1
|
Benny J, Saito T, Liu J. Nitrosation mechanisms, kinetics, and dynamics of the guanine and 9-methylguanine radical cations by nitric oxide-Radical-radical combination at different electron configurations. J Chem Phys 2024; 161:125101. [PMID: 39319660 DOI: 10.1063/5.0230367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2024] [Accepted: 09/06/2024] [Indexed: 09/26/2024] Open
Abstract
As a precursor to various reactive nitrogen species formed in biological systems, nitric oxide (•NO) participates in numerous processes, including enhancing DNA radiosensitivity in ionizing radiation-based radiotherapy. Forming guanine radical cations is another common DNA lesion resulting from ionization and oxidation damage. As such, the interaction of •NO with guanine radical cations (G•+) may contribute to the radiosensitization of •NO. An intriguing aspect of this process is the participation of multiple spin configurations in the reaction, including open-shell singlet 1,OS[G•+(↑)⋯(↓)•NO], closed-shell singlet 1,CS[G(↑↓)⋯NO+], and triplet 3[G•+(↑)⋯(↑)•NO]. In this study, the reactions of •NO with both unsubstituted guanine radical cations (in the 9HG•+ conformation) and 9-methylguanine radical cations (9MG•+, a guanosine-mimicking model compound) were investigated in the absence and presence of monohydration of radical cations. Kinetic-energy dependent reaction product ions and cross sections were measured using an electrospray ionization guided-ion beam tandem mass spectrometer. The reaction mechanisms, kinetics, and dynamics were comprehended by interpreting the reaction potential energy surface using spin-projected density functional theory, coupled cluster theory, and multiconfiguration complete active space second-order perturbation theory, followed by RRKM kinetics modeling. The combined experimental and computational findings revealed closed-shell singlet 1,CS[7-NO-9MG]+ as the major, exothermic product and triplet 3[8-NO-9MG]+ as the minor, endothermic product. Singlet biradical products were not detected due to high reaction endothermicities, activation barriers, and inherent instability.
Collapse
Affiliation(s)
- Jonathan Benny
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, USA
- The Ph.D. Program in Chemistry, the Graduate Center of the City University of New York, 365 5th Ave., New York, New York 10016, USA
| | - Toru Saito
- Department of Biomedical Information Science, Graduate School of Information Science, Hiroshima City University, 731-3194 Hiroshima, Japan
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, USA
- The Ph.D. Program in Chemistry, the Graduate Center of the City University of New York, 365 5th Ave., New York, New York 10016, USA
| |
Collapse
|
2
|
Cadet J, Angelov D, Di Mascio P, Wagner JR. Contribution of oxidation reactions to photo-induced damage to cellular DNA. Photochem Photobiol 2024; 100:1157-1185. [PMID: 38970297 DOI: 10.1111/php.13990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2024] [Revised: 06/14/2024] [Accepted: 06/15/2024] [Indexed: 07/08/2024]
Abstract
This review article is aimed at providing updated information on the contribution of immediate and delayed oxidative reactions to the photo-induced damage to cellular DNA/skin under exposure to UVB/UVA radiations and visible light. Low-intensity UVC and UVB radiations that operate predominantly through direct excitation of the nucleobases are very poor oxidizing agents giving rise to very low amounts of 8-oxo-7,8-dihydroguanine and DNA strand breaks with respect to the overwhelming bipyrimidine dimeric photoproducts. The importance of these two classes of oxidatively generated damage to DNA significantly increases together with a smaller contribution of oxidized pyrimidine bases upon UVA irradiation. This is rationalized in terms of sensitized photooxidation reactions predominantly mediated by singlet oxygen together with a small contribution of hydroxyl radical that appear to also be implicated in the photodynamic effects of the blue light component of visible light. Chemiexcitation-mediated formation of "dark" cyclobutane pyrimidine dimers in UVA-irradiated melanocytes is a recent major discovery that implicates in the initial stage, a delayed generation of reactive oxygen and nitrogen species giving rise to triplet excited carbonyl intermediate and possibly singlet oxygen. High-intensity UVC nanosecond laser radiation constitutes a suitable source of light to generate pyrimidine and purine radical cations in cellular DNA via efficient biphotonic ionization.
Collapse
Affiliation(s)
- Jean Cadet
- Département de Médecine nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Dimitar Angelov
- Laboratoire de Biologie et de Modélisation de la Cellule LMBC, Ecole Normale Supérieure de Lyon, CNRS, Université de Lyon, Lyon, France
- Izmir Biomedicine and Genome Center IBG, Dokuz Eylul University, Balçova, Izmir, Turkey
| | - Paolo Di Mascio
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - J Richard Wagner
- Département de Médecine nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| |
Collapse
|
3
|
Zhou Q, Guo W, Hu Z, Yan S, Jie J, Su H. Can methylated purine bases act as photoionization hotspots? Photochem Photobiol 2024; 100:368-379. [PMID: 37792888 DOI: 10.1111/php.13862] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 10/06/2023]
Abstract
The direct photoionization of DNA canonical bases under ultraviolet radiation is difficult due to the high ionization potentials. According to previous quantum chemical calculations, methylation can have great influence on the ionization potential. Are methylated nucleobases prone to photoionization and cause DNA damage? As an important epigenetic modification in transcription, expression, and regulation of genes, it is of great biological significance to explore the effect of methylation on base photoionization from the experimental perspective. Herein, we study the photoionization behavior of methylated purines 6 mA and 6mG at 266 nm using a nanosecond transient UV-Vis spectroscopy. The hydrated electron and methylated base radicals are observed, indicating the occurrence of photoionization for both 6mG and 6 mA. We measured one-photon ionization yields to be (5.0 ± 0.2) × 10-3 and (1.4 ± 0.2) × 10-3 for 6mG and 6 mA, respectively. These are higher than those of (dA)20 and (dA20 )·(dT20 ) previously reported, indicating that methylation significantly promotes base photoionization with a stronger effect than base stacking, consistent with calculations in literature. Given that the hydrated electrons and methylated base radicals from photoionization can trigger a cascade of deleterious reactions, the methylated purine bases may act as hotspots of DNA photoionization damage of living organisms.
Collapse
Affiliation(s)
- Qian Zhou
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Wenwen Guo
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Zheng Hu
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Shuyi Yan
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Jialong Jie
- College of Chemistry, Beijing Normal University, Beijing, China
| | - Hongmei Su
- College of Chemistry, Beijing Normal University, Beijing, China
| |
Collapse
|
4
|
Benny J, Liu J. Spin-orbit charge transfer from guanine and 9-methylguanine radical cations to nitric oxide radicals and the induced triplet-to-singlet intersystem crossing. J Chem Phys 2023; 159:085102. [PMID: 37638623 DOI: 10.1063/5.0160921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/08/2023] [Indexed: 08/29/2023] Open
Abstract
Nitric oxide (●NO) participates in many biological activities, including enhancing DNA radiosensitivity in ionizing radiation-based radiotherapy. To help understand the radiosensitization of ●NO, we report reaction dynamics between ●NO and the radical cations of guanine (a 9HG●+ conformer) and 9-methylguanine (9MG●+). On the basis of the formation of 9HG●+ and 9MG●+ in the gas phase and the collisions of the radical cations with ●NO in a guided-ion beam mass spectrometer, the charge transfer reactions of 9HG●+ and 9MG●+ with ●NO were examined. For both reactions, the kinetic energy-dependent product ion cross sections revealed a threshold energy that is 0.24 (or 0.37) eV above the 0 K product 9HG (or 9MG) + NO+ asymptote. To interrogate this abnormal threshold behavior, the reaction potential energy surface for [9MG + NO]+ was mapped out at closed-shell singlet, open-shell singlet, and triplet states using density functional and coupled cluster theories. The results showed that the charge transfer reaction requires the interaction of a triplet-state surface originating from a reactant-like precursor complex 3[9MG●+(↑)⋅(↑)●NO] with a closed-shell singlet-state surface evolving from a charge-transferred complex 1[9MG⋅NO+]. During the reaction, an electron is transferred from π∗(NO) to perpendicular π∗(9MG), which introduces a change in orbital angular momentum. The latter offsets the change in electron spin angular momentum and facilitates intersystem crossing. The reaction threshold in excess of the 0 K thermochemistry and the low charge-transfer efficiency are rationalized by the vibrational excitation in the product ion NO+ and the kinetic shift arising from a long-lived triplet intermediate.
Collapse
Affiliation(s)
- Jonathan Benny
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, USA
- The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, New York 10016, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, USA
- The Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, New York 10016, USA
| |
Collapse
|
5
|
Angelov D, Boopathi R, Lone IN, Menoni H, Dimitrov S, Cadet J. Capturing Protein-Nucleic Acid Interactions by High-Intensity Laser-Induced Covalent Crosslinking. Photochem Photobiol 2022; 99:296-312. [PMID: 35997098 DOI: 10.1111/php.13699] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/21/2022] [Indexed: 11/30/2022]
Abstract
Interactions of DNA with structural proteins such as histones, regulatory proteins, and enzymes play a crucial role in major cellular processes such as transcription, replication and repair. The in vivo mapping and characterization of the binding sites of the involved biomolecules are of primary importance for a better understanding of genomic deployment that is implicated in tissue and developmental stage-specific gene expression regulation. The most powerful and commonly used approach to date is immunoprecipitation of chemically cross-linked chromatin (XChIP) coupled with sequencing analysis (ChIP-seq). While the resolution and the sensitivity of the high-throughput sequencing techniques have been constantly improved little progress has been achieved in the crosslinking step. Because of its low efficiency the use of the conventional UVC lamps remains very limited while the formaldehyde method was established as the "gold standard" crosslinking agent. Efficient biphotonic crosslinking of directly interacting nucleic acid-protein complexes by a single short UV laser pulse has been introduced as an innovative technique for overcoming limitations of conventionally used chemical and photochemical approaches. In this survey, the main available methods including the laser approach are critically reviewed for their ability to generate DNA-protein crosslinks in vitro model systems and cells.
Collapse
Affiliation(s)
- Dimitar Angelov
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, CNRS UMR 5239, 46 Allée d'Italie, 69007, Lyon, France.,Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balçova, Izmir 35330, Turkey
| | - Ramachandran Boopathi
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, CNRS UMR 5239, 46 Allée d'Italie, 69007, Lyon, France.,Université Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS), 38000, Grenoble, France
| | - Imtiaz Nisar Lone
- Izmir Biomedicine and Genome Center, Dokuz Eylul University Health Campus, Balçova, Izmir 35330, Turkey
| | - Hervé Menoni
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700, La Tronche, France
| | - Stefan Dimitrov
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences (IAB), Site Santé - Allée des Alpes, 38700, La Tronche, France
| | - Jean Cadet
- Département de Médecine nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, J1H 5N4, Québec, Canada
| |
Collapse
|
6
|
Moe MM, Saito T, Tsai M, Liu J. Singlet O 2 Oxidation of the Radical Cation versus the Dehydrogenated Neutral Radical of 9-Methylguanine in a Watson-Crick Base Pair. Consequences of Structural Context. J Phys Chem B 2022; 126:5458-5472. [PMID: 35849846 DOI: 10.1021/acs.jpcb.2c03748] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In DNA, guanine is the most susceptible to oxidative damage by exogenously and endogenously produced electronically excited singlet oxygen (1O2). The reaction mechanism and the product outcome strongly depend on the nucleobase ionization state and structural context. Previously, exposure of a monomeric 9-methylguanine radical cation (9MG•+, a model guanosine compound) to 1O2 was found to result in the formation of an 8-peroxide as the initial product. The present work explores the 1O2 oxidation of 9MG•+ and its dehydrogenated neutral form [9MG - H]• within a Watson-Crick base pair consisting of one-electron-oxidized 9-methylguanine-1-methylcytosine [9MG·1MC]•+. Emphasis is placed on entangling the base pair structural context and intra-base pair proton transfer with and consequences thereof on the singlet oxygenation of guanine radical species. Electrospray ionization coupled with guided-ion beam tandem mass spectrometry was used to study the formation and reaction of guanine radical species in the gas phase. The 1O2 oxidation of both 9MG•+ and [9MG - H]• is exothermic and proceeds barrierlessly either in an isolated monomer or within a base pair. Single- and multi-referential theories were tested for treating spin contaminations and multi-configurations occurring in radical-1O2 interactions, and reaction potential energy surfaces were mapped out to support experimental findings. The work provides a comprehensive profile for the singlet oxygenation of guanine radicals in different charge states and in the absence and the presence of base pairing. All results point to an 8-peroxide as the major oxidation product in the experiment, and the oxidation becomes slightly more favorable in a neutral radical form. On the basis of a variety of reaction pathways and product profiles observed in the present and previous studies, the interplay between guanine structure, base pairing, and singlet oxygenation and its biological implications are discussed.
Collapse
Affiliation(s)
- May Myat Moe
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York 10016, United States
| | - Toru Saito
- Department of Biomedical Information Science, Graduate School of Information Science, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, 731-3194 Hiroshima, Japan
| | - Midas Tsai
- Department of Natural Sciences, LaGuardia Community College, 31-10 Thomson Avenue, Long Island City, New York 11101, United States
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York 10016, United States
| |
Collapse
|
7
|
Cadet J, Angelov D, Wagner JR. Hydroxyl radical is predominantly involved in oxidatively generated base damage to cellular DNA exposed to ionizing radiation. Int J Radiat Biol 2022; 98:1-7. [PMID: 35475423 DOI: 10.1080/09553002.2022.2067363] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/29/2022] [Accepted: 04/06/2022] [Indexed: 12/28/2022]
Affiliation(s)
- Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Canada
| | - Dimitar Angelov
- Laboratoire de Biologie et de Modélisation de la Cellule LBMC, Ecole Normale Supérieure de Lyon, CNRS, Université de Lyon, Lyon, France
- Izmir Biomedicine and Genome Center IBG, Dokuz Eylul University Health Campus, Balçova, Izmir, Turkey
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Canada
| |
Collapse
|
8
|
Angelov D, Lone IN, Menoni H, Cadet J. Interstrand Crosslinking Involving Guanine: A New Major UVC Laser-Induced Biphotonic Oxidatively Generated DNA Damage. Photochem Photobiol 2021; 98:662-670. [PMID: 34958483 DOI: 10.1111/php.13587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Accepted: 11/29/2021] [Indexed: 11/27/2022]
Abstract
Several classes of oxidatively generated DNA damage including oxidized purine and pyrimidine bases, interstrand base crosslinks and DNA-protein crosslinks have been previously shown to be generated in both isolated DNA and cellular DNA upon exposure to either 266 nm laser irradiation or one-electron oxidants. In this study, we provide evidence that biphotonic ionization of guanine bases by UVC laser irradiation of double-stranded deoxyoligonucleotides in aerated aqueous solutions induces the formation of interstrand cross-links (ICLs). This is supported by various experiments including sequencing gel analyses of formed photoproducts and effects of UVC laser intensity on their formation. This constitutes a novel example of the diversity of reactions of guanine radical cation that can be generated by various one-electron oxidants including UVC laser biphotonic ionization, direct effect of ionization radiation and type I photosensitizers. However, the exact structure of the interstrand base adducts that is a challenging analytical issue remains to be further established. Examples of relevant biochemical/structural applications of biphotonic induction of ICLs in DNA samples by high-intensity UVC laser pulses are provided.
Collapse
Affiliation(s)
- Dimitar Angelov
- Université de Lyon, Ecole Normale Supérieure de Lyon, CNRS, Laboratoire de Biologie et de Modélisation de la Cellule LBMC, 46 Allée d'Italie, 69007, Lyon, France.,Izmir Biomedicine and Genome Center IBG, Dokuz Eylul University Health Campus, Balçova, Izmir, 35330, Turkey
| | - Imtiaz Nisar Lone
- Izmir Biomedicine and Genome Center IBG, Dokuz Eylul University Health Campus, Balçova, Izmir, 35330, Turkey
| | - Hervé Menoni
- Université Grenoble Alpes, CNRS UMR 5309, INSERM U1209, Institute for Advanced Biosciences IAB, Site Santé - Allée des Alpes, 38700, La Tronche, France
| | - Jean Cadet
- Département de Médecine nucléaire et Radiobiologie, Faculté de Médecine, Université de Sherbrooke, Sherbrooke, Québec, Canada, J1H 5N4
| |
Collapse
|
9
|
Torii S, Miura F, Itamochi M, Haga K, Katayama K, Katayama H. Impact of the Heterogeneity in Free Chlorine, UV 254, and Ozone Susceptibilities Among Coxsackievirus B5 on the Prediction of the Overall Inactivation Efficiency. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:3156-3164. [PMID: 33583178 DOI: 10.1021/acs.est.0c07796] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The disinfection susceptibilities of viruses vary even among variants, yet the inactivation efficiency of a certain virus genotype, species, or genus was determined based on the susceptibility of its laboratory strain. The objectives were to evaluate the variability in susceptibilities to free chlorine, UV254, and ozone among 13 variants of coxsackievirus B5 (CVB5) and develop the model allowing for predicting the overall inactivation of heterogeneous CVB5. Our results showed that the susceptibilities differed by up to 3.4-fold, 1.3-fold, and 1.8-fold in free chlorine, UV254, and ozone, respectively. CVB5 in genogroup B exhibited significantly lower susceptibility to free chlorine and ozone than genogroup A, where the laboratory strain, Faulkner, belongs. The capsid protein in genogroup B contained a lower number of sulfur-containing amino acids, readily reactive to oxidants. We reformulated the Chick-Watson model by incorporating the probability distributions of inactivation rate constants to capture the heterogeneity. This expanded Chick-Watson model indicated that up to 4.2-fold larger free chlorine CT is required to achieve 6-log inactivation of CVB5 than the prediction by the Faulkner strain. Therefore, it is recommended to incorporate the variation in disinfection susceptibilities for predicting the overall inactivation of a certain type of viruses.
Collapse
Affiliation(s)
- Shotaro Torii
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| | - Fuminari Miura
- Center for Marine Environmental Studies (CMES), Ehime University, Bunkyo-cho 3, Matsuyama-shi, Ehime 790-8577, Japan
| | - Masae Itamochi
- Department of Virology, Toyama Institute of Health, 17-1 Nakataikoyama, Imizu-shi, Toyama 939-0363, Japan
| | - Kei Haga
- Laboratory of Viral Infection I, Department of Infection Control and Immunology, O̅mura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Kazuhiko Katayama
- Laboratory of Viral Infection I, Department of Infection Control and Immunology, O̅mura Satoshi Memorial Institute & Graduate School of Infection Control Sciences, Kitasato University, Tokyo 108-8641, Japan
| | - Hiroyuki Katayama
- Department of Urban Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8654, Japan
| |
Collapse
|
10
|
Sun Y, Moe MM, Liu J. Mass spectrometry and computational study of collision-induced dissociation of 9-methylguanine–1-methylcytosine base-pair radical cation: intra-base-pair proton transfer and hydrogen transfer, non-statistical dissociation, and reaction with a water ligand. Phys Chem Chem Phys 2020; 22:14875-14888. [DOI: 10.1039/d0cp01788d] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A combined experimental and theoretical study is presented on the collision-induced dissociation of 9-methylguanine–1-methylcytosine base-pair radical cation ([9MG·1MC]˙+) and its monohydrate ([9MG·1MC]˙+·H2O) with Xe and Ar gases.
Collapse
Affiliation(s)
- Yan Sun
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| | - May Myat Moe
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| | - Jianbo Liu
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| |
Collapse
|
11
|
Kerzig C, Wenger OS. Reactivity control of a photocatalytic system by changing the light intensity. Chem Sci 2019; 10:11023-11029. [PMID: 32206254 PMCID: PMC7069242 DOI: 10.1039/c9sc04584h] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 10/08/2019] [Indexed: 12/13/2022] Open
Abstract
By using simple optics such as a lens, switching between one- and two-photon driven reaction mechanisms became feasible, which allows the control over the main products of photochemical reactions.
We report a novel light-intensity dependent reactivity approach allowing us to selectively switch between triplet energy transfer and electron transfer reactions, or to regulate the redox potential available for challenging reductions. Simply by adjusting the light power density with an inexpensive lens while keeping all other parameters constant, we achieved control over one- and two-photon mechanisms, and successfully exploited our approach for lab-scale photoreactions using three substrate classes with excellent selectivities and good product yields. Specifically, our proof-of-concept study demonstrates that the irradiation intensity can be used to control (i) the available photoredox reactivity for reductive dehalogenations to selectively target either bromo- or chloro-substituted arenes, (ii) the photochemical cis–trans isomerization of olefins versus their photoreduction, and (iii) the competition between hydrogen atom abstraction and radical dimerization processes.
Collapse
Affiliation(s)
- Christoph Kerzig
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland . ;
| | - Oliver S Wenger
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , 4056 Basel , Switzerland . ;
| |
Collapse
|
12
|
Cadet J, Wagner JR, Angelov D. Biphotonic Ionization of DNA: From Model Studies to Cell. Photochem Photobiol 2018; 95:59-72. [PMID: 30380156 DOI: 10.1111/php.13042] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/16/2018] [Indexed: 12/13/2022]
Abstract
Oxidation reactions triggered by low-intensity UV photons represent a minor contribution with respect to the overwhelming pyrimidine base dimerization in both isolated and cellular DNA. The situation is totally different when DNA is exposed to high-intensity UVC radiation under conditions where biphotonic ionization of the four main purine and pyrimidine bases becomes predominant at the expense of singlet excitation processes. The present review article provides a critical survey of the main chemical reactions of the base radical cations thus generated by one-electron oxidation of nucleic acids in model systems and cells. These include oxidation of the bases with the predominant formation of 8-oxo-7,8-dihydroguanine as the result of preferential hole transfer to guanine bases that act as sinks in isolated and cellular DNA. In addition to hydration, other nucleophilic addition reactions involving the guanine radical cation give rise to intra- and interstrand cross-links together with DNA-protein cross-links. Information is provided on the utilization of high-intensity UV laser pulses as molecular biology tools for studying DNA conformational features, nucleic acid-protein interactions and nucleic acid reactivity through DNA-protein cross-links and DNA footprinting experiments.
Collapse
Affiliation(s)
- Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - Dimitar Angelov
- Laboratoire de Biologie et Modélisation de la Cellule LBMC, CNRS-UMR 5239, Université de Lyon, École Normale Supérieure de Lyon, Lyon, France
| |
Collapse
|
13
|
Sun Y, Zhou W, Moe MM, Liu J. Reactions of water with radical cations of guanine, 9-methylguanine, 2′-deoxyguanosine and guanosine: keto–enol isomerization, C8-hydroxylation, and effects of N9-substitution. Phys Chem Chem Phys 2018; 20:27510-27522. [DOI: 10.1039/c8cp05453c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The reactions of D2O with guanine radical cations in nucleobases and nucleosides were studied in the gas phase using the guided-ion-beam experiment and computational modeling.
Collapse
Affiliation(s)
- Yan Sun
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| | - Wenjing Zhou
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
| | - May Myat Moe
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry
- Queens College of the City University of New York
- Queens
- USA
- PhD Program in Chemistry
| |
Collapse
|
14
|
How Does Thymine DNA Survive Ultrafast Dimerization Damage? Molecules 2016; 22:molecules22010060. [PMID: 28042858 PMCID: PMC6155609 DOI: 10.3390/molecules22010060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2016] [Revised: 12/13/2016] [Accepted: 12/24/2016] [Indexed: 11/16/2022] Open
Abstract
The photodimerization reaction between the two adjacent thymine bases within a single strand has been the subject of numerous studies due to its potential to induce DNA mutagenesis and possible tumorigenesis in human skin cells. It is well established that the cycloaddition photoreaction takes place on a picosecond time scale along barrierless or low barrier singlet/triplet pathways. However, the observed dimerization quantum yield in different thymine multimer is considerable lower than might be expected. A reasonable explanation is required to understand why thymine in DNA is able to survive ultrafast dimerization damage. In this work, accurate quantum calculations based on the combined CASPT2//CASSCF/AMBER method were conducted to map the excited state relaxation pathways of the thymine monomer in aqueous solution and of the thymine oligomer in DNA. A monomer-like decay pathway, induced by the twisting of the methyl group, is found to provide a bypass channel to ensure the photostability of thymine in single-stranded oligomers. This fast relaxation path is regulated by the conical intersection between the bright SCT(¹ππ*) state with the intra-base charge transfer character and the ground state to remove the excess excitation energy, thereby achieving the ground-state recovery with high efficiency.
Collapse
|
15
|
Itri F, Monti DM, Della Ventura B, Vinciguerra R, Chino M, Gesuele F, Lombardi A, Velotta R, Altucci C, Birolo L, Piccoli R, Arciello A. Femtosecond UV-laser pulses to unveil protein-protein interactions in living cells. Cell Mol Life Sci 2016; 73:637-48. [PMID: 26265182 PMCID: PMC11108384 DOI: 10.1007/s00018-015-2015-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Revised: 07/30/2015] [Accepted: 08/06/2015] [Indexed: 12/30/2022]
Abstract
A hallmark to decipher bioprocesses is to characterize protein-protein interactions in living cells. To do this, the development of innovative methodologies, which do not alter proteins and their natural environment, is particularly needed. Here, we report a method (LUCK, Laser UV Cross-linKing) to in vivo cross-link proteins by UV-laser irradiation of living cells. Upon irradiation of HeLa cells under controlled conditions, cross-linked products of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were detected, whose yield was found to be a linear function of the total irradiation energy. We demonstrated that stable dimers of GAPDH were formed through intersubunit cross-linking, as also observed when the pure protein was irradiated by UV-laser in vitro. We proposed a defined patch of aromatic residues located at the enzyme subunit interface as the cross-linking sites involved in dimer formation. Hence, by this technique, UV-laser is able to photofix protein surfaces that come in direct contact. Due to the ultra-short time scale of UV-laser-induced cross-linking, this technique could be extended to weld even transient protein interactions in their native context.
Collapse
Affiliation(s)
- Francesco Itri
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Daria M Monti
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
- Istituto Nazionale di Biostrutture e Biosistemi (INBB), Rome, Italy
| | | | - Roberto Vinciguerra
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Marco Chino
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Felice Gesuele
- Department of Physics, University of Naples Federico II, 80126, Naples, Italy
| | - Angelina Lombardi
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Raffaele Velotta
- Department of Physics, University of Naples Federico II, 80126, Naples, Italy
- Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), UdR, Naples, Italy
| | - Carlo Altucci
- Department of Physics, University of Naples Federico II, 80126, Naples, Italy.
- Consorzio Nazionale Interuniversitario per le Scienze Fisiche della Materia (CNISM), UdR, Naples, Italy.
| | - Leila Birolo
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy.
| | - Renata Piccoli
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
- Istituto Nazionale di Biostrutture e Biosistemi (INBB), Rome, Italy
| | - Angela Arciello
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy.
- Istituto Nazionale di Biostrutture e Biosistemi (INBB), Rome, Italy.
| |
Collapse
|
16
|
Intriguing radical–radical interactions among double-electron oxidized adenine–thymine base pairs. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.11.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
17
|
Zhao H, Liu K, Song D, Su H. Physical quenching in competition with the formation of cyclobutane pyrimidine dimers in DNA photolesion. J Phys Chem A 2014; 118:9105-12. [PMID: 24964272 DOI: 10.1021/jp504944b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The potential energy profiles toward formation of cyclobutane pyrimidine dimers CPD and the physical quenching after UV excitation were explored for the dinucleotide thymine dinucleoside monophosphate (TpT) using density functional theory (ωB97XD) and the time-dependent density functional theory (TD-ωB97XD). The ωB97XD functional that includes empirical dispersion correction is shown to be an appropriate method to obtain rational results for the current large reaction system of TpT. Photophysical quenching is shown to be predominant over the photochemical CPD formation. Following the initial excitation to the (1)ππ* state, the underlying dark (1)nπ* state bifurcates the excited population to the prevailing IC to S0 and the small ISC to the long-lived triplet state T1 via T4 ((3)ππ*) state that has negligible energy gap with (1)nπ* state. Even for the reactive T1 state, two physical quenching pathways resulting in the conversion back to ground-state reactant via the T1/S0 crossing points are newly located, which are in strong competition with CPD formation. These results provide rationale for the recently observed nanosecond triplet decay rates in the single-stranded (dT)18 and inefficiency of deleterious CPD formation, which allow for a deeper understanding of DNA photostability.
Collapse
Affiliation(s)
- Hongmei Zhao
- Beijing National Laboratory for Molecular Sciences (BNLMS), State Key Laboratory of Molecular Reaction Dynamics, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, P. R. China
| | | | | | | |
Collapse
|
18
|
Benedetti R, Conte M, Carafa V, Della Ventura B, Altucci C, Velotta R, Stunnenberg HG, Altucci L, Nebbioso A. Analysis of chromatin-nuclear receptor interactions by laser-chromatin immunoprecipitation. Methods Mol Biol 2014; 1204:25-34. [PMID: 25182758 DOI: 10.1007/978-1-4939-1346-6_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Better defining the dynamics of biomolecular interactions is an important step in understanding molecular biology and cellular processes. DNA-protein interactions, and specifically hormone-triggered DNA-nuclear receptor interactions, are key events which are still poorly understood. To date, the most commonly used approach in studying chromatin interactions is the immunoprecipitation of chemically cross-linked chromatin (ChIP) coupled with single gene or global genomic analyses. Currently, establishing a stable interplay between nucleic acids and proteins (DNA-protein cross-link) is mainly obtained through conventional, diffusion-triggered, chemical methods using formaldehyde. Here we describe an alternative method, called Laser-ChIP (LChIP), for the specific analysis of interactions between chromatin and nuclear receptors driven by a UV laser energy source. Photo-induced cross-linking in LChIP is achieved very rapidly, allowing the study of transient interactions, depending on laser source parameters.
Collapse
Affiliation(s)
- Rosaria Benedetti
- Dipartimento di Biochimica, Biofisica e Patologia Generale-II Università di Napoli, Via L. De Crecchio, 7, 80138, Naples, Italy
| | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Zhao J, Wang M, Yang H, Zhang M, Liu P, Bu Y. Radical–Radical Interactions among Oxidized Guanine Bases Including Guanine Radical Cation and Dehydrogenated Guanine Radicals. J Phys Chem B 2013; 117:10698-710. [DOI: 10.1021/jp4042149] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jing Zhao
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, 250100, People’s Republic of China
| | - Mei Wang
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, 250100, People’s Republic of China
| | - Hongfang Yang
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, 250100, People’s Republic of China
| | - Meng Zhang
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, 250100, People’s Republic of China
| | - Ping Liu
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, 250100, People’s Republic of China
| | - Yuxiang Bu
- School of Chemistry and Chemical
Engineering, Shandong University, Jinan, 250100, People’s Republic of China
| |
Collapse
|
20
|
Leo G, Altucci C, Bourgoin-Voillard S, Gravagnuolo AM, Esposito R, Marino G, Costello CE, Velotta R, Birolo L. Ultraviolet laser-induced cross-linking in peptides. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:1660-8. [PMID: 23754800 PMCID: PMC3882510 DOI: 10.1002/rcm.6610] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2013] [Revised: 04/24/2013] [Accepted: 04/25/2013] [Indexed: 05/29/2023]
Abstract
RATIONALE The aim of this study was to demonstrate, and to characterize by high-resolution mass spectrometry that it is possible to preferentially induce covalent cross-links in peptides by using high-energy femtosecond ultraviolet (UV) laser pulses. The cross-link is readily formed only when aromatic amino acids are present in the peptide sequence. METHODS Three peptides, xenopsin, angiotensin I, and interleukin, individually or in combination, were exposed to high-energy femtosecond UV laser pulses, either alone or in the presence of spin trapping molecules, the reaction products being characterized by high resolution mass spectrometry. RESULTS High-resolution mass spectrometry and spin trapping strategies showed that cross-linking occurs readily, proceeds via a radical mechanism, and is the highly dominant reaction, proceeding without causing significant photo-damage in the investigated range of experimental parameters. CONCLUSIONS High-energy femtosecond UV laser pulses can be used to induce covalent cross-links between aromatic amino acids in peptides, overcoming photo-oxidation processes, that predominate as the mean laser pulse intensity approaches illumination conditions achievable with conventional UV light sources.
Collapse
Affiliation(s)
- Gabriella Leo
- Dipartimento di Scienze Chimiche, Università di Napoli “Federico II”, Complesso Universitario di Monte S. Angelo, 80126-Napoli, Italy
| | - Carlo Altucci
- Dipartimento di Scienze Fisiche, Università di Napoli “Federico II”, Complesso Universitario di Monte S. Angelo, 80126-Napoli, Italy
| | - Sandrine Bourgoin-Voillard
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Alfredo M. Gravagnuolo
- Dipartimento di Scienze Chimiche, Università di Napoli “Federico II”, Complesso Universitario di Monte S. Angelo, 80126-Napoli, Italy
| | - Rosario Esposito
- Dipartimento di Scienze Fisiche, Università di Napoli “Federico II”, Complesso Universitario di Monte S. Angelo, 80126-Napoli, Italy
| | - Gennaro Marino
- Dipartimento di Scienze Chimiche, Università di Napoli “Federico II”, Complesso Universitario di Monte S. Angelo, 80126-Napoli, Italy
| | - Catherine E. Costello
- Center for Biomedical Mass Spectrometry, Department of Biochemistry, Boston University School of Medicine, Boston, Massachusetts 02118, USA
| | - Raffaele Velotta
- Dipartimento di Scienze Fisiche, Università di Napoli “Federico II”, Complesso Universitario di Monte S. Angelo, 80126-Napoli, Italy
| | - Leila Birolo
- Dipartimento di Scienze Chimiche, Università di Napoli “Federico II”, Complesso Universitario di Monte S. Angelo, 80126-Napoli, Italy
| |
Collapse
|
21
|
Douki T, Ravanat JL, Angelov D, Wagner JR, Cadet J. Effects of Duplex Stability on Charge-Transfer Efficiency within DNA. Top Curr Chem (Cham) 2012. [DOI: 10.1007/b94409] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
|
22
|
Orzekowsky-Schroeder R, Klinger A, Martensen B, Blessenohl M, Gebert A, Vogel A, Hüttmann G. In vivo spectral imaging of different cell types in the small intestine by two-photon excited autofluorescence. JOURNAL OF BIOMEDICAL OPTICS 2011; 16:116025. [PMID: 22112130 DOI: 10.1117/1.3655587] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Spectrally resolved two-photon excited autofluorescence imaging is used to distinguish different cell types and functional areas during dynamic processes in the living gut. Excitation and emission spectra of mucosal tissue and tissue components are correlated to spectra of endogenous chromophores. We show that selective excitation with only two different wavelengths within the tuning range of a Ti:sapphire femtosecond laser system yields excellent discrimination between enterocytes, antigen presenting cells and lysosomes based on the excitation and emission properties of their autofluorescence. The method is employed for time-lapse microscopy over up to 8 h. Changes of the spectral signature with the onset of photodamage are demonstrated, and their origin is discussed.
Collapse
|
23
|
Kuetemeyer K, Lucas-Hahn A, Petersen B, Lemme E, Hassel P, Niemann H, Heisterkamp A. Combined multiphoton imaging and automated functional enucleation of porcine oocytes using femtosecond laser pulses. JOURNAL OF BIOMEDICAL OPTICS 2010; 15:046006. [PMID: 20799808 DOI: 10.1117/1.3463012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Since the birth of "Dolly" as the first mammal cloned from a differentiated cell, somatic cell cloning has been successful in several mammalian species, albeit at low success rates. The highly invasive mechanical enucleation step of a cloning protocol requires sophisticated, expensive equipment and considerable micromanipulation skill. We present a novel noninvasive method for combined oocyte imaging and automated functional enucleation using femtosecond (fs) laser pulses. After three-dimensional imaging of Hoechst-labeled porcine oocytes by multiphoton microscopy, our self-developed software automatically identified the metaphase plate. Subsequent irradiation of the metaphase chromosomes with the very same laser at higher pulse energies in the low-density-plasma regime was used for metaphase plate ablation (functional enucleation). We show that fs laser-based functional enucleation of porcine oocytes completely inhibited the parthenogenetic development without affecting the oocyte morphology. In contrast, nonirradiated oocytes were able to develop parthenogenetically to the blastocyst stage without significant differences to controls. Our results indicate that fs laser systems have great potential for oocyte imaging and functional enucleation and may improve the efficiency of somatic cell cloning.
Collapse
|
24
|
Abstract
Recent experimental and theoretical investigations dealing with model DNA double helices, composed of either adenine–thymine (A–T) or guanine–cytosine (G–C) base pairs, and G quadruplexes shed some light on the excited states populated by photon absorption and their relaxation, energy transfer among bases, and one-photon ionization. These studies revealed that the Franck–Condon excited states of DNA helices cannot be considered as the sum of their monomeric constituents because electronic coupling induces delocalization of the excitation over a few bases. Energy transfer takes place via intraband scattering in less than 100 fs. The fluorescence lifetimes of DNA helices detected by fluorescence upconversion and corresponding mainly to ππ* transitions are longer than that of an equimolar mixture of nucleotides; the only exception was observed for alternating G–C polymers. Moreover, nanosecond flash photolysis experiments showed that organization of bases within single and double helices may lead to a lowering of their ionization potential. Finally, the first determination regarding the time-scale needed for the formation of T dimers, the (6–4) adducts, was determined for the single strand (dT)20.
Collapse
|
25
|
Thøgersen J, Knudsen CS, Maetzke A, Jensen SJK, Keiding SR, Alsner J, Overgaard J. Reproductive death of cancer cells induced by femtosecond laser pulses. Int J Radiat Biol 2009; 83:289-99. [PMID: 17457754 DOI: 10.1080/09553000701283808] [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: 10/23/2022]
Abstract
PURPOSE High intensity femtosecond (1 fs = 10(-15) s) laser pulses may, via multi-photon processes, cause reproductive cell death at wavelengths that otherwise are harmless. We study the efficacy of inducing reproductive death of cancer cells by ultraviolet (UV), visible (VIS) and near infrared (IR) femtosecond laser pulses. MATERIALS AND METHODS Human squamous carcinoma cervical cancer cells are irradiated by femtosecond laser pulses at 800 nanometers (nm), 400 nm, 266 nm and 200 nm. The reproductive death is assessed by colony forming assay. The contribution from multi-photon processes is evaluated by comparing the cell reproduction subsequent to irradiation by collimated (low intensity) and focused (high intensity), pulsed laser beams with identical fluences. RESULTS Suitable femtosecond pulses are capable of arresting cell reproduction at all the tested wavelengths. Irradiation at 266 nm is far more efficient than the other wavelengths, both in terms of the fluence and the absorbed dose needed to induce reproductive cell death. The collimated 800 nm beam is unable to induce reproductive cell death even at a fluence of 230 Joule/square centimeters (J/cm2). However, focused 800 nm pulses with much higher intensities, but lower fluences efficiently arrest cell reproduction, thus highlighting the dramatic effect of multi-photon processes. At the intensities used in the present work focusing the 400 nm beam improves its efficacy by an order of magnitude, whereas focusing the 266 nm beam does not improve its efficacy. CONCLUSION Femtosecond pulses at 200, 266, 400 and 800 nm induce reproductive cell death if the intensity is sufficiently high. Multi-photon processes can improve the efficacy substantially and even result in reproductive cell death at wavelengths, where single-photon processes are harmless.
Collapse
Affiliation(s)
- Jan Thøgersen
- Department of Chemistry, University of Aarhus, Denmark.
| | | | | | | | | | | | | |
Collapse
|
26
|
Candeias LP, O'Neill P, Jones GD, Steenken S. Ionization of Polynucleotides and DNA in Aqueous Solution by 193nm Pulsed Laser Light: Identification of Base-derived Radicals. Int J Radiat Biol 2009; 61:15-20. [PMID: 1345926 DOI: 10.1080/09553009214550571] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- L P Candeias
- Max-Planck-Institut für Strahlenchemie, Mülheim, Germany
| | | | | | | |
Collapse
|
27
|
Affiliation(s)
- Angelo Bongiorno
- School of Chemistry & Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400
| |
Collapse
|
28
|
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: 9.3] [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.
Collapse
Affiliation(s)
- Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
| | | | | |
Collapse
|
29
|
Fecko CJ, Munson KM, Saunders A, Sun G, Begley TP, Lis JT, Webb WW. Comparison of femtosecond laser and continuous wave UV sources for protein-nucleic acid crosslinking. Photochem Photobiol 2008; 83:1394-404. [PMID: 18028214 DOI: 10.1111/j.1751-1097.2007.00179.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Crosslinking proteins to the nucleic acids they bind affords stable access to otherwise transient regulatory interactions. Photochemical crosslinking provides an attractive alternative to formaldehyde-based protocols, but irradiation with conventional UV sources typically yields inadequate product amounts. Crosslinking with pulsed UV lasers has been heralded as a revolutionary technique to increase photochemical yield, but this method had only been tested on a few protein-nucleic acid complexes. To test the generality of the yield enhancement, we have investigated the benefits of using approximately 150 fs UV pulses to crosslink TATA-binding protein, glucocorticoid receptor and heat shock factor to oligonucleotides in vitro. For these proteins, we find that the quantum yields (and saturating yields) for forming crosslinks using the high-peak intensity femtosecond laser do not improve on those obtained with low-intensity continuous wave (CW) UV sources. The photodamage to the oligonucleotides and proteins also has comparable quantum yields. Measurements of the photochemical reaction yields of several small molecules selected to model the crosslinking reactions also exhibit nearly linear dependences on UV intensity instead of the previously predicted quadratic dependence. Unfortunately, these results disprove earlier assertions that femtosecond pulsed laser sources provide significant advantages over CW radiation for protein-nucleic acid crosslinking.
Collapse
Affiliation(s)
- Christopher J Fecko
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
| | | | | | | | | | | | | |
Collapse
|
30
|
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: 7.9] [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.
Collapse
Affiliation(s)
- Wai-Ming Kwok
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong S. A. R., P. R. China
| | | | | |
Collapse
|
31
|
Angelov D, Charra M, Müller CW, Cadet J, Dimitrov S. Solution Study of the NF-κB p50-DNA Complex by UV Laser Protein-DNA Cross-linking¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2003)0770592ssotnp2.0.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]
|
32
|
Crespo-Hernández CE, Arce R. Photoionization of DNA and RNA Bases, Nucleosides and Nucleotides Through a Combination of One- and Two-photon Pathways upon 266 nm Nanosecond Laser Excitation¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2002)0760259podarb2.0.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]
|
33
|
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: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
34
|
Marguet S, Markovitsi D, Talbot F. One- and Two-Photon Ionization of DNA Single and Double Helices Studied by Laser Flash Photolysis at 266 nm. J Phys Chem B 2006; 110:11037-9. [PMID: 16771360 DOI: 10.1021/jp062578m] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ionization of the DNA single and double helices (dA)20, (dT)20, (dAdT)10(dAdT)10 and (dA)20(dT)20, induced by nanosecond pulses at 266 nm, is studied by time-resolved absorption spectroscopy. The variation of the hydrated electron concentration with the absorbed laser intensity shows that, in addition to two-photon ionization, one-photon ionization takes place for (dAdT)10(dAdT)10, (dA)20(dT)20 and (dA)20 but not for (dT)20. The spectra of all adenine-containing oligomers at the microsecond time-scale correspond to the adenine deprotonated radical formed in concentrations comparable to that of the hydrated electron. The quantum yield for one-photon ionization of the oligomers (ca. 10(-3)) is higher by at least 1 order of magnitude than that of dAMP, showing clearly that organization of the bases in single and double helices leads to an important lowering of the ionization potential. The propensity of (dAdT)10(dAdT)10, containing alternating adenine-thymine sequences, to undergo one-photon ionization is lower than that of (dA)20(dT)20 and (dA)20, containing adenine runs. Pairing of the (dA)20 with the complementary strand leads to a decrease of quantum yield for one photon ionization by about a factor of 2.
Collapse
|
35
|
Sun G, Fecko CJ, Nicewonger RB, Webb WW, Begley TP. DNA−Protein Cross-Linking: Model Systems for Pyrimidine−Aromatic Amino Acid Cross-Linking. Org Lett 2006; 8:681-3. [PMID: 16468741 DOI: 10.1021/ol052876m] [Citation(s) in RCA: 30] [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
[reaction: see text] We have synthesized simple model systems to explore the possibility of photo-cross-linking between the pyrimidine bases and the side chains of the aromatic amino acids. Thymine/phenylalanine and thymine/tyrosine models gave cross-links, and thymine/tryptophan models gave complex mixtures; the cytosine/phenylalanine model was unreactive. The quantum yields for the model cross-linking reactions were 18-46 times smaller than those for thymine dimer formation. Biphotonic excitation contributes little to the yield of these reactions.
Collapse
Affiliation(s)
- Guangxing Sun
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | | | | | | | | |
Collapse
|
36
|
Markovitsi D, Onidas D, Gustavsson T, Talbot F, Lazzarotto E. Collective Behavior of Franck−Condon Excited States and Energy Transfer in DNA Double Helices. J Am Chem Soc 2005; 127:17130-1. [PMID: 16332029 DOI: 10.1021/ja054955z] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Absorption of UV radiation by DNA bases is known to induce carcinogenic mutations. The lesion distribution depends on the sequence around the hotspots, suggesting cooperativity between bases. Here we show that such cooperativity may intervene at the very first step of a cascade of events by formation of Franck-Condon states delocalized over several bases and subsequent energy transfer faster than 100 fs. Our study focuses on the double helix poly(dA).poly(dT), whose fluorescence, induced by femtosecond pulses at 267 nm, is probed by the upconversion technique and time-correlated single photon counting, over a large time domain (100 fs to 100 ns). The time-resolved fluorescence decays and fluorescence anisotropy decays are discussed in relation with the steady-state absorption and fluorescence spectra in the frame of exciton theory.
Collapse
Affiliation(s)
- Dimitra Markovitsi
- Laboratoire Francis Perrin, CEA/DSM/DRECAM/SPAM, CNRS URA 2453, CEA Saclay, 91191 Gif-sur-Yvette, France.
| | | | | | | | | |
Collapse
|
37
|
Abstract
The formation of thymine dimers in the single-stranded oligonucleotide, (dT)20, is studied at room temperature by laser flash photolysis using 266 nm excitation. It is shown that the (6-4) adduct is formed within 4 ms via a reactive intermediate. The formation of cyclobutane dimers is faster than 200 ns. The overall quantum yield for the (6-4) formation is (3.7 +/- 0.3) x 10-3, and that of the cyclobutane dimers is (2.8 +/- 0.2) x 10-2. No triplet absorption is detected, showing that either the intersystem crossing yield decreases by 1 order of magnitude upon oligomerization (<1.4 x 10-3) or the triplet state reacts with unit efficiency in less than 200 ns to yield cyclobutane dimers.
Collapse
Affiliation(s)
- Sylvie Marguet
- Laboratoire Francis Perrin, CEA/DSM/DRECAM/SPAM-CNRS, URA 2453, CEA Saclay, 91191 Gif-sur-Yvette, France
| | | |
Collapse
|
38
|
Angelov D, Beylot B, Spassky A. Origin of the heterogeneous distribution of the yield of guanyl radical in UV laser photolyzed DNA. Biophys J 2004; 88:2766-78. [PMID: 15613625 PMCID: PMC1305372 DOI: 10.1529/biophysj.104.049015] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Oxidative guanine lesions were analyzed, at the nucleotide level, within DNA exposed to nanosecond ultraviolet (266 nm) laser pulses of variable intensity (0.002-0.1 J/cm(2)). Experiments were carried out, at room temperature, in TE buffer (20 mM Tris-HCl, pH 7.5; 1 mM EDTA) containing 35 mM NaCl, on 5'-end radioactively labeled double-stranded and single-stranded oligomer DNA at a size of 33-37 nucleobases. Lesions were analyzed on polyacrylamide gel electrophoresis by taking advantage of the specific removal of 8-oxodG from DNA by the formamidopyrimidine DNA glycosylase (Fpg protein) and of the differential sensitivity of 8-oxodG and oxazolone to piperidine. The quantum yields of lesions at individual sites, determined from the normalized intensities of bands, were plotted against the irradiation energy levels. Simplified model fitting of the experimental data enabled to evaluate the spectroscopic parameters characterizing excitation and photoionization processes. Results show that the distribution of guanine residues, excited to the lowest triplet state or photoionized, is heterogeneous and depends on the primary and secondary DNA structure. These findings are generalized in terms of excitation energy and charge-migration mediated biphotonic ionization. On the basis of the changes in the yield of the guanyl radical resulting from local helical perturbations in the DNA pi-stack, it can be assessed that the distance range of migration is <6-8 bp.
Collapse
Affiliation(s)
- Dimitar Angelov
- UMR 8113 French National Center for Scientific Research, Institut Gustave Roussy, 94805 Villejuif, France
| | | | | |
Collapse
|
39
|
Crespo-Hernández CE, Arce R. Formamidopyrimidines as major products in the low- and high-intensity UV irradiation of guanine derivatives. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2004; 73:167-75. [PMID: 14975405 DOI: 10.1016/j.jphotobiol.2003.11.006] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2002] [Revised: 06/30/2003] [Accepted: 11/24/2003] [Indexed: 11/20/2022]
Abstract
Two major UV-induced transformation products of guanosine (Guo) in oxygen-free aqueous solution were isolated and characterized using reverse-phase HPLC-ESI-MS and UV absorption spectrophotometric techniques. These products were identified as two different sugar isomers of 2,6-diamino-4-hydroxy-5-formamidopyrimidine ribonucleosides, FapyGuo. A formation quantum yield of the order of 10(-3) for these products was obtained at a 75 microM concentration of Guo, while an increase in the ground state concentration of Guo from 10(-5) to 10(-4) M decreased their formation yield by a factor of ten. The formation of FapydGuo was also observed in the 254 nm photolysis of 2'-deoxyguanosine. In addition, the formation FapyGua was identified in the UV photolysis of all the guanine derivatives investigated. A formation quantum yield of the order of 10(-4) was obtained for the latter product, except in the photolysis of Gua in which a higher formation yield (10(-3)) was determined. These results suggest that hydration of the radical cation of guanine, followed by opening of the imidazole ring to form Fapy products, is one of the main low-intensity UV radiation-induced photo-transformation pathway of the guanine derivatives in oxygen-free aqueous solutions. Furthermore, the formation of the Fapy products and base release occurs through a similar photo-transformation pathways using a high-intensity UV radiation source.
Collapse
Affiliation(s)
- Carlos E Crespo-Hernández
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, P.O. Box 23346, San Juan PR 00931-3346, Puerto Rico
| | | |
Collapse
|
40
|
Close DM. Calculation of the Ionization Potentials of the DNA Bases in Aqueous Medium. J Phys Chem A 2004. [DOI: 10.1021/jp046660y] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- David M. Close
- Department of Physics, Box 70652, East Tennessee State University, Johnson City, Tennessee 37614
| |
Collapse
|
41
|
Angelov D, Lenouvel F, Hans F, Müller CW, Bouvet P, Bednar J, Moudrianakis EN, Cadet J, Dimitrov S. The histone octamer is invisible when NF-kappaB binds to the nucleosome. J Biol Chem 2004; 279:42374-82. [PMID: 15269206 DOI: 10.1074/jbc.m407235200] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The transcription factor NF-kappaB is involved in the transcriptional control of more than 150 genes, but the way it acts at the level of nucleosomal templates is not known. Here we report on a study examining the interaction of NF-kappaB p50 with its DNA recognition sequence in a positioned nucleosome. We demonstrate that NF-kappaB p50 was able to bind to the nucleosome with an apparent association constant close to that for free DNA. In agreement with this, the affinity of NF-kappaB p50 binding does not depend on the localization of its recognition sequence relative to the nucleosome dyad axis. In addition, the binding of NF-kappaB p50 does not induce eviction of histones and does not perturb the overall structure of the nucleosome. The NF-kappaB p50-nucleosome complex exhibits, however, local structural alterations within the NF-kappaB p50 recognition site. Importantly, these alterations were very similar to those found in the NF-kappaB p50-DNA complex. Our data suggest that NF-kappaB p50 can accommodate the distorted, bent DNA within the nucleosome. This peculiar property of NF-kappaB p50 might have evolved to meet the requirements for its function as a central switch for stress responses.
Collapse
Affiliation(s)
- Dimitar Angelov
- Laboratoire de Biologie Moléculaire et Cellulaire de la Différenciation, INSERM U309, Institut Albert Bonniot, Domaine de la Merci, 38706 La Tronche Cedex, France
| | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Crespo-Hernández CE, Arce R, Ishikawa Y, Gorb L, Leszczynski J, Close DM. Ab Initio Ionization Energy Thresholds of DNA and RNA Bases in Gas Phase and in Aqueous Solution. J Phys Chem A 2004. [DOI: 10.1021/jp049270k] [Citation(s) in RCA: 110] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
| | | | | | | | | | - David M. Close
- Department of Physics, East Tennessee State University, Johnson City, Tennessee 37614
| |
Collapse
|
43
|
Shafirovich V, Geacintov NE. Proton-Coupled Electron Transfer Reactions at a Distance in DNA Duplexes. Top Curr Chem (Cham) 2004. [DOI: 10.1007/b94475] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
|
44
|
Angelov D, Charra M, Müller CW, Cadet J, Dimitrov S. Solution study of the NF-kappaB p50-DNA complex by UV laser protein-DNA cross-linking. Photochem Photobiol 2003; 77:592-6. [PMID: 12870843 DOI: 10.1562/0031-8655(2003)077<0592:ssotnp>2.0.co;2] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
In this study, we describe a new approach for studying protein-DNA interactions in solution. The approach is based on mapping the UV laser-induced protein-DNA cross-links between the amino acids of the protein and the DNA bases that are in direct contact. The approach was applied for studying the solution structure of the human necrosis factor (NF)-kappaB p50 homodimer bound to a 37 base pair DNA. Several points of contact identical to those observed in the NF-kappaB-DNA crystal structure were found between the two biomolecules. Evidence is provided for the occurrence of two new contact points, one for each DNA strand. These new points of contact are located symmetrically a base apart from the extremity of the binding sequence.
Collapse
Affiliation(s)
- Dimitar Angelov
- Laboratoire de Biologie Moléculaire et Cellulaire de la Différenciation, INSERM Institut Albert Bonniot, Domaine de la Merci, La Tronche Cedex, France
| | | | | | | | | |
Collapse
|
45
|
Crespo-Hernández CE, Arce R. Near Threshold Photo-Oxidation of Dinucleotides Containing Purines upon 266 nm Nanosecond Laser Excitation. The Role of Base Stacking, Conformation, and Sequence. J Phys Chem B 2003. [DOI: 10.1021/jp026408v] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carlos E. Crespo-Hernández
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, P.O. Box 23346, San Juan, PR 00931-3346
| | - Rafael Arce
- Department of Chemistry, University of Puerto Rico, Río Piedras Campus, P.O. Box 23346, San Juan, PR 00931-3346
| |
Collapse
|
46
|
Spassky A, Angelov D. Temperature-dependence of UV laser one-electron oxidative guanine modifications as a probe of local stacking fluctuations and conformational transitions. J Mol Biol 2002; 323:9-15. [PMID: 12368094 DOI: 10.1016/s0022-2836(02)00878-1] [Citation(s) in RCA: 14] [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
By monitoring R(pip)/R(Fpg), i.e. the relative sensitivity to hot piperidine and to formamidopyrimidine DNA glycosylase (Fpg protein) of the guanine lesions induced in DNA exposed to UV laser irradiation, we have previously observed that the formation of the two major types of one-electron oxidative guanine modifications, oxazolone and 7,8-dihydro-8-oxoguanine (8-oxodG), depends on DNA conformational features. While oxazolone is largely predominant at each site of single-stranded DNA (R(pip)>R(Fpg)), 8-oxodG is the major lesion at most of the sites of double-stranded DNA (R(pip)<R(Fpg)). In the present study, we investigated the temperature dependence of R(pip) and R(Fpg) at individual sites of a DNA sequence during the transition between the double-stranded and the melted random coiled states. The striking result is that the transition curves of the ratio R(pip)/R(Fpg) display a shape similar to the helix-coil melting profile of the DNA fragment determined from UV absorbance measurements with, at individual sites, subtle differences in the slope of the curves and in the temperature at the mid-point of the transitions. At a few guanine residues of the DNA duplex, R(pip)>R(Fpg) at 20 degrees C and the ratio R(pip)/R(Fpg) does not vary significantly during the melting process. Interestingly, these guanine residues display a high sensitivity to dimethyl sulfoxide methylation while the opposite cytosine residues are unsensitive, suggesting that the prevalence of R(pip) over R(Fpg) is related not to base-pairing disruption but rather to the local helical alteration of the B-DNA stacking geometry. This leads us to propose that the slight variations in the ratios R(pip)/R(Fpg) observed, at individual sites, at temperatures below the helix-coil transition reflect local small-scale breathing motions, unstacking single dinucleotide steps prior to opening. Our results thus support the view that the temperature dependence of the ratio of R(pip)/R(Fpg) at sites of B-DNA provides a sensitive probe of the DNA internal local thermal stability and are discussed in relation with the mechanisms proposed for the intramolecular rearrangement of the guanyl radical.
Collapse
Affiliation(s)
- Annick Spassky
- UMR 8532-CNRS, Institut Gustave Roussy, Villejuif, 94805, France.
| | | |
Collapse
|
47
|
Crespo-Hernández CE, Arce R. Photoionization of DNA and RNA bases, nucleosides and nucleotides through a combination of one- and two-photon pathways upon 266 nm nanosecond laser excitation. Photochem Photobiol 2002; 76:259-67. [PMID: 12403446 DOI: 10.1562/0031-8655(2002)076<0259:podarb>2.0.co;2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The 266 nm nanosecond laser photolysis of various purine and pyrimidine derivatives results in their photoionization (PI) as one of the primary photochemical pathways. Electron photoejection occurs through a combination of one- and two-photon mechanisms. The PI values depend on the substituents attached to the chromophore of the base. The net PI of the purine bases at 266 nm are of the same order of magnitude (10(-2)) as those of the pyrimidine bases under similar experimental conditions. The monophotonic component is approximately one-third of the net PI yield of the bases. A nonrelaxed singlet excited state intermediate is tentatively proposed for this pathway. It is proposed that this state is significantly stabilized by water solvation, transforming it into a charge transfer to solvent state from which the hydrated electron evolves.
Collapse
|
48
|
Crespo-Hernández CE, Martı́nez L, González-Sierra AE, Robles-Irizarry L, Dı́az-Vázquez A, Arce R. The 254 nm low intensity and 266 nm laser photochemistry of adenosine. J Photochem Photobiol A Chem 2002. [DOI: 10.1016/s1010-6030(02)00131-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
|
49
|
|
50
|
Douki T, Angelov D, Cadet J. UV laser photolysis of DNA: effect of duplex stability on charge-transfer efficiency. J Am Chem Soc 2001; 123:11360-6. [PMID: 11707110 DOI: 10.1021/ja016426a] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The distribution of the final base damage was determined within isolated DNA exposed to pulses of 266 nm laser light. Studied lesions included oxidation products arising from biphotonic ionization of DNA bases and pyrimidine dimeric photoproducts arising from monophotonic processes. The distribution of the latter class of damage was found to be correlated with the stability of the DNA duplex. The quantum yield for formation of 8-oxo-7,8-dihydroguanine was much higher than that of other oxidized nucleosides arising from the degradation of thymine and adenine. This observation, together with the shape of the intensity dependence curves, provided evidence for the occurrence of charge-transfer processes within DNA. In addition, increase in the ionic strength of the irradiated DNA and stabilization of the DNA duplex were found to induce a drastic decrease in the yield of thymine and adenine oxidation products. Concurrently, an increase in the yield of 8-oxo-7,8-dihydroguanine was observed. This was rationalized in terms of an increase in the overall charge-transfer efficiency. Therefore, it may be concluded that stabilization of the double-helix favors charge-transfer process toward guanine bases.
Collapse
Affiliation(s)
- T Douki
- DRFMC/Service de Chimie Inorganique et Biologique UMR 5046; Laboratoire des Lésions des Acides Nucléiques; CEA/Grenoble, 17, rue des Martyrs, F-38054 Grenoble Cedex 9, France
| | | | | |
Collapse
|