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Gustavsson T, Markovitsi D. The Ubiquity of High-Energy Nanosecond Fluorescence in DNA Duplexes. J Phys Chem Lett 2023; 14:2141-2147. [PMID: 36802626 DOI: 10.1021/acs.jpclett.2c03884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
During the past few years, several studies reported that a significant part of the intrinsic fluorescence of DNA duplexes decays with surprisingly long lifetimes (1-3 ns) at wavelengths shorter than the ππ* emission of their monomeric constituents. This high-energy nanosecond emission (HENE), hardly discernible in the steady-state fluorescence spectra of most duplexes, was investigated by time-correlated single-photon counting. The ubiquity of HENE contrasts with the paradigm that the longest-lived excited states correspond to low-energy excimers/exciplexes. Interestingly, the latter were found to decay faster than the HENE. So far, the excited states responsible for HENE remain elusive. In order to foster future studies for their characterization, this Perspective presents a critical summary of the experimental observations and the first theoretical approaches. Moreover, some new directions for further work are outlined. Finally, the obvious need for computations of the fluorescence anisotropy considering the dynamic conformational landscape of duplexes is stressed.
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Affiliation(s)
- Thomas Gustavsson
- Université Paris-Saclay, CEA, CNRS, LIDYL, 91191 Gif-sur-Yvette, France
| | - Dimitra Markovitsi
- Université Paris-Saclay, CNRS, Institut de Chimie Physique, UMR8000, 91405 Orsay, France
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2
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Reveguk ZV, Khoroshilov EV, Sharkov AV, Pomogaev VA, Buglak AA, Tarnovsky AN, Kononov AI. Exciton Absorption and Luminescence in i-Motif DNA. Sci Rep 2019; 9:15988. [PMID: 31690734 PMCID: PMC6831829 DOI: 10.1038/s41598-019-52242-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 08/17/2019] [Indexed: 11/08/2022] Open
Abstract
We have studied the excited-state dynamics for the i-motif form of cytosine chains (dC)10, using the ultrafast fluorescence up-conversion technique. We have also calculated vertical electronic transition energies and determined the nature of the corresponding excited states in a model tetramer i-motif structure. Quantum chemical calculations of the excitation spectrum of a tetramer i-motif structure predict a significant (0.3 eV) red shift of the lowest-energy transition in the i-motif form relative to its absorption maximum, which agrees with the experimental absorption spectrum. The lowest excitonic state in i-(dC)10 is responsible for a 2 ps red-shifted emission at 370 nm observed in the decay-associated spectra obtained on the femtosecond time-scale. This delocalized (excitonic) excited state is likely a precursor to a long-lived excimer state observed in previous studies. Another fast 310 fs component at 330 nm is assigned to a monomer-like locally excited state. Both emissive states form within less than the available time resolution of the instrument (100 fs). This work contributes to the understanding of excited-state dynamics of DNA within the first few picoseconds, which is the most interesting time range with respect to unraveling the photodamage mechanism, including the formation of the most dangerous DNA lesions such as cyclobutane pyrimidine dimers.
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Affiliation(s)
- Zakhar V Reveguk
- Department of Molecular Biophysics and Polymer Physics, Saint-Petersburg State University, 199034, St. Petersburg, Russia
| | - Evgeny V Khoroshilov
- P.N. Lebedev Physical Institute, Russian Academy of Sciences, 53 Leninsky Pr., 119991, Moscow, Russia
| | - Andrey V Sharkov
- P.N. Lebedev Physical Institute, Russian Academy of Sciences, 53 Leninsky Pr., 119991, Moscow, Russia
| | - Vladimir A Pomogaev
- Department of Physics, Tomsk State University, Tomsk, 634050, Russia
- Department of Chemistry and Green-Nano Materials Research Center, College of Natural Sciences, Kyungpook National University 1370 Sankyuk-dong, Buk-gu, Daegu, 702-701, Republic of Korea
| | - Andrey A Buglak
- Department of Molecular Biophysics and Polymer Physics, Saint-Petersburg State University, 199034, St. Petersburg, Russia
| | - Alexander N Tarnovsky
- Department of Chemistry and the Center for Photochemical Sciences, Bowling Green State University, Bowling Green, OH, USA
| | - Alexei I Kononov
- Department of Molecular Biophysics and Polymer Physics, Saint-Petersburg State University, 199034, St. Petersburg, Russia.
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3
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Ma C, Chan RCT, Chan CTL, Wong AKW, Chung BPY, Kwok WM. Fluorescence and Ultrafast Fluorescence Unveil the Formation, Folding Molecularity, and Excitation Dynamics of Homo-Oligomeric and Human Telomeric i-Motifs at Acidic and Neutral pH. Chem Asian J 2018; 13:3706-3717. [PMID: 30230251 DOI: 10.1002/asia.201801117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 08/28/2018] [Indexed: 01/07/2023]
Abstract
i-Motifs are tetraplex DNAs known to be stable at acidic pH. The structure of i-motifs is important in DNA nanotechnology; i-motif-forming sequences with consecutive cytosine (C) molecules are abundant throughout the human genome. There is, however, little information on the structure of C-rich DNAs under physiologically relevant neutral conditions. The electron dynamics of i-motifs, crucial to both biology and materials applications, also remains largely unexplored. In this work, we report a combined femtosecond and nanosecond broadband time-resolved fluorescence (TRF) and steady-state fluorescence investigation on homo-oligomer dC20 , a human telomeric sequence (HTS) 5'-dC3 (TA2 C3 )3 , and its analogue performed with different excitation at both acidic and neutral pH. Our study provides direct observation of intrinsic fluorescence and the first full probe of the real-time dynamics of the intrinsic fluorescence from i-motifs formed from varied sequences and pH conditions. The results obtained demonstrate concrete evidence for the existence at neutral pH of i-motifs from both dC20 and the HTS. It also identifies that, under neutral conditions, the i-motif from dC20 adopting the bimolecular folding structure is significantly more stable than the HTS i-motif featuring the unimolecular topology. Our femtosecond and nanosecond TRF study unveils excitation dynamics distinctive of the interdigitated architecture of i-motifs with the excited states involved exhibiting deactivation over a remarkably broad timescale through multiple channels involving proton-coupled electron transfer lasting tens of picoseconds, as signified by the solvent kinetic isotope effect, and structure-dependent charge recombination in the hundreds of picoseconds to tens of nanoseconds time regime.
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Affiliation(s)
- Chensheng Ma
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, P. R. China
| | - Ruth Chau-Ting Chan
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China
| | - Chris Tsz-Leung Chan
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, P. R. China
| | - Allen Ka-Wa Wong
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China
| | - Bowie Po-Yee Chung
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China
| | - Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, P. R. China
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4
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Dong B, Almassalha LM, Soetikno BT, Chandler JE, Nguyen TQ, Urban BE, Sun C, Zhang HF, Backman V. Stochastic fluorescence switching of nucleic acids under visible light illumination. OPTICS EXPRESS 2017; 25:7929-7944. [PMID: 28380910 PMCID: PMC5810907 DOI: 10.1364/oe.25.007929] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/03/2017] [Accepted: 03/06/2017] [Indexed: 05/20/2023]
Abstract
We report detailed characterizations of stochastic fluorescence switching of unmodified nucleic acids under visible light illumination. Although the fluorescent emission from nucleic acids under the visible light illumination has long been overlooked due to their apparent low absorption cross section, our quantitative characterizations reveal the high quantum yield and high photon count in individual fluorescence emission events of nucleic acids at physiological concentrations. Owing to these characteristics, the stochastic fluorescence switching of nucleic acids could be comparable to that of some of the most potent exogenous fluorescence probes for localization-based super-resolution imaging. Therefore, utilizing the principle of single-molecule photon-localization microscopy, native nucleic acids could be ideal candidates for optical label-free super-resolution imaging.
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Affiliation(s)
- Biqin Dong
- Biomedical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
- Mechanical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
| | - Luay M. Almassalha
- Biomedical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
| | - Brian T. Soetikno
- Biomedical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
| | - John E. Chandler
- Biomedical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
| | - The-Quyen Nguyen
- Biomedical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
| | - Ben E. Urban
- Biomedical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
| | - Cheng Sun
- Mechanical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
| | - Hao F. Zhang
- Biomedical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
| | - Vadim Backman
- Biomedical Engineering Department, Northwestern University, Evanston, IL 60208,
USA
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5
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Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast. Proc Natl Acad Sci U S A 2016; 113:9716-21. [PMID: 27535934 DOI: 10.1073/pnas.1602202113] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Visualizing the nanoscale intracellular structures formed by nucleic acids, such as chromatin, in nonperturbed, structurally and dynamically complex cellular systems, will help expand our understanding of biological processes and open the next frontier for biological discovery. Traditional superresolution techniques to visualize subdiffractional macromolecular structures formed by nucleic acids require exogenous labels that may perturb cell function and change the very molecular processes they intend to study, especially at the extremely high label densities required for superresolution. However, despite tremendous interest and demonstrated need, label-free optical superresolution imaging of nucleotide topology under native nonperturbing conditions has never been possible. Here we investigate a photoswitching process of native nucleotides and present the demonstration of subdiffraction-resolution imaging of cellular structures using intrinsic contrast from unmodified DNA based on the principle of single-molecule photon localization microscopy (PLM). Using DNA-PLM, we achieved nanoscopic imaging of interphase nuclei and mitotic chromosomes, allowing a quantitative analysis of the DNA occupancy level and a subdiffractional analysis of the chromosomal organization. This study may pave a new way for label-free superresolution nanoscopic imaging of macromolecular structures with nucleotide topologies and could contribute to the development of new DNA-based contrast agents for superresolution imaging.
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6
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Sherlock ME, Rumble CA, Kwok CK, Breffke J, Maroncelli M, Bevilacqua PC. Steady-State and Time-Resolved Studies into the Origin of the Intrinsic Fluorescence of G-Quadruplexes. J Phys Chem B 2016; 120:5146-58. [PMID: 27267433 DOI: 10.1021/acs.jpcb.6b03790] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Stretches of guanines in DNA and RNA can fold into guanine quadruplex structures (GQSs). These structures protect telomeres in DNA and regulate gene expression in RNA. GQSs have an intrinsic fluorescence that is sensitive to different parameters, including loop sequence and length. However, the dependence of GQS fluorescence on solution and sequence parameters and the origin of this fluorescence are poorly understood. Herein we examine effects of dangling nucleotides and cosolute conditions on GQS fluorescence using both steady-state and time-resolved fluorescence spectroscopy. The quantum yield of dGGGTGGGTGGGTGGG, termed "dG3T", is found to be modest at ∼2 × 10(-3). Nevertheless, dG3T and its variants are significantly brighter than the common nucleic acid fluorophore 2-aminopurine (2AP) largely due to their sizable extinction coefficients. Dangling 5'-end nucleotides generally reduce emission and blue-shift the resultant spectrum, whereas dangling 3'-end nucleotides slightly enhance fluorescence, particularly on the red side of the emission band. Time-resolved fluorescence decays are broadly distributed in time and require three exponential components for accurate fits. Time-resolved emission spectra suggest the presence of two emitting populations centered at ∼330 and ∼390 nm, with the redder component being a well-defined long-lived (∼1 ns) entity. Insights into GQS fluorescence obtained here should be useful in designing brighter intrinsic RNA and DNA quadruplexes for use in label-free biotechnological applications.
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Affiliation(s)
- Madeline E Sherlock
- Department of Chemistry, ‡Center for RNA Molecular Biology, and §Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Christopher A Rumble
- Department of Chemistry, ‡Center for RNA Molecular Biology, and §Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Chun Kit Kwok
- Department of Chemistry, ‡Center for RNA Molecular Biology, and §Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Jens Breffke
- Department of Chemistry, ‡Center for RNA Molecular Biology, and §Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Mark Maroncelli
- Department of Chemistry, ‡Center for RNA Molecular Biology, and §Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
| | - Philip C Bevilacqua
- Department of Chemistry, ‡Center for RNA Molecular Biology, and §Department of Biochemistry and Molecular Biology, Pennsylvania State University , University Park, Pennsylvania 16802, United States
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7
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Conti I, Nenov A, Höfinger S, Flavio Altavilla S, Rivalta I, Dumont E, Orlandi G, Garavelli M. Excited state evolution of DNA stacked adenines resolved at the CASPT2//CASSCF/Amber level: from the bright to the excimer state and back. Phys Chem Chem Phys 2015; 17:7291-302. [DOI: 10.1039/c4cp05546b] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
La and excimer state population exchange, along the common puckering decay coordinate, explains the longest DNA lifetime component.
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Affiliation(s)
- Irene Conti
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
| | - Artur Nenov
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
| | - Siegfried Höfinger
- Zentraler Informatikdienst
- Technische Universität Wien
- 1040 Wien, Austria
- Department of Physics
- Michigan Technological University
| | | | - Ivan Rivalta
- Université de Lyon
- CNRS
- Institut de Chimie de Lyon
- École Normale Supérieure de Lyon
- F-69364 Lyon Cedex 07, France
| | - Elise Dumont
- Laboratoire de Chimie
- Ecole Normale Supérieure de Lyon
- Lyon, France
| | - Giorgio Orlandi
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
| | - Marco Garavelli
- Dipartimento di Chimica “G. Ciamician”
- Università di Bologna
- Bologna, Italy
- Laboratoire de Chimie
- Ecole Normale Supérieure de Lyon
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8
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Plasser F, Lischka H. Electronic excitation and structural relaxation of the adenine dinucleotide in gas phase and solution. Photochem Photobiol Sci 2014; 12:1440-52. [PMID: 23737069 DOI: 10.1039/c3pp50032b] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The excited states and potential surfaces of the adenine dinucleotide are analyzed in gas phase and in solution using a correlated ab initio methodology in a QM/MM framework. In agreement with previous studies, a rather flat S1 surface with a number of minima of different character is found. Specifically, our results suggest that exciplexes with remarkably short intermolecular separation down to ~2.0 Å are formed. A detailed analysis shows that due to strong orbital interactions their character differs significantly from any states present in the Franck-Condon region. The lowest S1 energy minimum is a ππ* exciplex with only a small amount of charge transfer. It possesses appreciable oscillator strength with a polarization almost perpendicular to the planes of the two adenine molecules.
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Affiliation(s)
- Felix Plasser
- Institute for Theoretical Chemistry, University of Vienna, Währingerstr. 17, 1090 Vienna, Austria.
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9
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Electronic Excitation Processes in Single-Strand and Double-Strand DNA: A Computational Approach. PHOTOINDUCED PHENOMENA IN NUCLEIC ACIDS II 2014; 356:1-37. [DOI: 10.1007/128_2013_517] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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10
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Dao NT, Haselsberger R, Michel-Beyerle ME, Phan AT. Excimer formation by stacking G-quadruplex blocks. Chemphyschem 2013; 14:2667-71. [PMID: 23780713 DOI: 10.1002/cphc.201300481] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2013] [Indexed: 01/15/2023]
Affiliation(s)
- Nguyen Thuan Dao
- School of Physical and Mathematical Science, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Singapore
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11
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12
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Zelený T, Ruckenbauer M, Aquino AJ, Müller T, Lankaš F, Dršata T, Hase WL, Nachtigallova D, Lischka H. Strikingly Different Effects of Hydrogen Bonding on the Photodynamics of Individual Nucleobases in DNA: Comparison of Guanine and Cytosine. J Am Chem Soc 2012; 134:13662-9. [DOI: 10.1021/ja3028845] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tomáš Zelený
- Regional Centre of
Advanced
Technologies and Materials, Department of Physical Chemistry, Faculty
of Science, Palacky University Olomouc,
17. listopadu 1192/12, 771 46 Olomouc, Czech Republic
| | - Matthias Ruckenbauer
- Institute of Theoretical Chemistry, University of Vienna, Währingerstraße 17,
A-1090 Vienna, Austria
| | - Adelia J.A. Aquino
- Institute of Theoretical Chemistry, University of Vienna, Währingerstraße 17,
A-1090 Vienna, Austria
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United
States
- Institute of Soil
Research, University of Natural Resources and Life Sciences,
Peter-Jordan-Straße 82, A-1190 Vienna, Austria
| | - Thomas Müller
- Institute of Advanced Simulation, Jülich Supercomuter Centre, Forschungszentrum
Jülich, D-52425 Jülich, Germany
| | - Filip Lankaš
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Tomáš Dršata
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - William L. Hase
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United
States
| | - Dana Nachtigallova
- Institute of Organic Chemistry
and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, 166 10 Prague, Czech Republic
| | - Hans Lischka
- Institute of Theoretical Chemistry, University of Vienna, Währingerstraße 17,
A-1090 Vienna, Austria
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United
States
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13
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Dou Y, Yuan S, Zhang W, Tang H, Lo GV. Bonded exciplex formation from stacked thymine and adenine: semiclassical simulations. Mol Phys 2012. [DOI: 10.1080/00268976.2012.663944] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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15
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Keane PM, Wojdyla M, Doorley GW, Kelly JM, Clark IP, Parker AW, Greetham GM, Towrie M, Magno LM, Quinn SJ. Ultrafast IR spectroscopy of polymeric cytosine nucleic acids reveal the long-lived species is due to a localised state. Phys Chem Chem Phys 2012; 14:6307-11. [PMID: 22358255 DOI: 10.1039/c2cp23774a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The decay pathways of UV-excited cytosine polymers are investigated using picosecond time-resolved infrared spectroscopy. Similar yields of a non-emissive (1)nπ* state are found in the single-stranded dC(30) polymer as in the dCMP monomer, but with a longer lifetime in the polymer (80 ps vs. 39 ps). A longer lifetime is also found in the d(CpC) dinucleotide. No evidence of excimer states is observed, suggesting that localised (1)nπ* excited states are the most significant intermediates present on the picosecond timescale.
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Affiliation(s)
- Páraic M Keane
- School of Chemistry and Centre for Synthesis and Chemical Biology, Trinity College, Dublin 2, Ireland
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16
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Conti I, Altoè P, Stenta M, Garavelli M, Orlandi G. Adenine deactivation in DNA resolved at the CASPT2//CASSCF/AMBER level. Phys Chem Chem Phys 2010; 12:5016-23. [DOI: 10.1039/b926608a] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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de la Harpe K, Crespo-Hernández CE, Kohler B. The excited-state lifetimes in a G x C DNA duplex are nearly independent of helix conformation and base-pairing motif. Chemphyschem 2009; 10:1421-5. [PMID: 19301308 DOI: 10.1002/cphc.200900004] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
DNA photophysics: Femtosecond transient absorption experiments reveal that excited states produced by UV light in a duplex DNA oligonucleotide decay at essentially the same rate in B and Z helix conformers (see figure).
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Affiliation(s)
- Kimberly de la Harpe
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210, USA
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18
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González-Ramírez I, Climent T, Serrano-Pérez JJ, González-Luque R, Merchán M, Serrano-Andrés L. The role of pyrimidine nucleobase excimers in DNA photophysics and photoreactivity. PURE APPL CHEM 2009. [DOI: 10.1351/pac-con-08-08-31] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Quantum chemical studies using the accurate CASPT2//CASSCF procedure show that π-stacked interactions in biochromophores such as pyrimidine (Pyr) DNA/RNA nucleobases pairs yield excimer-like situations which behave as precursors of processes like charge transfer (CT) or photoreactivity and are the source of the emissive properties in DNA. Examples are the CT between adjacent DNA nucleobases in a strand of oligonucleotides and the photodimerization taking place in cytosine (C) pairs leading to cyclobutanecytosine (CBC) mutants. These processes take place through nonadiabatic photochemical mechanisms whose evolution is determined by the presence and accessibility of conical intersections (CIs) and other surface crossings between different electronic states.
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Affiliation(s)
- Israel González-Ramírez
- 1Instituto de Ciencia Molecular, Universitat de València, Apartado de Correos 22085, ES-46071 Valencia, Spain
| | - Teresa Climent
- 1Instituto de Ciencia Molecular, Universitat de València, Apartado de Correos 22085, ES-46071 Valencia, Spain
| | - Juan José Serrano-Pérez
- 1Instituto de Ciencia Molecular, Universitat de València, Apartado de Correos 22085, ES-46071 Valencia, Spain
| | - Remedios González-Luque
- 1Instituto de Ciencia Molecular, Universitat de València, Apartado de Correos 22085, ES-46071 Valencia, Spain
| | - Manuela Merchán
- 1Instituto de Ciencia Molecular, Universitat de València, Apartado de Correos 22085, ES-46071 Valencia, Spain
| | - Luis Serrano-Andrés
- 1Instituto de Ciencia Molecular, Universitat de València, Apartado de Correos 22085, ES-46071 Valencia, Spain
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19
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Kwok WM, Ma C, Phillips DL. “Bright” and “Dark” Excited States of an Alternating AT Oligomer Characterized by Femtosecond Broadband Spectroscopy. J Phys Chem B 2009; 113:11527-34. [DOI: 10.1021/jp906265c] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - Chensheng Ma
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong
| | - David Lee Phillips
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, and Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong
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20
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Olaso-González G, Merchán M, Serrano-Andrés L. The role of adenine excimers in the photophysics of oligonucleotides. J Am Chem Soc 2009; 131:4368-77. [PMID: 19317507 DOI: 10.1021/ja808280j] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Energies and structures of different arrangements of the stacked adenine homodimer have been computed at the ab initio CASPT2 level of theory in isolation and in an aqueous environment. Adenine dimers are shown to form excimer singlet states with different degrees of stacking and interaction. A model for a 2-fold decay dynamics of adenine oligomers can be supported in which, after initial excitation in the middle UV range, unstacked or slightly stacked pairs of nucleobases will relax by an ultrafast internal conversion to the ground state, localizing the excitation in the monomer and through the corresponding conical intersection with the ground state. On the other hand, long-lifetime intrastrand stacked excimer singlet states will be formed in different conformations, including neutral and charge transfer dimers, which originate the red-shifted emission observed in the oligonucleotide chains and that will evolve toward the same monomer decay channel after surmounting an energy barrier. By computing the transient absorption spectra for the different structures considered and their relative stability in vacuo and in water, it is concluded that in the adenine homodimers the maximum-overlap face-to-face orientations are the most stable excimer conformations observed in experiment.
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Affiliation(s)
- Gloria Olaso-González
- Instituto de Ciencia Molecular, Universitat de Valencia, Apartado 22085, ES-46071 Valencia, Spain
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Middleton CT, de La Harpe K, Su C, Law YK, Crespo-Hernández CE, Kohler B. DNA excited-state dynamics: from single bases to the double helix. Annu Rev Phys Chem 2009; 60:217-39. [PMID: 19012538 DOI: 10.1146/annurev.physchem.59.032607.093719] [Citation(s) in RCA: 602] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ultraviolet light is strongly absorbed by DNA, producing excited electronic states that sometimes initiate damaging photochemical reactions. Fully mapping the reactive and nonreactive decay pathways available to excited electronic states in DNA is a decades-old quest. Progress toward this goal has accelerated rapidly in recent years, in large measure because of ultrafast laser experiments. Here we review recent discoveries and controversies concerning the nature and dynamics of excited states in DNA model systems in solution. Nonradiative decay by single, solvated nucleotides occurs primarily on the subpicosecond timescale. Surprisingly, excess electronic energy relaxes one or two orders of magnitude more slowly in DNA oligo- and polynucleotides. Highly efficient nonradiative decay pathways guarantee that most excited states do not lead to deleterious reactions but instead relax back to the electronic ground state. Understanding how the spatial organization of the bases controls the relaxation of excess electronic energy in the double helix and in alternative structures is currently one of the most exciting challenges in the field.
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Affiliation(s)
- Chris T Middleton
- Department of Chemistry, The Ohio State University, Columbus, Ohio 43210, USA
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22
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Serrano-Pérez JJ, González-Ramírez I, Coto PB, Merchán M, Serrano-Andrés L. Theoretical insight into the intrinsic ultrafast formation of cyclobutane pyrimidine dimers in UV-irradiated DNA: thymine versus cytosine. J Phys Chem B 2008; 112:14096-8. [PMID: 18928316 DOI: 10.1021/jp806794x] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The higher formation yields measured in the ultrafast photoinduced formation of cyclobutane thymine dimers (T<>T) with respect to those of cytosine (C<>C) are explained, on the basis of ab initio CASPT2 results, by the existence in thymine of more reactive orientations and a less efficient photoreversibility, whereas in cytosine the funnel toward the photolesion becomes competitive with that mediating the internal conversion of the excited-cytosine monomer.
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Affiliation(s)
- Juan José Serrano-Pérez
- Instituto de Ciencia Molecular, Universitat de València, Apartado 22085, ES-46071 Valencia, Spain
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23
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UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases. Proc Natl Acad Sci U S A 2008; 105:10285-90. [PMID: 18647840 DOI: 10.1073/pnas.0802079105] [Citation(s) in RCA: 143] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Excited electronic states created by UV excitation of the diribonucleoside monophosphates ApA, ApG, ApC, ApU, and CpG were studied by the femtosecond transient-absorption technique. Bleach recovery signals recorded at 252 nm show that long-lived excited states are formed in all five dinucleosides. The lifetimes of these states exceed those measured in equimolar mixtures of the constituent mononucleotides by one to two orders of magnitude, indicating that electronic coupling between proximal nucleobases dramatically slows the relaxation of excess electronic energy. The decay rates of the long-lived states decrease with increasing energy of the charge-transfer state produced by transferring an electron from one base to another. The charge-transfer character of the long-lived states revealed by this analysis supports their assignment to excimer or exciplex states. Identical bleach recovery signals were seen for ApA, (A)(4), and poly(A) at delay times >10 ps after photoexcitation. This indicates that excited states localized on a stack of just two bases are the common trap states independent of the number of stacked nucleotides. The fraction of initial excitations that decay to long-lived exciplex states is approximately equal to the fraction of stacked bases determined by NMR measurements. This supports a model in which excitations associated with two stacked bases decay to exciplex states, whereas excitations in unstacked bases decay via ultrafast internal conversion. These results establish the importance of charge transfer-quenching pathways for UV-irradiated RNA and DNA in room-temperature solution.
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Roca-Sanjuán D, Olaso-González G, González-Ramírez I, Serrano-Andrés L, Merchán M. Molecular basis of DNA photodimerization: intrinsic production of cyclobutane cytosine dimers. J Am Chem Soc 2008; 130:10768-79. [PMID: 18627152 DOI: 10.1021/ja803068n] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Based on CASPT2 results, the present contribution establishes for the first time that cytosine photodimer formation (C< >C) is mediated along the triplet and singlet manifold by a singlet-triplet crossing, (T1/S0)X, and by a conical intersection, (S1/S0)CI, respectively. The former can be accessed in a barrierless way from a great variety of photochemical avenues and exhibits a covalent single bond between the ethene C6-C6' carbon atoms of each monomer. The efficiency of the stepwise triplet mechanism, however, would be modulated by the effectiveness of the intersystem crossing mechanism. The results provide the grounds for the understanding of the potential photogenotoxicity of endogenous and exogenous compounds via triplet-triplet sensitization, with a lower bound for cytosine oligonucleotides predicted to be 2.70 eV, and give support to the traditional view of the primary role of triplet excited states in the photochemistry of DNA, a well-known source of photoproducts in solution under triplet photosensitization conditions. The function played by singlet excimers (excited dimers) to explain both the red-shifted fluorescence and photoreaction is highlighted. A rationale on the pronounced wavelength dependence of the observed fluorescence is offered. Geometrical arrangements at the time of light irradiation close to, but energetically above, (S1/S0)CI are suggested as reactive orientations that become prone to produce C< >C directly, with no energy barrier. Because of the outstanding intrinsic ability of cytosine to form stable relaxed excimers, the system located near the bound relaxed excimer has to accumulate enough vibrational energy to surmount a small barrier of 0.2 eV to reach (S1/S0)CI, making the overall process to proceed at a slower relative rate as compared to other compounds such as thymine, which is not susceptible of forming so stable excimers.
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Affiliation(s)
- Daniel Roca-Sanjuán
- Instituto de Ciencia Molecular, Universitat de València, Apartado 22085, ES-46071 Valencia, Spain
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25
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Abstract
The excited-state dynamics of the RNA homopolymer of cytosine and of the 18-mer (dC)(18) were studied by steady-state and time-resolved absorption and emission spectroscopy. At pH 6.8, excitation of poly(rC) by a femtosecond UV pump pulse produces excited states that decay up to one order of magnitude more slowly than the excited states formed in the mononucleotide cytidine 5'-monophosphate under the same conditions. Even slower relaxation is observed for the hemiprotonated, self-associated form of poly(rC), which is stable at acidic pH. Transient absorption and time-resolved fluorescence signals for (dC)(18) at pH 6.8 are similar to ones observed for poly(rC) near pH 4, indicating that hemiprotonated structures are found in DNA C tracts at neutral pH. In both systems, there is evidence for two kinds of emitting states with lifetimes of ~100 ps and slightly more than 1 ns. The former states are responsible for the bulk of emission from the hemiprotonated structures. Evidence suggests that slow electronic relaxation in these self-complexes is the result of vertical base stacking. The similar signals from RNA and DNA C tracts suggest a common base-stacked structure, which may be identical with that of i-motif DNA.
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Affiliation(s)
| | | | - Bern Kohler
- Corresponding author: e-mail: , Telephone +1-614-688-3944, Fax +1-614-292-1685
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26
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Roca-Sanjuán D, Merchán M, Serrano-Andrés L. Modeling hole transfer in DNA: Low-lying excited states of oxidized cytosine homodimer and cytosine–adenine heterodimer. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.02.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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27
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Kwok WM, Ma C, Phillips DL. A doorway state leads to photostability or triplet photodamage in thymine DNA. J Am Chem Soc 2008; 130:5131-9. [PMID: 18335986 DOI: 10.1021/ja077831q] [Citation(s) in RCA: 158] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultraviolet irradiation of DNA produces electronic excited states that predominantly eliminate the excitation energy by returning to the ground state (photostability) or following minor pathways into mutagenic photoproducts (photodamage). The cyclobutane pyrimidine dimer (CPD) formed from photodimerization of thymines in DNA is the most common form of photodamage. The underlying molecular processes governing photostability and photodamage of thymine-constituted DNA remain unclear. Here, a combined femtosecond broadband time-resolved fluorescence and transient absorption spectroscopies were employed to study a monomer thymidine and a single-stranded thymine oligonucleotide. We show that the protecting deactivation of a thymine multimer is due to an ultrafast single-base localized stepwise mechanism where the initial excited state decays via a doorway state to the ground state or proceeds via the doorway state to a triplet state identified as a major precursor for CPD photodamage. These results provide new mechanistic characterization of and a dynamic link between the photoexcitation of DNA and DNA photostability and photodamage.
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Affiliation(s)
- Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
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28
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Nachtigallová D, Hobza P, Ritze HH. Electronic splitting in the excited states of DNA base homodimers and -trimers: an evaluation of short-range and Coulombic interactions. Phys Chem Chem Phys 2008; 10:5689-97. [DOI: 10.1039/b806323k] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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29
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Photostability and Photoreactivity in Biomolecules: Quantum Chemistry of Nucleic Acid Base Monomers and Dimers. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2008. [DOI: 10.1007/978-1-4020-8184-2_16] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
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30
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31
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Improta R. The excited states of π-stacked 9-methyladenine oligomers: a TD-DFT study in aqueous solution. Phys Chem Chem Phys 2008; 10:2656-64. [DOI: 10.1039/b718562f] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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32
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Frank JH, Elder AD, Swartling J, Venkitaraman AR, Jeyasekharan AD, Kaminski CF. A white light confocal microscope for spectrally resolved multidimensional imaging. J Microsc 2007; 227:203-15. [PMID: 17760615 DOI: 10.1111/j.1365-2818.2007.01803.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Spectrofluorometric imaging microscopy is demonstrated in a confocal microscope using a supercontinuum laser as an excitation source and a custom-built prism spectrometer for detection. This microscope system provides confocal imaging with spectrally resolved fluorescence excitation and detection from 450 to 700 nm. The supercontinuum laser provides a broad spectrum light source and is coupled with an acousto-optic tunable filter to provide continuously tunable fluorescence excitation with a 1-nm bandwidth. Eight different excitation wavelengths can be simultaneously selected. The prism spectrometer provides spectrally resolved detection with sensitivity comparable to a standard confocal system. This new microscope system enables optimal access to a multitude of fluorophores and provides fluorescence excitation and emission spectra for each location in a 3D confocal image. The speed of the spectral scans is suitable for spectrofluorometric imaging of live cells. Effects of chromatic aberration are modest and do not significantly limit the spatial resolution of the confocal measurements.
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Affiliation(s)
- J H Frank
- Combustion Research Facility, Sandia National Laboratories, Livermore, CA 94611, USA.
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33
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Hu L, Zhao Y, Wang F, Chen G, Ma C, Kwok WM, Phillips DL. Are adenine strands helical H-aggregates? J Phys Chem B 2007; 111:11812-6. [PMID: 17880195 DOI: 10.1021/jp070403m] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
On the basis of our quantum mechanical calculation, we propose that homogeneous single-stranded adenine bases (Ade-DNA) form helical H aggregates, and the photoexcited states can be described as Frenkel excitons. The calculated excitonic coupling between adjacent transition dipoles is in good agreement with the measured absorption spectrum of 20-base homogeneous adenine stacks that exhibits a blue shift of 2.6 nm relative to that of the monomeric species.
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Affiliation(s)
- Lihong Hu
- Department of Chemistry and Centre of Theoretical and Computational Physics, University of Hong Kong, Hong Kong, PR China
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34
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Kwok WM, Ma C, Phillips DL. Femtosecond time- and wavelength-resolved fluorescence and absorption spectroscopic study of the excited states of adenosine and an adenine oligomer. J Am Chem Soc 2007; 128:11894-905. [PMID: 16953630 DOI: 10.1021/ja0622002] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
By employing broadband femtosecond Kerr-gated time-resolved fluorescence (KTRF) and transient absorption (TA) techniques, we report the first (to our knowledge) femtosecond combined time- and wavelength-resolved study on an ultraviolet-excited nucleoside and a single-stranded oligonucleotide (namely adenosine (Ado) and single-stranded adenine oligomer (dA)(20)) in aqueous solution. With the advantages of the ultrafast time resolution, the broad spectral and temporal probe window, and a high sensitivity, our KTRF and TA results enable the real time monitoring and spectral characterization of the excited-state relaxation processes of the Ado nucleoside and (dA)(20) oligonucleotide investigated. The temporal evolution of the 267 nm excited Ado KTRF spectra indicates there are two emitting components with lifetimes of approximately 0.13 ps and approximately 0.45 ps associated with the L(a) and L(b) pipi* excited states, respectively. These Ado results reveal no obvious evidence for the involvement of the npi* state along the irradiative internal conversion pathway. A distinct mechanism involving only the two pipi* states has been proposed for the ultrafast Ado deactivation dynamics in aqueous solution. The time dependence of the 267 nm excited (dA)(20) KTRF and TA spectra reveals temporal evolution from an ultrafast "A-like" state (with a approximately 0.39 ps decay time) to a relatively long-lived E(1) "excimer" (approximately 4.3 ps decay time) and an E(2) "excimer-like" (approximately 182 ps decay time) state. The "A-like" state has a spectral character closely resembling the excited state of Ado. Comparison of the spectral evolution between the results for Ado and (dA)(20) provides unequivocal evidence for the local excitation character of the initially photoexcited (dA)(20). The rapid transformation of the locally excited (dA)(20) component into the delocalized E(1) "excimer" state which then further evolves into the E(2) "excimer-like" state indicates that base stacking has a high ability to modify the excited-state deactivation pathway. This modification appears to occur by suppressing the internal conversion pathway of an individually excited base component where the stacking interaction mediates efficient interbase energy transfer and promotes formation of the collective excited states. This feature of the local excitation that is subsequently followed by rapid energy delocalization into nearby bases may occur in many base multimer systems. Our results provide an important new contribution to better understanding DNA photophysics.
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Affiliation(s)
- Wai-Ming Kwok
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong S. A. R., P. R. China
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35
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Santoro F, Barone V, Improta R. Influence of base stacking on excited-state behavior of polyadenine in water, based on time-dependent density functional calculations. Proc Natl Acad Sci U S A 2007; 104:9931-6. [PMID: 17545308 PMCID: PMC1891264 DOI: 10.1073/pnas.0703298104] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A thorough study of the excited-state properties of the stacked dimers and trimers of 9-methyladenine in B-DNA conformation has been performed in aqueous solution by using time-dependent density functional calculations and the solvent polarizable continuum model, and results were compared with experimental results on polyadenine oligomers. The effect of base stacking on the absorption and emission spectra is fully reproduced by our calculations. Although light absorption leads to a state (S(B)) delocalized over several nucleobases, excited-state geometry optimization indicates that S(B) subsequently evolves into a state in which the excitation is localized on a single base. Analysis of the excited-state potential energy surfaces shows that S(B) can easily decay into the lowest energy excited state, S(CT), which is a dark excimer produced by intermonomer charge transfer between two stacked bases. The subpicosecond features of the time-resolved experiments are interpreted in terms of ultrafast decay from S(B). After localization, two easy, radiationless decay channels are indeed open for S(B): (i) ground-state recovery, according to the same mechanisms proposed for isolated adenine and/or (ii) decay to S(CT). Our calculations suggest that the slowest part of the excited-state dynamics detected experimentally involves the S(CT) state.
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Affiliation(s)
- F. Santoro
- Istituto per i Processi Chimico–Fisici, Consiglio Nazionale delle Ricerche (CNR), Area della Ricerca del CNR, Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - V. Barone
- Dipartimento di Chimica and Interuniversitario Nazionale per la Scienza e la Tecnologia dei Materiali, Università Federico II, Complesso Monte S. Angelo, Via Cintia, I-80126 Napoli, Italy; and
| | - R. Improta
- Dipartimento di Chimica and Interuniversitario Nazionale per la Scienza e la Tecnologia dei Materiali, Università Federico II, Complesso Monte S. Angelo, Via Cintia, I-80126 Napoli, Italy; and
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy
- To whom correspondence should be addressed. E-mail:
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36
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Krawczyk S, Luchowski R. Electronic excited States of polynucleotides: a study by electroabsorption spectroscopy. J Phys Chem B 2007; 111:1213-21. [PMID: 17266277 DOI: 10.1021/jp0652953] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electroabsorption spectra were obtained for single-stranded polynucleotides poly(U), poly(C), poly(A), and poly(G) in glycerol/water glass at low temperature, and the differences in permanent dipole moment (Deltamu) and polarizability (Deltaalpha) were estimated for several spectral ranges covering the lowest energy absorption band around 260 nm. In each spectral range, the electrooptical parameters associated with apparent features in the absorption spectrum exhibit distinct values representing either a dominant single transition or the resultant value for a group of a relatively narrow cluster of overlapping transitions. The estimated spacing in energy between electronic origins of these transitions is larger than the electronic coupling within the Coulombic interaction model which is usually adopted in computational studies. The electroabsorption data allow us to distinguish a weak electronic transition associated with a wing in polynucleotide absorption spectra, at an energy below the electronic origin in absorption spectra of monomeric nucleobases. In poly(C) and poly(G), these low-energy transitions are related to increased values of Deltamu and Deltaalpha, possibly indicating a weak involvement of charge resonance in the respective excited states. A model capable of explaining the origin of low-energy excited states, based on the interaction of pipi* and npi* transitions in neighboring bases, is introduced and briefly discussed on the grounds of point dipole interaction.
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Affiliation(s)
- Stanislaw Krawczyk
- Institute of Physics, Maria Curie-Sklodowska University, 20-031 Lublin, Poland.
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37
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Gabelica V, Rosu F, Tabarin T, Kinet C, Antoine R, Broyer M, De Pauw E, Dugourd P. Base-dependent electron photodetachment from negatively charged DNA strands upon 260-nm laser irradiation. J Am Chem Soc 2007; 129:4706-13. [PMID: 17378565 DOI: 10.1021/ja068440z] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
DNA multiply charged anions stored in a quadrupole ion trap undergo one-photon electron ejection (oxidation) when subjected to laser irradiation at 260 nm (4.77 eV). Electron photodetachment is likely a fast process, given that photodetachment is able to compete with internal conversion or radiative relaxation to the ground state. The DNA [6-mer]3- ions studied here show a marked sequence dependence of electron photodetachment yield. Remarkably, the photodetachment yield (dG6 > dA6 > dC6 > dT6) is inversely correlated with the base ionization potentials (G < A < C < T). Sequences with guanine runs show increased photodetachment yield as the number of guanine increases, in line with the fact that positive holes are the most stable in guanine runs. This correlation between photodetachment yield and the stability of the base radical may be explained by tunneling of the electron through the repulsive Coulomb barrier. Theoretical calculations on dinucleotide monophosphates show that the HOMO and HOMO-1 orbitals are localized on the bases. The wavelength dependence of electron detachment yield was studied for dG63-. Maximum electron photodetachment is observed in the wavelength range corresponding to base absorption (260-270 nm). This demonstrates the feasibility of gas-phase UV spectroscopy on large DNA anions. The calculations and the wavelength dependence suggest that the electron photodetachment is initiated at the bases and not at the phosphates. This also indicates that, although direct photodetachment could also occur, autodetachment from excited states, presumably corresponding to base excitation, is the dominant process at 260 nm. Excited-state dynamics of large DNA strands still remains largely unexplored, and photo-oxidation studies on trapped DNA multiply charged anions can help in bridging the gap between gas-phase studies on isolated bases or base pairs and solution-phase studies on full DNA strands.
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Affiliation(s)
- Valérie Gabelica
- Laboratoire de Spectrométrie de Masse, Université de Liège, Institut de Chimie Bat B6c, B-4000 Liège, Belgium.
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38
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Ritze HH, Hobza P, Nachtigallová D. Electronic coupling in the excited electronic state of stacked DNA base homodimers. Phys Chem Chem Phys 2007; 9:1672-5. [PMID: 17396177 DOI: 10.1039/b618382d] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The nature of the electronic coupling of stacked nucleic acid bases adenine (A), thymine (T), and cytosine (C), in A-A, T-T, and C-C complexes in their excited states was investigated; a different character of the electronic coupling for the T-T complex was shown.
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Affiliation(s)
- Hans-Hermann Ritze
- Max Born Institute for Nonlinear Optics and Short Pulse Spectroscopy, Max-Born-Strasse 2A, D-12489 Berlin, Germany.
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39
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Olaso-González G, Roca-Sanjuán D, Serrano-Andrés L, Merchán M. Toward the understanding of DNA fluorescence: the singlet excimer of cytosine. J Chem Phys 2007; 125:231102. [PMID: 17190539 DOI: 10.1063/1.2408411] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
By using the multiconfigurational second-order perturbation method CASPT2, including corrections for the basis set superposition error, the lowest-singlet excited state of the face-to-face pi-stacked cytosine homodimer is revealed to be bound by about half an eV, being the source of an emissive feature consistent with the observed redshifted fluorescence.
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Affiliation(s)
- Gloria Olaso-González
- Instituto de Ciencia Molecular, Universitat de València, Apartado 22085, ES-46071 Valencia, Spain
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40
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Markovitsi D, Gustavsson T, Talbot F. Excited states and energy transfer among DNA bases in double helices. Photochem Photobiol Sci 2007; 6:717-24. [PMID: 17609764 DOI: 10.1039/b705674e] [Citation(s) in RCA: 100] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The study of excited states and energy transfer in DNA double helices has recently gained new interest connected to the development of computational techniques and that of femtosecond spectroscopy. The present article points out contentious questions regarding the nature of the excited states and the occurrence of energy transfer and shows how they are currently approached. Using as example the polymer poly(dA) . poly(dT), composed of about 2000 adenine-thymine pairs, a model is proposed on the basis of time-resolved measurements (fluorescence decays, fluorescence anisotropy decays and fluorescence spectra, obtained with femtosecond resolution), associated to steady-state spectra. According to this qualitative model, excitation at 267 nm populates excited states that are delocalized over a few bases (excitons). Ultrafast internal conversion directs the excited state population to the lower part of the exciton band giving rise to fluorescence. Questions needing further investigations, both theoretical and experimental, are underlined with particular emphasis on delicate points related to the complexity and the plasticity of these systems.
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Affiliation(s)
- Dimitra Markovitsi
- Laboratoire Francis Perrin, CEA/DSM/DRECAM/SPAM-CNRS URA 2453, CEA/Saclay, 91191, Gif-sur-Yvette, France
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41
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Daniels M, Hart LP, Ho PS, Ballini JP, Vigny P, Brochon JC. Intrinsic fluorescence of B and Z forms of poly d(G-m5C)·poly d(G-m5C), a synthetic double-stranded DNA: spectra and lifetimes by the maximum entropy method. Photochem Photobiol Sci 2007; 6:883-93. [PMID: 17668119 DOI: 10.1039/b615670c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A study has been made of the fluorescence of poly d(G-m5C).poly d(G-m5C), a synthetic double-stranded DNA, in buffered neutral aqueous solution at room temperature, excited by synchrotron radiation at 280 nm and 250 nm and by a frequency-doubled pulse dye laser at 290 nm. Exciting at 280 nm, the B form shows a uni-modal UV spectrum with lambdaf(max) approximately 340 nm. The Z form has in addition a visible emission lambdaf(max) at 450 nm. The spectral positions remain unchanged on exciting at 250 nm but the relative intensities change considerably. Decay profiles have been obtained at 360 nm and 450 nm for both the B and Z forms and have been analyzed by fitting to a pseudo-continuous distribution of 100 (and occasionally 200) exponentials, ranging from 10 ps to 20 ns, by optimizing the 'entropy' of the signal (the method of maximum entropy). We find the mean lifetimes for both wavelengths of emission and for both structural forms fall into three well-separated regions in the ranges indicated tau1 approximately 0.04-0.21 ns, tau2 approximately 0.9-1.26 ns, and tau3 approximately 5.1-6.5 ns. The UV emission, from its spectral position and half-width, correlates with monomeric emission from m5C (and from C for poly d(G-C)). However the lifetime tau1 is approximately 2 orders of magnitude longer than the monomers and points to an involvement of protonated guanosine (GH+, tauf approximately 200 ps) in the overall absorption/emission sequence. In the UV the tau3 emission is predominant, with fractional time-integrated emission approximately 86% for B DNA and approximately 64% for Z. We suggest it results from exciton (stacked) absorption followed by dissociative emission. For Z DNA the visible (450 nm) emission is dominated by a tau3 species (approximately 91%) with a lifetime of 6.5 ns and we suggest it represents a hetero-excimer emission consequent upon absorption by the strongly overlapped base-stacking, which differs from that in B DNA. The weak emission corresponding to tau2 is made more apparent by scanned gated detection of the emission from laser excitation (290 nm) of single-crystal d(m5C-G)3. A central role is attributed to the tight stacking of the bases in the Z form which correlates with enhanced hypochromism at 250 nm vs. 280 nm and with the reversal of the fluorescence intensity ratios UV-visible between these wavelengths.
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Affiliation(s)
- Malcolm Daniels
- Chemistry Department & Radiation Center, Oregon State University, Corvallis, OR 97331, USA
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Markovitsi D, Onidas D, Talbot F, Marguet S, Gustavsson T, Lazzarotto E. UVB/UVC induced processes in model DNA helices studied by time-resolved spectroscopy: Pitfalls and tricks. J Photochem Photobiol A Chem 2006. [DOI: 10.1016/j.jphotochem.2006.05.029] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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43
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Crespo-Hernández CE, Kohler B. Influence of Secondary Structure on Electronic Energy Relaxation in Adenine Homopolymers. J Phys Chem B 2004. [DOI: 10.1021/jp0496046] [Citation(s) in RCA: 98] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Bern Kohler
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, Ohio 43210
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Crespo-Hernández CE, Cohen B, Hare PM, Kohler B. Ultrafast Excited-State Dynamics in Nucleic Acids. Chem Rev 2004; 104:1977-2019. [PMID: 15080719 DOI: 10.1021/cr0206770] [Citation(s) in RCA: 965] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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46
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Lotte K, Plessow R, Brockhinke A. Static and time-resolved fluorescence investigations of tryptophan analogues--a solvent study. Photochem Photobiol Sci 2004; 3:348-59. [PMID: 15052363 DOI: 10.1039/b312436c] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The fluorescence properties of tryptophan, polytryptophan and seven of its analogues (7-azatryptophan, 5-hydroxytryptophan, 5-methoxytryptophan, 5-fluorotryptophan, 5-methyltryptophan, 5-bromotryptophan, and 6-fluorotryptophan) are studied using two novel fluorescence spectroscopic techniques for a wide range of solvent polarities. Two-dimensional mapping of all emission and all fluorescence spectra using excitation-emission spectroscopy (EES) has been used to determine quantum yields, positions of emission maxima, full widths at half maximum (FWHMs) as well as Stokes' shifts. Additionally, fluorescence lifetimes obtained from time-resolved experiments using a picosecond laser system are presented and compared with the data acquired from the static setup. This systematic study of the fluorescence characteristics is a prerequisite to assess the potential of these analogues to act as structure-conserving substitutes for tryptophan in protein fluorescence experiments. The potential of these analogues, to act as probes for the local environment, and allow estimation of the polarity in the vicinity of the fluorophore and its exposure to the solvent, is discussed.
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Affiliation(s)
- Kirsten Lotte
- Physikalische Chemie I, Fakultät für Chemie, Universität Bielefeld, Universitätsstrasse 25, D-33615 Bielefeld, Germany
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47
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König J, Lotte K, Plessow R, Brockhinke A, Baier M, Dietz KJ. Reaction mechanism of plant 2-Cys peroxiredoxin. Role of the C terminus and the quaternary structure. J Biol Chem 2003; 278:24409-20. [PMID: 12702727 DOI: 10.1074/jbc.m301145200] [Citation(s) in RCA: 136] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Barley 2-cysteine peroxiredoxin (2-Cys Prx) was analyzed for peroxide reduction, quaternary structure, thylakoid attachment, and function as well as in vivo occurrence of the inactivated form, with emphasis on the role of specific amino acid residues. Data presented show the following. 1) 2-Cys Prx has a broad substrate specificity and reduces even complex lipid peroxides such as phosphatidylcholine dilineoyl hydroperoxide, although at low rates. 2) 2-Cys Prx partly becomes irreversibly oxidized by peroxide substrates during the catalytic cycle in a concentration-dependent manner, particularly by bulky hydroperoxides. 3) Using dithiothreitol and thioredoxin (Trx) as reductants, amino acids were identified that are important for peroxide reduction (Cys64, Arg140, and Arg163), regeneration by Trx (Cys185), and conformation changes from dimer to oligomer (Thr66, Trp99, and Trp189). 4) Oligomerization decreased the rate of Trx-dependent peroxide detoxification. 5) Comparison of PrxWT, W99L, and W189L using static and time-resolved LIF techniques demonstrated the contributions of the tryptophan residues and yielded information about their local environment. Data indicated protein dynamics in the catalytic site and the carboxyl terminus during the reduction-oxidation cycle. 6) Reduced and inactivated barley 2-Cys Prx oligomerized and attached to the thylakoid membrane in isolated chloroplasts. The in vivo relevance of inactivation was shown in leaves subjected to cold and wilting stress and during senescence. Based on these results, it is hypothesized that in addition to its function in peroxide detoxification, 2-Cys Prx may play a role as a structural redox sensor in chloroplasts.
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Affiliation(s)
- Janine König
- Biochemistry and Physiology of Plants, University of Bielefeld, Germany
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Markovitsi D, Sharonov A, Onidas D, Gustavsson T. The effect of molecular organisation in DNA oligomers studied by femtosecond fluorescence spectroscopy. Chemphyschem 2003; 4:303-5. [PMID: 12674606 DOI: 10.1002/cphc.200390050] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Dimitra Markovitsi
- Laboratoire Francis Perrin, CEA/DSM/DRECAM/SPAM-CNRS URA 2453, CEA Saclay, 91191 Gif-sur-Yvette, France.
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Brockhinke A, Plessow R, Kohse-Höinghaus K, Herrmann C. Structural changes in the Ras protein revealed by fluorescence spectroscopy. Phys Chem Chem Phys 2003. [DOI: 10.1039/b303262k] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Lakowicz JR, Shen Y, D'Auria S, Malicka J, Fang J, Gryczynski Z, Gryczynski I. Radiative decay engineering. 2. Effects of Silver Island films on fluorescence intensity, lifetimes, and resonance energy transfer. Anal Biochem 2002; 301:261-77. [PMID: 11814297 PMCID: PMC6909932 DOI: 10.1006/abio.2001.5503] [Citation(s) in RCA: 369] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Metallic surfaces can have unusual effects on fluorophores such as increasing or decreasing the rates of radiative decay and the rates of resonance energy transfer (RET). In the present article we describe the effects of metallic silver island films on the emission spectra, lifetimes, and energy transfer for several fluorophores. The fluorophores are not covalently coupled to the silver islands so that there are a range of fluorophore-to-metal distances. We show that proximity of fluorophores to the silver islands results in increased fluorescence intensity, with the largest enhancement for the lowest-quantum-yield fluorophores. Importantly, the metal-induced increases in intensity are accompanied by decreased lifetimes and increased photostability. These effects demonstrate that the silver islands have increased the radiative decay rates of the fluorophore. For solvent-sensitive fluorophores the emission spectra shifted to shorted wavelengths in the presence of the silver islands, which is consistent with a decrease of the apparent lifetime for fluorophores near the metal islands. We also observed an increased intensity and blue spectral shift for the protein human glyoxalase, which displays a low quantum yield for its intrinsic tryptophan emission. In this case the blue shift is thought to be due to increased emission from a buried low-quantum-yield tryptophan residue. Increased intensities were also observed for the intrinsic emission of the nucleic acid bases adenine and thymine and for single-stranded 15-mers poly(T) and poly(C). And finally, we observed increased RET for donors and acceptors in solution and when bound to double-helical DNA. These results demonstrate that metallic particles can be used to modify the emission from intrinsic and extrinsic fluorophores in biochemical systems.
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Affiliation(s)
- Joseph R Lakowicz
- Center for Fluorescence Spectroscopy, Department of Biochemistry and Molecular Biology, University of Maryland Baltimore, 725 West Lombard Street, Baltimore, Maryland 21201, USA
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