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Jixin Chen - One of the best experts on this subject based on the ideXlab platform.
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Ultrafast Transient Absorption Spectra of Photoexcited YOYO-1 molecules call for additional investigations of their fluorescence quenching mechanism.
Journal of photochemistry and photobiology. A Chemistry, 2018Co-Authors: Lei Wang, Joseph R. Pyle, Katherine Cimatu, Jixin ChenAbstract: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 ∼0%). 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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Correction: Photobleaching of YOYO-1 in super-resolution single DNA fluorescence imaging.
Beilstein journal of nanotechnology, 2018Co-Authors: Joseph R. Pyle, Jixin ChenAbstract:[This corrects the article DOI: 10.3762/bjnano.8.229.].
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Photobleaching of YOYO-1 in Super-Resolution Single DNA Fluorescence Imaging
Beilstein journal of nanotechnology, 2017Co-Authors: Joseph R. Pyle, Jixin ChenAbstract: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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Charge Transfer Initializes Photoexcited YOYO-1 Intramolecular Rotation and Fluorescent Quenching
2017Co-Authors: Jixin Chen, Lei Wang, Joseph R. PyleAbstract:YOYO-1 is a commonly used cyanine dye for DNA staining that is fluorescently bright in DNA but very dim in water. The major assumption of its excited electron decay pathway is thermal relaxation via the rotation at a bridging methine that connects the two moieties of the molecule, i.e. photo-isomerization. In this report, we use femtosecond transient absorption spectroscopy to directly measure the excited electron decay, the hole refill, and the hot ground state rise and decay. The data suggest that the first step of the photo-isomerization involves a charge transfer to quench the holes and vibrational activation of the molecules to a hot ground state.
Xuguang Xi - One of the best experts on this subject based on the ideXlab platform.
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direct visualization of recq helicase dna interaction with fluorescence microscopy and atomic force microscopy
Science and Technology of Advanced Materials, 2005Co-Authors: Pengye Wang, Yaxin Jiang, Weichi Wang, Xiaohong Fang, Xuguang XiAbstract:RecQ helicase–DNA interactions were directly visualized with fluorescence microscopy. DNA–RecQ complexes formed in binding and unwinding reaction were stretched onto the hydrophobic surface by molecular combing method. The complexes can be observed with fluorescence microscope because the DNA molecules were labeled with dye molecules of YOYO-1. The DNA binding and unwinding activity of RecQ helicase leads to reduced lengths of the observed DNA molecules. More direct observations with atomic force microscopy were also made. It was seen that RecQ is mainly monomeric both in solution and after binding to DNA.
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Direct visualization of RecQ helicase–DNA interaction with fluorescence microscopy and atomic force microscopy
Science and Technology of Advanced Materials, 2005Co-Authors: Pengye Wang, Yaxin Jiang, Weichi Wang, Xiaohong Fang, Xuguang XiAbstract:RecQ helicase–DNA interactions were directly visualized with fluorescence microscopy. DNA–RecQ complexes formed in binding and unwinding reaction were stretched onto the hydrophobic surface by molecular combing method. The complexes can be observed with fluorescence microscope because the DNA molecules were labeled with dye molecules of YOYO-1. The DNA binding and unwinding activity of RecQ helicase leads to reduced lengths of the observed DNA molecules. More direct observations with atomic force microscopy were also made. It was seen that RecQ is mainly monomeric both in solution and after binding to DNA.
Jirí Velemínský - One of the best experts on this subject based on the ideXlab platform.
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DNA staining with the fluorochromes EtBr, DAPI and YOYO-1 in the comet assay with tobacco plants after treatment with ethyl methanesulphonate, hyperthermia and DNase-I.
Mutation research, 2006Co-Authors: Tomás Gichner, Anita Mukherjee, Jirí VelemínskýAbstract:We applied the alkaline version of the single-cell gel electrophoresis (comet) assay to roots and leaves of tobacco (Nicotiana tabacum var. xanthi) seedlings or isolated leaf nuclei treated with: (1) the alkylating agent ethyl methanesulphonate, (2) necrotic heat treatments at 50 degrees C, and (3) DNase-I. All three treatments induced a dose-dependent increase in DNA migration, expressed as percentage of tail DNA. A comparison of the fluorochrome DNA dyes ethidium bromide, DAPI and YOYO-1 demonstrated that for the alkaline version of the comet assay in plants, the commonly used fluorescent dye ethidium bromide can be used with the same efficiency as DAPI or YOYO-1.
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DNA staining with the fluorochromes EtBr, DAPI and YOYO-1 in the comet assay with tobacco plants after treatment with ethyl methanesulphonate, hyperthermia and DNase-I.
Mutation Research-genetic Toxicology and Environmental Mutagenesis, 2006Co-Authors: Tomás Gichner, Anita Mukherjee, Jirí VelemínskýAbstract:Abstract We applied the alkaline version of the single-cell gel electrophoresis (comet) assay to roots and leaves of tobacco (Nicotiana tabacum var. xanthi) seedlings or isolated leaf nuclei treated with: (1) the alkylating agent ethyl methanesulphonate, (2) necrotic heat treatments at 50 °C, and (3) DNase-I. All three treatments induced a dose-dependent increase in DNA migration, expressed as percentage of tail DNA. A comparison of the fluorochrome DNA dyes ethidium bromide, DAPI and YOYO-1 demonstrated that for the alkaline version of the comet assay in plants, the commonly used fluorescent dye ethidium bromide can be used with the same efficiency as DAPI or YOYO-1.
Joseph R. Pyle - One of the best experts on this subject based on the ideXlab platform.
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Ultrafast Transient Absorption Spectra of Photoexcited YOYO-1 molecules call for additional investigations of their fluorescence quenching mechanism.
Journal of photochemistry and photobiology. A Chemistry, 2018Co-Authors: Lei Wang, Joseph R. Pyle, Katherine Cimatu, Jixin ChenAbstract: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 ∼0%). 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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Correction: Photobleaching of YOYO-1 in super-resolution single DNA fluorescence imaging.
Beilstein journal of nanotechnology, 2018Co-Authors: Joseph R. Pyle, Jixin ChenAbstract:[This corrects the article DOI: 10.3762/bjnano.8.229.].
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Photobleaching of YOYO-1 in Super-Resolution Single DNA Fluorescence Imaging
Beilstein journal of nanotechnology, 2017Co-Authors: Joseph R. Pyle, Jixin ChenAbstract: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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Charge Transfer Initializes Photoexcited YOYO-1 Intramolecular Rotation and Fluorescent Quenching
2017Co-Authors: Jixin Chen, Lei Wang, Joseph R. PyleAbstract:YOYO-1 is a commonly used cyanine dye for DNA staining that is fluorescently bright in DNA but very dim in water. The major assumption of its excited electron decay pathway is thermal relaxation via the rotation at a bridging methine that connects the two moieties of the molecule, i.e. photo-isomerization. In this report, we use femtosecond transient absorption spectroscopy to directly measure the excited electron decay, the hole refill, and the hot ground state rise and decay. The data suggest that the first step of the photo-isomerization involves a charge transfer to quench the holes and vibrational activation of the molecules to a hot ground state.
Pengye Wang - One of the best experts on this subject based on the ideXlab platform.
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direct visualization of recq helicase dna interaction with fluorescence microscopy and atomic force microscopy
Science and Technology of Advanced Materials, 2005Co-Authors: Pengye Wang, Yaxin Jiang, Weichi Wang, Xiaohong Fang, Xuguang XiAbstract:RecQ helicase–DNA interactions were directly visualized with fluorescence microscopy. DNA–RecQ complexes formed in binding and unwinding reaction were stretched onto the hydrophobic surface by molecular combing method. The complexes can be observed with fluorescence microscope because the DNA molecules were labeled with dye molecules of YOYO-1. The DNA binding and unwinding activity of RecQ helicase leads to reduced lengths of the observed DNA molecules. More direct observations with atomic force microscopy were also made. It was seen that RecQ is mainly monomeric both in solution and after binding to DNA.
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Direct visualization of RecQ helicase–DNA interaction with fluorescence microscopy and atomic force microscopy
Science and Technology of Advanced Materials, 2005Co-Authors: Pengye Wang, Yaxin Jiang, Weichi Wang, Xiaohong Fang, Xuguang XiAbstract:RecQ helicase–DNA interactions were directly visualized with fluorescence microscopy. DNA–RecQ complexes formed in binding and unwinding reaction were stretched onto the hydrophobic surface by molecular combing method. The complexes can be observed with fluorescence microscope because the DNA molecules were labeled with dye molecules of YOYO-1. The DNA binding and unwinding activity of RecQ helicase leads to reduced lengths of the observed DNA molecules. More direct observations with atomic force microscopy were also made. It was seen that RecQ is mainly monomeric both in solution and after binding to DNA.