| | - Meizhen Yin
- State Key Laboratory of Chemical Resource Engineering, Beijing Laboratory of Biomedical Materials, Beijing University of Chemical Technology, Beijing 100029, China.
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9
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Pyle JR, Chen J. Photobleaching of YOYO-1 in super-resolution single DNA fluorescence imaging. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2017; 8:2296-2306. [PMID: 29181286 PMCID: PMC5687005 DOI: 10.3762/bjnano.8.229] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 10/05/2017] [Indexed: 06/07/2023]
Abstract
Super-resolution imaging of single DNA molecules via point accumulation for imaging in nanoscale topography (PAINT) has great potential to visualize fine DNA structures with nanometer resolution. In a typical PAINT video acquisition, dye molecules (YOYO-1) in solution sparsely bind to the target surfaces (DNA) whose locations can be mathematically determined by fitting their fluorescent point spread function. Many YOYO-1 molecules intercalate into DNA and remain there during imaging, and most of them have to be temporarily or permanently fluorescently bleached, often stochastically, to allow for the visualization of a few fluorescent events per DNA per frame of the video. Thus, controlling the fluorescence on-off rate is important in PAINT. In this paper, we study the photobleaching of YOYO-1 and its correlation with the quality of the PAINT images. At a low excitation laser power density, the photobleaching of YOYO-1 is too slow and a minimum required power density was identified, which can be theoretically predicted with the proposed method in this report.
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Affiliation(s)
- Joseph R Pyle
- Department of Chemistry and Biochemistry, Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, Ohio 45701, USA
| | - Jixin Chen
- Department of Chemistry and Biochemistry, Nanoscale and Quantum Phenomena Institute, Ohio University, Athens, Ohio 45701, USA
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10
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Noda M, Ma Y, Yoshikawa Y, Imanaka T, Mori T, Furuta M, Tsuruyama T, Yoshikawa K. A single-molecule assessment of the protective effect of DMSO against DNA double-strand breaks induced by photo-and γ-ray-irradiation, and freezing. Sci Rep 2017; 7:8557. [PMID: 28819291 PMCID: PMC5561226 DOI: 10.1038/s41598-017-08894-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 07/14/2017] [Indexed: 11/09/2022] Open
Abstract
Dimethyl sulfoxide (DMSO) is widely used as a cryoprotectant for organs, tissues, and cell suspension in storage. In addition, DMSO is known to be a useful free radical scavenger and a radio-protectant. To date, many in vitro assays using cultured cells have been performed for analysing the protective effect of DMSO against genomic DNA damage; however, currently it has been rather difficult to detect DNA double strand breaks (DSBs) in a quantitative manner. In the present study, we aimed to observe the extent of DNA damage by use of single molecular observation with a fluorescence microscope to evaluate DSBs induced by photo- and γ-ray-irradiation, or freeze/thawing in variable concentrations of DMSO. As a result, we found that 2% DMSO conferred the maximum protective effect against all of the injury sources tested, and these effects were maintained at higher concentrations. Further, DMSO showed a significantly higher protective effect against freezing-induced damage than against photo- and γ-ray-irradiation-induced damage. Our study provides significant data for the optimization of DNA cryopreservation with DMSO, as well as for the usage of DNA as the protective agent against the injuries caused by active oxygen and radiations.
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Affiliation(s)
- Masami Noda
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0321, Japan
| | - Yue Ma
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0321, Japan
| | - Yuko Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0321, Japan
| | - Tadayuki Imanaka
- Research Organization of Science and Technology, Ritsumeikan University, Shiga, 525-8577, Japan
| | - Toshiaki Mori
- Graduate School of Engineering, Department of Quantum and Radiation Technology, Osaka Prefecture University, Osaka, 599-8570, Japan
| | - Masakazu Furuta
- Graduate School of Engineering, Department of Quantum and Radiation Technology, Osaka Prefecture University, Osaka, 599-8570, Japan
| | - Tatsuaki Tsuruyama
- Drug Discovery and Medicine, Department of Pathology, Graduate School of Medicine, Kyoto University, Kyoto, 606-8501, Japan
| | - Kenichi Yoshikawa
- Faculty of Life and Medical Sciences, Doshisha University, Kyoto, 610-0321, Japan.
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11
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Maschmann A, Kounovsky-Shafer KL. Determination of restriction enzyme activity when cutting DNA labeled with the TOTO dye family. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2017; 36:406-417. [PMID: 28362164 DOI: 10.1080/15257770.2017.1300665] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Optical mapping, a single DNA molecule genome analysis platform that can determine methylation profiles, uses fluorescently labeled DNA molecules that are elongated on the surface and digested with a restriction enzyme to produce a barcode of that molecule. Understanding how the cyanine fluorochromes affect enzyme activity can lead to other fluorochromes used in the optical mapping system. The effects of restriction digestion on fluorochrome labeled DNA (Ethidium Bromide, DAPI, H33258, EthD-1, TOTO-1) have been analyzed previously. However, TOTO-1 is a part of a family of cyanine fluorochromes (YOYO-1, TOTO-1, BOBO-1, POPO-1, YOYO-3, TOTO-3, BOBO-3, and POPO-3) and the rest of the fluorochromes have not been examined in terms of their effects on restriction digestion. In order to determine if the other dyes in the TOTO-1 family inhibit restriction enzymes in the same way as TOTO-1, lambda DNA was stained with a dye from the TOTO family and digested. The restriction enzyme activity in regards to each dye, as well as each restriction enzyme, was compared to determine the extent of digestion. YOYO-1, TOTO-1, and POPO-1 fluorochromes inhibited ScaI-HF, PmlI, and EcoRI restriction enzymes. Additionally, the mobility of labeled DNA fragments in an agarose gel changed depending on which dye was intercalated.
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Affiliation(s)
- April Maschmann
- a Department of Chemistry , University of Nebraska-Kearney , Kearney , NE , USA
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12
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Ma Y, Cui Z, He Z, Li W, Zhang Z, Zhang X, Zhang XE, Tan T. Delaying Photobleaching of a Light-Switch Complex for Real-Time Imaging of Single Viral Particle Uncoating. Anal Chem 2016; 88:10675-10679. [DOI: 10.1021/acs.analchem.6b03127] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Yingxin Ma
- Beijing Key Lab
of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People’s Republic of China
- State Key Laboratory
of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, People’s Republic of China
| | - Zongqiang Cui
- State Key Laboratory
of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, People’s Republic of China
| | - Zhike He
- Key Laboratory
of Analytical Chemistry for Biology and Medicine, Ministry of Education,
College of Chemistry and Sciences, Wuhan University, Wuhan, Hubei 430072, People’s Republic of China
| | - Wei Li
- State Key Laboratory
of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, People’s Republic of China
| | - Zhiping Zhang
- State Key Laboratory
of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, People’s Republic of China
| | - Xiaowei Zhang
- State Key Laboratory
of Virology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, People’s Republic of China
| | - Xian-En Zhang
- National
Laboratory
of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Tianwei Tan
- Beijing Key Lab
of Bioprocess, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, People’s Republic of China
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13
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Guan L, Li A, Song Y, Yan M, Gao D, Zhang X, Li B, Wang L. Nonplanar Monocyanines: Meso-Substituted Thiazole Orange with High Photostability and Their Synthetic Strategy as well as a Cell Association Study. J Org Chem 2016; 81:6303-13. [DOI: 10.1021/acs.joc.6b00928] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Li Guan
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry,
Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, People’s Republic of China
| | - Anyang Li
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry,
Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, People’s Republic of China
| | - Yinyin Song
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry,
Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, People’s Republic of China
| | - Mengqi Yan
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry,
Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, People’s Republic of China
| | - Dengfeng Gao
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry,
Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, People’s Republic of China
| | - Xianghan Zhang
- School
of Life Sciences and Technology, Xidian University, Xi’an 710071, People’s Republic of China
| | - Bin Li
- Key
Laboratory of Resource Biology and Biotechnology in Western China,
Ministry of Education, Northwest University, Xi’an 710069, People’s Republic of China
| | - Lanying Wang
- Key
Laboratory of Synthetic and Natural Functional Molecule Chemistry,
Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, People’s Republic of China
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14
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Chen Y, Guan R, Zhang C, Huang J, Ji L, Chao H. Two-photon luminescent metal complexes for bioimaging and cancer phototherapy. Coord Chem Rev 2016. [DOI: 10.1016/j.ccr.2015.09.010] [Citation(s) in RCA: 146] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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15
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Huang JQ, Cai ZB, Jin F, Li SL, Tian YP. A new series of two-photon blue/violet fluorescent trans-alkenes: Green synthesis and optical properties. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 154:164-170. [PMID: 26520477 DOI: 10.1016/j.saa.2015.10.034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 08/19/2015] [Accepted: 10/22/2015] [Indexed: 06/05/2023]
Abstract
A new series of trans-alkenes (3a-3e) containing different electron-donating groups were synthesized by the solvent-free Horner-Wadsworth-Emmons reaction, and characterized by infrared, hydrogen nuclear magnetic resonance, mass spectrometry and elemental analysis. Their UV-visible absorption, one-photon excited fluorescence, two-photon absorption, and two-photon excited fluorescence were systematically investigated in different solvents. Experimental results show different trends in linear and nonlinear optical properties with different donor units. 3a with triphenylamine donor exhibits the best optical properties. It emits strong blue up-converted fluorescence, and the two-photon absorption cross-section can be as large as 218 GM in DCM.
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Affiliation(s)
- Jiu-Qiang Huang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Zhi-Bin Cai
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Fan Jin
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, PR China
| | - Sheng-Li Li
- Department of Chemistry, Anhui Province Key Laboratory of Functional Inorganic Materials, Anhui University, Hefei 230039, PR China
| | - Yu-Peng Tian
- Department of Chemistry, Anhui Province Key Laboratory of Functional Inorganic Materials, Anhui University, Hefei 230039, PR China
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16
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Rombouts K, Braeckmans K, Remaut K. Fluorescent Labeling of Plasmid DNA and mRNA: Gains and Losses of Current Labeling Strategies. Bioconjug Chem 2015; 27:280-97. [PMID: 26670733 DOI: 10.1021/acs.bioconjchem.5b00579] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Live-cell imaging has provided the life sciences with insights into the cell biology and dynamics. Fluorescent labeling of target molecules proves to be indispensable in this regard. In this Review, we focus on the current fluorescent labeling strategies for nucleic acids, and in particular mRNA (mRNA) and plasmid DNA (pDNA), which are of interest to a broad range of scientific fields. By giving a background of the available techniques and an evaluation of the pros and cons, we try to supply scientists with all the information needed to come to an informed choice of nucleic acid labeling strategy aimed at their particular needs.
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Affiliation(s)
- K Rombouts
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Braeckmans
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
| | - K Remaut
- Laboratory of general biochemistry and physical pharmacy, Faculty of pharmacy and ‡Centre for Nano- and Biophotonics, Ghent University , Ghent 9000, Belgium
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17
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Kabatc J, Jurek K, Kostrzewska K, Orzeł Ł. Hemicyanine dyes derived from 2,3,3-trimethyl-3H-indolium as candidates for non-covalent protein probes. J Pharm Biomed Anal 2015; 114:433-40. [DOI: 10.1016/j.jpba.2015.06.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2015] [Revised: 06/11/2015] [Accepted: 06/17/2015] [Indexed: 10/23/2022]
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18
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Moradpour Hafshejani S, Watson SMD, Tuite EM, Pike AR. Click Modification of Diazido Acridine Intercalators: A Versatile Route towards Decorated DNA Nanostructures. Chemistry 2015. [DOI: 10.1002/chem.201501836] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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19
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The fluorescence properties and binding mechanism of SYTOX green, a bright, low photo-damage DNA intercalating agent. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2015; 44:337-48. [PMID: 26024786 DOI: 10.1007/s00249-015-1027-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Revised: 04/05/2015] [Accepted: 04/08/2015] [Indexed: 10/23/2022]
Abstract
DNA intercalators are widely used in cancer therapeutics, to probe protein-DNA interactions and to investigate the statistical-mechanical properties of DNA. Here, we employ single-molecule fluorescence microscopy, magnetic tweezers, and ensemble-binding assays to investigate the fluorescence properties and binding mechanism of SYTOX green, a DNA labeling dye previously used for staining dead cells and becoming of common use for single-molecule methodologies. Specifically, we show that SYTOX green presents several advantages with respect to other dyes: (1) binds DNA rapidly and with high affinity; (2) has a good signal-to-noise ratio even at low concentrations; (3) exhibits a low photobleaching rate; and (4) induces lower light-induced DNA degradation. Finally, we show that SYTOX green is a DNA intercalator that binds DNA cooperatively with a binding site of 3.5 bp, increasing the DNA length upon binding by 43%, while not affecting its mechanical properties.
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Kabatc J, Jurek K, Orzeł Ł. New N-(carboxyethyl)-2-methylbenzothiazole-based hemicyanine dyes: Synthesis, spectra, photostability and association with bovine serum albumin. J Mol Struct 2015. [DOI: 10.1016/j.molstruc.2014.12.032] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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21
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Kim D, Ryu HG, Ahn KH. Recent development of two-photon fluorescent probes for bioimaging. Org Biomol Chem 2014; 12:4550-66. [DOI: 10.1039/c4ob00431k] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Fluorescent probes are essential tools for studying biological systems.
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Affiliation(s)
- Dokyoung Kim
- Department of Chemistry and Center for Electro-Photo Behaviors in Advanced Molecular Systems
- Gyungbuk, Korea 790-784
| | - Hye Gun Ryu
- Department of Chemistry and Center for Electro-Photo Behaviors in Advanced Molecular Systems
- Gyungbuk, Korea 790-784
| | - Kyo Han Ahn
- Department of Chemistry and Center for Electro-Photo Behaviors in Advanced Molecular Systems
- Gyungbuk, Korea 790-784
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22
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Oxidative cleavage of DNA by pentamethine carbocyanine dyes irradiated with long-wavelength visible light. Bioorg Med Chem Lett 2013; 24:214-9. [PMID: 24332091 DOI: 10.1016/j.bmcl.2013.11.035] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Revised: 11/14/2013] [Accepted: 11/15/2013] [Indexed: 12/26/2022]
Abstract
Here we report the synthesis of seven symmetrical carbocyanine dyes in which two nitrogen-substituted benz[e]indolium rings are joined by a pentamethine bridge that is meso-substituted with chlorine or bromine versus hydrogen. The heteroatom of benz[e]indolium is modified with a phenylpropyl, methyl, or cationic quaternary ammonium group. In reactions containing micro molar concentrations of halogenated dye, irradiation at 575, 588, 623, or 700nm produces good photocleavage of plasmid DNA. UV-visible spectra show that the carbocyanines are in their H-aggregated and monomeric forms. Scavenger experiments point to the involvement of singlet oxygen and hydroxyl radicals in DNA photocleavage.
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Selective G-quadruplex DNA recognition by a new class of designed cyanines. Molecules 2013; 18:13588-607. [PMID: 24192912 PMCID: PMC4457452 DOI: 10.3390/molecules181113588] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Revised: 10/26/2013] [Accepted: 10/29/2013] [Indexed: 12/15/2022] Open
Abstract
A variety of cyanines provide versatile and sensitive agents acting as DNA stains and sensors and have been structurally modified to bind in the DNA minor groove in a sequence dependent manner. Similarly, we are developing a new set of cyanines that have been designed to achieve highly selective binding to DNA G-quadruplexes with much weaker binding to DNA duplexes. A systematic set of structurally analogous trimethine cyanines has been synthesized and evaluated for quadruplex targeting. The results reveal that elevated quadruplex binding and specificity are highly sensitive to the polymethine chain length, heterocyclic structure and intrinsic charge of the compound. Biophysical experiments show that the compounds display significant selectivity for quadruplex binding with a higher preference for parallel stranded quadruplexes, such as cMYC. NMR studies revealed the primary binding through an end-stacking mode and SPR studies showed the strongest compounds have primary KD values below 100 nM that are nearly 100-fold weaker for duplexes. The high selectivity of these newly designed trimethine cyanines for quadruplexes as well as their ability to discriminate between different quadruplexes are extremely promising features to develop them as novel probes for targeting quadruplexes in vivo.
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Yasui T, Motoyama K, Kaji N, Tokeshi M, Baba Y. Enzyme-catalysed reaction for long-term fluorescent observation of single DNA molecules. RSC Adv 2013. [DOI: 10.1039/c3ra22999h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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25
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Schoen I, Ries J, Klotzsch E, Ewers H, Vogel V. Binding-activated localization microscopy of DNA structures. NANO LETTERS 2011; 11:4008-11. [PMID: 21838238 DOI: 10.1021/nl2025954] [Citation(s) in RCA: 130] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Many nucleic acid stains show a strong fluorescence enhancement upon binding to double-stranded DNA. Here we exploit this property to perform superresolution microscopy based on the localization of individual binding events. The dynamic labeling scheme and the optimization of fluorophore brightness yielded a resolution of ∼14 nm (fwhm) and a spatial sampling of 1/nm. We illustrate our approach with two different DNA-binding dyes and apply it to visualize the organization of the bacterial chromosome in fixed Escherichia coli cells. In general, the principle of binding-activated localization microscopy (BALM) can be extended to other dyes and targets such as protein structures.
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Affiliation(s)
- Ingmar Schoen
- Laboratory for Biologically Oriented Materials, ETH Zurich, Zurich, Switzerland.
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26
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Persson F, Bingen P, Staudt T, Engelhardt J, Tegenfeldt JO, Hell SW. Fluorescence nanoscopy of single DNA molecules by using stimulated emission depletion (STED). Angew Chem Int Ed Engl 2011; 50:5581-3. [PMID: 21557413 PMCID: PMC3229986 DOI: 10.1002/anie.201100371] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2011] [Indexed: 11/29/2022]
Affiliation(s)
- F Persson
- Department of Physics, University of GothenburgFysikgränd 3, 412 96 Gothenburg (Sweden)
| | - P Bingen
- Optical Nanoscopy Division, German Cancer Research Center (DKFZ)Im Neuenheimer Feld 280, 69120 Heidelberg (Germany), Fax: (+49) 6221-54-51210
| | - T Staudt
- Optical Nanoscopy Division, German Cancer Research Center (DKFZ)Im Neuenheimer Feld 280, 69120 Heidelberg (Germany), Fax: (+49) 6221-54-51210
| | - J Engelhardt
- Optical Nanoscopy Division, German Cancer Research Center (DKFZ)Im Neuenheimer Feld 280, 69120 Heidelberg (Germany), Fax: (+49) 6221-54-51210
| | - J O Tegenfeldt
- Department of Physics, University of GothenburgFysikgränd 3, 412 96 Gothenburg (Sweden)
| | - Stefan W Hell
- Optical Nanoscopy Division, German Cancer Research Center (DKFZ)Im Neuenheimer Feld 280, 69120 Heidelberg (Germany), Fax: (+49) 6221-54-51210
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27
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Persson F, Bingen P, Staudt T, Engelhardt J, Tegenfeldt JO, Hell SW. Fluoreszenznanoskopie einzelner DNA-Moleküle mit Fluoreszenzverhinderung durch stimulierte Emission (STED). Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201100371] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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28
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Flors C. DNA and chromatin imaging with super-resolution fluorescence microscopy based on single-molecule localization. Biopolymers 2010; 95:290-7. [PMID: 21184489 DOI: 10.1002/bip.21574] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2010] [Revised: 11/25/2010] [Accepted: 12/06/2010] [Indexed: 12/12/2022]
Abstract
With the expansion of super-resolution fluorescence microscopy methods, it is now possible to access the organization of cells and materials at the nanoscale by optical means. This review discusses recent progress in super-resolution imaging of isolated and cell DNA using single-molecule localization methods. A high labeling density of photoswitchable fluorophores is crucial for these techniques, which can be provided by sequence independent DNA stains in which photoblinking reactions can be induced. In particular, unsymmetrical cyanine intercalating dyes in combination with special buffers can be used to image isolated DNA with a spatial resolution of 30-40 nm. For super-resolution imaging of chromatin, cell permeant cyanine dyes that bind the minor groove of DNA have the potential to become a useful alternative to the labeling of histones and other DNA-associated proteins. Other recent developments that are interesting in this context such as high density labeling methods or new DNA probes with photoswitching functionalities are also surveyed. Progress in labeling, optics, and single-molecule localization algorithms is being rapid, and it is likely to provide real insight into DNA structuring in cells and materials.
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Affiliation(s)
- Cristina Flors
- School of Chemistry and Collaborative Optical Spectroscopy, Micromanipulation and Imaging Center (COSMIC), University of Edinburgh, Joseph Black Building, The King's Buildings, West Mains Road, EH9 3JJ Edinburgh, UK.
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29
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Yoshikawa Y, Mori T, Suzuki M, Imanaka T, Yoshikawa K. Comparative study of kinetics on DNA double-strand break induced by photo- and gamma-irradiation: Protective effect of water-soluble flavonoids. Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.11.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Flors C. Photoswitching of monomeric and dimeric DNA-intercalating cyanine dyes for super-resolution microscopy applications. Photochem Photobiol Sci 2010; 9:643-8. [DOI: 10.1039/b9pp00119k] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Flors C, Ravarani CNJ, Dryden DTF. Super-Resolution Imaging of DNA Labelled with Intercalating Dyes. Chemphyschem 2009; 10:2201-4. [DOI: 10.1002/cphc.200900384] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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32
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Ozhalici-Unal H, Armitage BA. Fluorescent DNA nanotags based on a self-assembled DNA tetrahedron. ACS NANO 2009; 3:425-433. [PMID: 19236081 DOI: 10.1021/nn800727x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Progress in fluorescence detection and imaging technologies depends on the availability of fluorescent labels with strong light absorption/emission characteristics. We have synthesized intercalator dye arrays on a compact 3-dimensional DNA-tetrahedron nanostructure. The template tolerates the structural distortions introduced by intercalation and allows concentration of multiple fluorophores within a small volume, resulting in brightly fluorescent nanotags with effective extinction coefficients in the order of 10(6) M(-1) cm(-1). Efficient energy transfer from intercalated donor dyes to covalently attached acceptor dyes in the nanotags allows the emission wavelength to be shifted to the red relative to the excitation light, providing wavelength tunability. The compact nature of the supramolecular DNA tetrahedron also provides a protective medium for the fluorophores, leading to improved photostability and enhanced resistance to nuclease digestion, relative to one- or two-dimensional nanotags described previously.
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Affiliation(s)
- Hayriye Ozhalici-Unal
- Department of Chemistry and Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, USA
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33
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Fürstenberg A, Deligeorgiev TG, Gadjev NI, Vasilev AA, Vauthey E. Structure-fluorescence contrast relationship in cyanine DNA intercalators: toward rational dye design. Chemistry 2008; 13:8600-9. [PMID: 17642070 DOI: 10.1002/chem.200700665] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The fluorescence enhancement mechanisms of a series of DNA stains of the oxazole yellow (YO) family have been investigated in detail using steady-state and ultrafast time-resolved fluorescence spectroscopy. The strong increase in the fluorescence quantum yield of these dyes upon DNA binding is shown to originate from the inhibition of two distinct processes: 1) isomerisation through large-amplitude motion that non-radiatively deactivates the excited state within a few picoseconds and 2) formation of weakly emitting H-dimers. As the H-dimers are not totally non-fluorescent, their formation is less efficient than isomerisation as a fluorescent contrast mechanism. The propensity of the dyes to form H-dimers and thus to reduce their fluorescence contrast upon DNA binding is shown to depend on several of their structural parameters, such as their monomeric (YO) or homodimeric (YOYO) nature, their substitution and their electric charge. Moreover, these parameters also have a substantial influence on the affinity of the dyes for DNA and on the ensuing sensitivity for DNA detection. The results give new insight into the development and optimisation of fluorescent DNA probes with the highest contrast.
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Affiliation(s)
- Alexandre Fürstenberg
- Physical Chemistry Department, University of Geneva, Quai Ernest-Ansermet 30, 1211 Genève 4, Switzerland
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Ohulchanskyy TY, Gannon MK, Ye M, Skripchenko A, Wagner SJ, Prasad PN, Detty MR. “Switched-On” Flexible Chalcogenopyrylium Photosensitizers. Changes in Photophysical Properties upon Binding to DNA. J Phys Chem B 2007; 111:9686-92. [PMID: 17645329 DOI: 10.1021/jp073270d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
2,4-Bis(4-dimethylaminophenyl)-6-alkylthiopyrylium and selenopyrylium dyes are essentially nonfluorescent (phi F < 0.001) and are poor generators of singlet oxygen in aqueous solution. However, upon complexation to calf thymus DNA, quantum yields for both fluorescence and generation of singlet oxygen increased dramatically. Irradiation of the dye-DNA complexes produced strand breaks in the DNA. The photodamage is not observed in the absence of oxygen and is suppressed by the addition of the singlet oxygen quencher imidazole. The inactivation of the pseudo-rabies virus upon treatment of oxygenated leukodepleted 20% hematocrit red blood cell suspensions with the chalcogenopyrylium dyes and light followed the same trend observed with quantum yields for the generation of singlet oxygen in the dye-DNA complexes.
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Affiliation(s)
- Tymish Y Ohulchanskyy
- Institute for Lasers, Photonics, and Biophotonics, Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, USA
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35
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Bowen BP, Enderlein J, Woodbury NW. Single-molecule Fluorescence Spectroscopy of TOTO on Poly-AT and Poly-GC DNA¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2003)0780576sfsoto2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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36
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Gaigalas AK, Wang L, Vogt RF. Frequency-domain Measurement of the PhotodegradationProcess of Fluorescein¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2002)0760022fdmotp2.0.co2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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37
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Silva GL, Ediz V, Yaron D, Armitage BA. Experimental and computational investigation of unsymmetrical cyanine dyes: understanding torsionally responsive fluorogenic dyes. J Am Chem Soc 2007; 129:5710-8. [PMID: 17411048 PMCID: PMC2535610 DOI: 10.1021/ja070025z] [Citation(s) in RCA: 136] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Unsymmetrical cyanine dyes are widely used in biomolecular detection due to their fluorogenic behavior, whereby fluorescence quantum yields can be very low in fluid solution but are significantly enhanced in conformationally restricted environments. Herein we describe a series of fluorinated analogues of the dye thiazole orange that exhibit improved fluorescence quantum yields and photostabilities. In addition, computational studies on these dyes revealed that twisting about the monomethine bridge beyond an interplanar angle of 60 degrees leads to a dark state that decays nonradiatively to the ground state, accounting for the observed fluorogenic behavior. The effects of position and number of fluorine substituents correlate with both observed quantum yield and calculated activation energy for twisting beyond this critical angle.
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Affiliation(s)
- Gloria L Silva
- Department of Chemistry, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213, USA
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38
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Allain C, Schmidt F, Lartia R, Bordeau G, Fiorini-Debuisschert C, Charra F, Tauc P, Teulade-Fichou MP. Vinyl-Pyridinium Triphenylamines: Novel Far-Red Emitters with High Photostability and Two-Photon Absorption Properties for Staining DNA. Chembiochem 2007; 8:424-33. [PMID: 17279593 DOI: 10.1002/cbic.200600483] [Citation(s) in RCA: 106] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A series of mono-, bis- and trisvinyl-pyridinium triphenylamines (TP-py) has been synthesised and evaluated for its one- and two-photon absorption (2PA) induced-fluorescence properties under biological conditions. Interestingly, these compounds are only weakly fluorescent in water, whereas their fluorescence emissions are strongly restored (exaltation factors of 20-100) upon binding to double-stranded DNA. Additional measurements in glycerol indicate that the fluorescence increases are the result of immobilisation of the dyes in the DNA matrix, which inhibits rotational de-excitation modes. This particular feature is especially remarkable in the case of the bis and tris derivatives (TP-2 py, TP-3 py), which each display a high affinity (K(d) ~ microM) for dsDNA. TPIF measurements have shown that TP-2 py and TP-3 py each have a large 2PA cross section (delta up to 700 GM) both in glycerol and in the presence of DNA, which ranks them amongst the best 2PA biological fluorophores. Finally, one- and two-photon confocal imaging in cells revealed that these compounds perform red staining (lambda(em)=660-680 nm) of nuclear DNA with excellent contrast. The remarkable optical properties of the TP-py series, combined with their high photostability and their easy synthetic access, make these compounds extremely attractive for use in confocal and 2PA microscopy.
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Affiliation(s)
- Clémence Allain
- Institut Curie UMR 176, Centre Universitaire, Bâtiment 110, 91405 Orsay, France
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Jia K, Wan Y, Xia A, Li S, Gong F, Yang G. Characterization of Photoinduced Isomerization and Intersystem Crossing of the Cyanine Dye Cy3. J Phys Chem A 2007; 111:1593-7. [PMID: 17295461 DOI: 10.1021/jp067843i] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several important photophysical properties of the cyanine dye Cy3 have been determined by laser flash photolysis. The triplet-state absorption and photoisomerization of Cy3 are distinguished by using the heavy-atom effects and oxygen-induced triplet --> triplet energy transfer. Furthermore, the triplet-state extinction coefficient and quantum yield of Cy3 are also measured via triplet-triplet energy-transfer method and comparative actinometry, respectively. It is found that the triplet --> triplet (T1-->Tn) absorptions of trans-Cy3 largely overlap the ground-state absorption of cis-Cy3. Unlike what occurred in Cy5, we have not observed the triplet-state T1-->Tn absorption of cis-Cy3 and the phosphorescence from triplet state of cis-Cy3 following a singlet excitation (S0-S1) of trans-Cy3, indicating the absence of a lowest cis-triplet state as an isomerization intermediate upon excitation in Cy3. The detailed spectra of Cy3 reported in this paper could help us interpret the complicated photophysics of cyanine dyes.
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Affiliation(s)
- Ke Jia
- The State Key Laboratory of Molecular Reaction Dynamics, and Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing-100080, P. R. China
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40
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Cole KD, Gaigalas A, Akerman B. Single-molecule measurements of trapped and migrating circular DNA during electrophoresis in agarose gels. Electrophoresis 2006; 27:4396-407. [PMID: 17117465 DOI: 10.1002/elps.200600347] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The effect of agarose gel concentration and field strength on the electrophoretic trapping of open (relaxed) circular DNA was investigated using microscopic measurements of individual molecules stained with a fluorescent dye. Three open circles with sizes of 52.5, 115, and 220 kbp were trapped by the electric field (6 V/cm) and found to be predominately fixed and stretched at a single point in the gel. The length of the stretched circles did not significantly change with agarose concentration of the gels (mass fractions of 0.0025, 0.01, and 0.02). The relaxation kinetics of the trapped circles was also measured in the gels. The relaxation of the large open circles was found to be a slow process, taking several seconds. The velocity and average length of the 52.5 kbp open circles and 48.5 kbp linear DNA were measured during electrophoresis in the agarose gels. The velocity increased when the agarose concentrations were lowered, but the average length of the open-circle DNA (during electrophoresis) did not significantly change with agarose gel concentrations. The circles move through the gels by cycles of stretching and relaxation during electrophoresis. Linear dichroism was also used to investigate the trapping and alignment of the 52.5 kbp open circles. The results in this study provide information that can be used to improve electrophoretic separations of circular DNA, an important form of genetic material and commonly used to clone DNA.
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Affiliation(s)
- Kenneth D Cole
- National Institute of Standards and Technology, Gaithersburg, MD, USA.
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41
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Tomlinson JT, Park G, Misenheimer JA, Kucera GL, Hesp K, Manderville RA. Photoinduced Cytotoxicity and Thioadduct Formation by a Prodigiosin Analogue. Org Lett 2006; 8:4951-4. [PMID: 17020344 DOI: 10.1021/ol061998r] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
[reaction: see text] The prodigiosin alkaloid 1 and the synthetic analogue 2 show photoinduced cytotoxicity against HL-60 cancer cells. Photoirradiation of 1 and 2 causes photofading, photooxidation, and thioadduct formation. These results provide a model for the redox properties of prodigiosins that play a role in their biological activity and provide a new way to functionalize their pyrromethene entity with water-soluble thiol groups.
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Affiliation(s)
- John T Tomlinson
- Department of Chemistry, Wake Forest University, Winston-Salem, North Carolina 27109-7486, USA
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42
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Guillo C, Ferrance JP, Landers JP. Use of a capillary electrophoresis instrument with laser-induced fluorescence detection for DNA quantitation. J Chromatogr A 2006; 1113:239-43. [PMID: 16483583 DOI: 10.1016/j.chroma.2006.01.111] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2005] [Revised: 12/29/2005] [Accepted: 01/25/2006] [Indexed: 11/26/2022]
Abstract
Highly selective and sensitive assays are required for detection and quantitation of the small masses of DNA typically encountered in clinical and forensic settings. High detection sensitivity is achieved using fluorescent labeling dyes and detection techniques such as spectrofluorometers, microplate readers and cytometers. This work describes the use of a laser-induced fluorescence (LIF) detector in conjunction with a commercial capillary electrophoresis instrument for DNA quantitation. PicoGreen and YO-PRO-1, two fluorescent DNA labeling dyes, were used to assess the potential of the system for routine DNA analysis. Linearity, reproducibility, sensitivity, limits of detection and quantitation, and sample stability were examined for the two assays. The LIF detector response was found to be linear (R2 > 0.999) and reproducible (RSD < 9%) in both cases. The PicoGreen assay displayed lower limits of detection and quantitation (20 pg and 60 pg, respectively) than the YO-PRO-1 assay (60 pg and 260 pg, respectively). Although a small variation in fluorescence was observed for the DNA/dye complexes over time, quantitation was not significantly affected and the solutions were found to be relatively stable for 80 min. The advantages of the technique include a 4- to 40-fold reduction in the volume of sample required compared to traditional assays, a 2- to 20-fold reduction in the volume of reagents consumed, fast and automated analysis, and low cost (no specific instrumentation required).
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Affiliation(s)
- Christelle Guillo
- Department of Chemistry, University of Virginia, Charlottesville, VA 22904, USA
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43
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Huang Z, Ji D, Wang S, Xia A, Koberling F, Patting M, Erdmann R. Spectral Identification of Specific Photophysics of Cy5 by Means of Ensemble and Single Molecule Measurements. J Phys Chem A 2005; 110:45-50. [PMID: 16392838 DOI: 10.1021/jp0562936] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The triplet-state characteristics of the Cy5 molecule related to trans-cis isomerization are investigated by means of ensemble and single molecule measurements. Cy5 has been used frequently in the past 10 years in single molecule spectroscopic applications, e.g., as a probe or fluorescence resonance energy transfer acceptor in large biomolecules. However, the unknown spectral properties of the triplet state and the lack of knowledge on the photoisomerization do not allow us to interpret precisely the unexpected single molecule behaviors. This limits the application of Cy5. The laser photolysis experiments demonstrate that the trans triplet state of Cy5 absorbs about 625 nm, the cis ground state absorbs about 690 nm, and the cis triplet state also absorbs about 690 nm. In other words, the T1-Tn absorptions largely overlap the ground-state absorptions for both trans and cis isomers, respectively. Furthermore, the observation of the cis triplet state indicates an important isomerization pathway from the trans-S1 state to the cis-T1 state upon excitation. The detailed spectra presented in this article let us clearly interpret the exact mechanisms responsible for several important and unexpected photophysical behaviors of single Cy5 molecules such as reverse intersystem crossing (RISC), the observation of dim states with a lower emission intensity and slightly red-shifted fluorescence, and unusual energy transfer from donor molecules to dark Cy5 molecules acting as acceptors in single molecule fluorescence resonance energy transfer (FRET) measurements. Spectral results show that the dim state in the single molecule fluorescence intensity time traces originated from cis-Cy5 because of a lower excitation rate, resulting from the red-shifted ground-state absorption of cis-Cy5 compared to that of the trans-Cy5.
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Affiliation(s)
- Zhengxi Huang
- State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100080, People's Republic of China
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44
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Yoshikawa Y, Hizume K, Oda Y, Takeyasu K, Araki S, Yoshikawa K. Protective effect of vitamin C against double-strand breaks in reconstituted chromatin visualized by single-molecule observation. Biophys J 2005; 90:993-9. [PMID: 16284271 PMCID: PMC1367124 DOI: 10.1529/biophysj.105.069963] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Direct attack to genomic DNA by reactive oxygen species causes various types of lesions, including base modifications and strand breaks. The most significant lesion is considered to be an unrepaired double-strand break that can lead to fatal cell damage. We directly observed double-strand breaks of DNA in reconstituted chromatin stained by a fluorescent cyanine dye, YOYO (quinolinium, 1,1'-[1,3- propanediylbis[(dimethyliminio)-3,1- propanediyl]]bis[4-[(3-methyl-2(3H)-benzoxazolylidene)methyl]]-, tetraiodide), in solution, where YOYO is known to have the ability to photo-cleave DNAs by generating reactive oxygen species. Reconstituted chromatin was assembled from large circular DNA (106 kbp) with core histone proteins. We also investigated the effect of vitamin C (ascorbic acid) on preventing photo-induced double-strand breaks in a quantitative manner. We found that DNA is protected against double-strand breaks by the addition of ascorbic acid, and this protective effect is dose dependent. The effective kinetic constant of the breakage reaction in the presence of 5 mM ascorbic acid is 20 times lower than that in the absence of ascorbic acid. This protective effect of ascorbic acid in reconstituted chromatin is discussed in relation to the highly compacted polynucleosomal structure. The results highlight the fact that single-molecule observation is a useful tool for studying double-strand breaks in giant DNA and chromatin.
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Affiliation(s)
- Yuko Yoshikawa
- Department of Food and Nutrition, Nagoya Bunri College, Nagoya 451-0077, Japan.
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45
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Huang Z, Ji D, Xia A, Koberling F, Patting M, Erdmann R. Direct Observation of Delayed Fluorescence from a Remarkable Back-Isomerization in Cy5. J Am Chem Soc 2005; 127:8064-6. [PMID: 15926831 DOI: 10.1021/ja050050+] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The direct observations of delayed fluorescence and phosphorescence from the cyanine dye Cy5 are reported. The delayed fluorescence is generated from the S(1) state of trans-Cy5 through a reserve intersystem crossing from the cis-triplet state T(1) to the trans-singlet state S(1) via thermal activation. The lowest cis-triplet state is evidenced to be involved in the formation of the isomer. The back-isomerization from cis-triplet state to trans-singlet state crossing, a remarkably back-isomerization pathway that has not been reported before, plays a significant role in this unusual delayed fluorescence.
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Affiliation(s)
- Zhengxi Huang
- State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, P. R. China
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46
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SUZUTO M, OHNISHI H, HIRAKAWA Y, MASUJIMA T. Manipulation of a Single DNA Molecule under the Pin-Fiber Video Scope. BUNSEKI KAGAKU 2005. [DOI: 10.2116/bunsekikagaku.54.455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Masashi SUZUTO
- Graduate School of Biomedical Sciences, Hiroshima University
| | - Hitoshi OHNISHI
- Graduate School of Biomedical Sciences, Hiroshima University
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47
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Renikuntla BR, Rose HC, Eldo J, Waggoner AS, Armitage BA. Improved photostability and fluorescence properties through polyfluorination of a cyanine dye. Org Lett 2004; 6:909-12. [PMID: 15012062 DOI: 10.1021/ol036081w] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
[structure: see text] A polyfluorinated cyanine dye has been synthesized and characterized. Compared with the nonfluorinated analogue, the dye exhibits significantly reduced aggregation in aqueous media, enhanced fluorescence quantum yield, greater resistance to photobleaching upon direct irradiation, and reduced reactivity toward singlet oxygen. All of these properties are favorable for use of cyanine dyes as fluorescent labels and point toward fluorination as a general strategy for improving performance in imaging applications.
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Affiliation(s)
- Babu Rao Renikuntla
- Department of Chemistry, Molecular Biosensor and Imaging Center, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213-3890, USA
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48
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Ling L, Jiang Y, Wang C, Fang X, Wan L, He Z, Bai C, Chen D. Delaying photobleaching and recovering luminescence of a DNA molecular light switch in DNA analysis. Anal Biochem 2004; 329:334-6. [PMID: 15158495 DOI: 10.1016/j.ab.2004.02.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2003] [Indexed: 11/29/2022]
Affiliation(s)
- Liansheng Ling
- Center of Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100080, People's Republic of China
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49
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Yoshikawa Y, Suzuki M, Yamada N, Yoshikawa K. Double-strand break of giant DNA: protection by glucosyl-hesperidin as evidenced through direct observation on individual DNA molecules. FEBS Lett 2004; 566:39-42. [PMID: 15147865 DOI: 10.1016/j.febslet.2004.04.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2004] [Revised: 04/06/2004] [Accepted: 04/06/2004] [Indexed: 11/19/2022]
Abstract
We have performed a real-time observation of photo-induced breakage on individual long DNA molecules stained by a cyanine dye, YOYO, under the intense illumination (lambda=450-490 nm) in solution. It was shown that the double-strand breakage is accelerated by Fenton's reagent (Fe2+/H2O2). In addition, it was found that the breakage reaction is protected in the presence of a water-soluble flavonoid, glucosyl-hesperidin. To interpret the kinetic process of the double-strand breakage reaction, a two-step mechanism is proposed: under light illumination on giant DNA molecules, single-strand breaks are generated to induce nicks in a stochastic manner, and then reactive oxygen attacks these nicks causing the double-strand break.
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Affiliation(s)
- Yuko Yoshikawa
- Department of Food and Nutrition, Nagoya Bunri College, Nagoya 451-0077, Japan.
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50
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Bowen BP, Enderlein J, Woodbury NW. Single-molecule fluorescence spectroscopy of TOTO on poly-AT and poly-GC DNA. Photochem Photobiol 2004; 78:576-81. [PMID: 14743865 DOI: 10.1562/0031-8655(2003)078<0576:sfsoto>2.0.co;2] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Excited state lifetime and amplitude measurements were made on thiazole orange dimer (TOTO), a dimeric DNA-intercalating fluorophore, at single-molecule concentrations. As expected from previous study, the excited state lifetime of TOTO intercalated in DNA is dependent on the sequence of the double-stranded DNA, having values of 2.2 ns in poly-GC DNA and 1.8 ns in poly-AT DNA. The distribution of excited state lifetimes of single molecules of TOTO intercalated into oligonucleotides having varying proportions of poly-GC sequences relative to poly-AT sequences were analyzed as a function of the fraction of poly-GC. By using excited state lifetime distributions from the purely GC and purely AT oligonucleotides as a basis set, it was possible to estimate the GC content of oligonucleotides with intermediate GC composition to within a few percent error. This serves as a model for the analysis of equilibrium binding distributions in DNA using single-molecule methods.
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Affiliation(s)
- Benjamin P Bowen
- Department of Chemical and Materials Engineering, Arizona State University, Tempe, AZ 85287, USA.
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