1
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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: 0.5] [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.
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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
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2
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Karamanos TK, Kalverda AP, Radford SE. Generating Ensembles of Dynamic Misfolding Proteins. Front Neurosci 2022; 16:881534. [PMID: 35431773 PMCID: PMC9008329 DOI: 10.3389/fnins.2022.881534] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 03/08/2022] [Indexed: 01/09/2023] Open
Abstract
The early stages of protein misfolding and aggregation involve disordered and partially folded protein conformers that contain a high degree of dynamic disorder. These dynamic species may undergo large-scale intra-molecular motions of intrinsically disordered protein (IDP) precursors, or flexible, low affinity inter-molecular binding in oligomeric assemblies. In both cases, generating atomic level visualization of the interconverting species that captures the conformations explored and their physico-chemical properties remains hugely challenging. How specific sub-ensembles of conformers that are on-pathway to aggregation into amyloid can be identified from their aggregation-resilient counterparts within these large heterogenous pools of rapidly moving molecules represents an additional level of complexity. Here, we describe current experimental and computational approaches designed to capture the dynamic nature of the early stages of protein misfolding and aggregation, and discuss potential challenges in describing these species because of the ensemble averaging of experimental restraints that arise from motions on the millisecond timescale. We give a perspective of how machine learning methods can be used to extract aggregation-relevant sub-ensembles and provide two examples of such an approach in which specific interactions of defined species within the dynamic ensembles of α-synuclein (αSyn) and β2-microgloblulin (β2m) can be captured and investigated.
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Affiliation(s)
- Theodoros K. Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
| | | | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, Leeds, United Kingdom
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3
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Benedetti R, Bajardi F, Capozziello S, Carafa V, Conte M, Del Sorbo MR, Nebbioso A, Singh M, Stunnenberg HG, Valadan M, Altucci L, Altucci C. Different Approaches to Unveil Biomolecule Configurations and Their Mutual Interactions. ANAL LETT 2021. [DOI: 10.1080/00032719.2020.1716241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- R. Benedetti
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Università degli Studi della Campania “L. Vanvitelli”, Napoli, Italy
| | - F. Bajardi
- Dipartimento di Fisica “Ettore Pancini”, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Sez. di Napoli, Napoli, Italy
| | - S. Capozziello
- Dipartimento di Fisica “Ettore Pancini”, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Sez. di Napoli, Napoli, Italy
- Gran Sasso Science Institute, L’Aquila, Italy
| | - V. Carafa
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Università degli Studi della Campania “L. Vanvitelli”, Napoli, Italy
| | - M. Conte
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Università degli Studi della Campania “L. Vanvitelli”, Napoli, Italy
| | - M. R. Del Sorbo
- Istituto Statale d’Istruzione Superiore “Leonardo da Vinci”, Poggiomarino, NA, Italy
| | - A. Nebbioso
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Università degli Studi della Campania “L. Vanvitelli”, Napoli, Italy
| | - M. Singh
- Dipartimento di Fisica “Ettore Pancini”, Università degli Studi di Napoli “Federico II”, Napoli, Italy
| | - H. G. Stunnenberg
- Department of Molecular Biology, NCMLS, Radboud University, Nijmegen, the Netherlands
| | - M. Valadan
- Dipartimento di Fisica “Ettore Pancini”, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Sez. di Napoli, Napoli, Italy
| | - L. Altucci
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Università degli Studi della Campania “L. Vanvitelli”, Napoli, Italy
| | - C. Altucci
- Dipartimento di Fisica “Ettore Pancini”, Università degli Studi di Napoli “Federico II”, Napoli, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Sez. di Napoli, Napoli, Italy
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4
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Stützer A, Welp LM, Raabe M, Sachsenberg T, Kappert C, Wulf A, Lau AM, David SS, Chernev A, Kramer K, Politis A, Kohlbacher O, Fischle W, Urlaub H. Analysis of protein-DNA interactions in chromatin by UV induced cross-linking and mass spectrometry. Nat Commun 2020; 11:5250. [PMID: 33067435 PMCID: PMC7567871 DOI: 10.1038/s41467-020-19047-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 09/24/2020] [Indexed: 02/08/2023] Open
Abstract
Protein–DNA interactions are key to the functionality and stability of the genome. Identification and mapping of protein–DNA interaction interfaces and sites is crucial for understanding DNA-dependent processes. Here, we present a workflow that allows mass spectrometric (MS) identification of proteins in direct contact with DNA in reconstituted and native chromatin after cross-linking by ultraviolet (UV) light. Our approach enables the determination of contact interfaces at amino-acid level. With the example of chromatin-associated protein SCML2 we show that our technique allows differentiation of nucleosome-binding interfaces in distinct states. By UV cross-linking of isolated nuclei we determined the cross-linking sites of several factors including chromatin-modifying enzymes, demonstrating that our workflow is not restricted to reconstituted materials. As our approach can distinguish between protein–RNA and DNA interactions in one single experiment, we project that it will be possible to obtain insights into chromatin and its regulation in the future. Cross-linking mass spectrometry (XLMS) allows mapping of protein-protein and protein-RNA interactions, but the analysis of protein-DNA complexes remains challenging. Here, the authors develop a UV light-based XLMS workflow to determine protein-DNA interfaces in reconstituted chromatin and isolated nuclei.
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Affiliation(s)
- Alexandra Stützer
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Luisa M Welp
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Monika Raabe
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Timo Sachsenberg
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076, Tübingen, Germany.,Applied Bioinformatics, Department for Computer Science, University of Tübingen, 72076, Tübingen, Germany
| | - Christin Kappert
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.,Somatosensory Signaling and Systems Biology Group, Max Planck Institute of Experimental Medicine, 37075, Göttingen, Germany
| | - Alexander Wulf
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Andy M Lau
- Department of Chemistry, King's College London, London, SE1 1DB, UK
| | - Stefan-Sebastian David
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.,King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, 23955, Thuwal, Saudi Arabia
| | - Aleksandar Chernev
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | | | - Argyris Politis
- Department of Chemistry, King's College London, London, SE1 1DB, UK
| | - Oliver Kohlbacher
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, 72076, Tübingen, Germany.,Applied Bioinformatics, Department for Computer Science, University of Tübingen, 72076, Tübingen, Germany.,Institute for Translational Bioinformatics, University Hospital Tübingen, 72076, Tübingen, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, 72076, Tübingen, Germany
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany.,King Abdullah University of Science and Technology (KAUST), Biological and Environmental Science and Engineering Division, Laboratory of Chromatin Biochemistry, 23955, Thuwal, Saudi Arabia
| | - Henning Urlaub
- Bioanalytical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany. .,Bioanalytics Group, Institute for Clinical Chemistry, University Medical Center Göttingen, 37075, Göttingen, Germany.
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5
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Reim A, Ackermann R, Font-Mateu J, Kammel R, Beato M, Nolte S, Mann M, Russmann C, Wierer M. Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry. Nat Commun 2020; 11:3019. [PMID: 32541649 PMCID: PMC7295792 DOI: 10.1038/s41467-020-16837-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 05/27/2020] [Indexed: 11/09/2022] Open
Abstract
Transcription factors (TFs) regulate target genes by specific interactions with DNA sequences. Detecting and understanding these interactions at the molecular level is of fundamental importance in biological and clinical contexts. Crosslinking mass spectrometry is a powerful tool to assist the structure prediction of protein complexes but has been limited to the study of protein-protein and protein-RNA interactions. Here, we present a femtosecond laser-induced crosslinking mass spectrometry (fliX-MS) workflow, which allows the mapping of protein-DNA contacts at single nucleotide and up to single amino acid resolution. Applied to recombinant histone octamers, NF1, and TBP in complex with DNA, our method is highly specific for the mapping of DNA binding domains. Identified crosslinks are in close agreement with previous biochemical data on DNA binding and mostly fit known complex structures. Applying fliX-MS to cells identifies several bona fide crosslinks on DNA binding domains, paving the way for future large scale ex vivo experiments.
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Affiliation(s)
- Alexander Reim
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Roland Ackermann
- Institute of Applied Physics, Abbe Center of Photonics, Friedrich-Schiller-Universität Jena, Albert-Einstein-Straße 15, 07745, Jena, Germany
| | - Jofre Font-Mateu
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Robert Kammel
- Institute of Applied Physics, Abbe Center of Photonics, Friedrich-Schiller-Universität Jena, Albert-Einstein-Straße 15, 07745, Jena, Germany
| | - Miguel Beato
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
- University Pompeu Fabra (UPF), 08002, Barcelona, Spain
| | - Stefan Nolte
- Institute of Applied Physics, Abbe Center of Photonics, Friedrich-Schiller-Universität Jena, Albert-Einstein-Straße 15, 07745, Jena, Germany
- Fraunhofer Institute for Applied Optics and Engineering (IOF), Albert-Einstein-Straße 7, 07745, Jena, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Christoph Russmann
- University of Applied Sciences and Arts Hildesheim/Holzminden/Goettingen (HAWK), Von-Ossietzky-Straße 99, 37085, Göttingen, Germany.
- Brigham and Women's Hospital, Harvard Medical School, 75 Francis Street, Boston, MA, 02115, USA.
| | - Michael Wierer
- Department of Proteomics and Signal Transduction, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
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6
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Guo L, Zhao Y, Liu D, Liu Z, Chen C, Xu R, Tian M, Wang X, Chen H, Kong MG. Cold atmospheric-pressure plasma induces DNA-protein crosslinks through protein oxidation. Free Radic Res 2018; 52:783-798. [PMID: 29722278 DOI: 10.1080/10715762.2018.1471476] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Reactive oxygen and nitrogen species (ROS and RNS) generated by cold atmospheric-pressure plasma could damage genomic DNA, although the precise types of these DNA damage induced by plasma are poorly characterized. Understanding plasma-induced DNA damage will help to elucidate the biological effect of plasma and guide the application of plasma in ROS-based therapy. In this study, it was shown that ROS and RNS generated by physical plasma could efficiently induce DNA-protein crosslinks (DPCs) in bacteria, yeast, and human cells. An in vitro assay showed that plasma treatment resulted in the formation of covalent DPCs by activating proteins to crosslink with DNA. Mass spectrometry and hydroperoxide analysis detected oxidation products induced by plasma. DPC formation were alleviated by singlet oxygen scavenger, demonstrating the importance of singlet oxygen in this process. These results suggested the roles of DPC formation in DNA damage induced by plasma, which could improve the understanding of the biological effect of plasma and help to develop a new strategy in plasma-based therapy including infection and cancer therapy.
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Affiliation(s)
- Li Guo
- a Center for Plasma Biomedicine, State Key Laboratory of Electrical Insulation and Power Equipment , Xi'an Jiaotong University , Xi'an , PR China
| | - Yiming Zhao
- b School of Life Science and Technology , Xi'an Jiaotong University , Xi'an , PR China
| | - Dingxin Liu
- a Center for Plasma Biomedicine, State Key Laboratory of Electrical Insulation and Power Equipment , Xi'an Jiaotong University , Xi'an , PR China
| | - Zhichao Liu
- a Center for Plasma Biomedicine, State Key Laboratory of Electrical Insulation and Power Equipment , Xi'an Jiaotong University , Xi'an , PR China
| | - Chen Chen
- a Center for Plasma Biomedicine, State Key Laboratory of Electrical Insulation and Power Equipment , Xi'an Jiaotong University , Xi'an , PR China
| | - Ruobing Xu
- b School of Life Science and Technology , Xi'an Jiaotong University , Xi'an , PR China
| | - Miao Tian
- b School of Life Science and Technology , Xi'an Jiaotong University , Xi'an , PR China
| | - Xiaohua Wang
- a Center for Plasma Biomedicine, State Key Laboratory of Electrical Insulation and Power Equipment , Xi'an Jiaotong University , Xi'an , PR China
| | - Hailan Chen
- c Frank Reidy Center for Bioelectrics , Old Dominion University , Norfolk , VA , USA
| | - Michael G Kong
- a Center for Plasma Biomedicine, State Key Laboratory of Electrical Insulation and Power Equipment , Xi'an Jiaotong University , Xi'an , PR China.,c Frank Reidy Center for Bioelectrics , Old Dominion University , Norfolk , VA , USA.,d Department of Electrical and Computer Engineering , Old Dominion University , Norfolk , VA , USA
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7
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Time-resolved analysis of DNA-protein interactions in living cells by UV laser pulses. Sci Rep 2017; 7:11725. [PMID: 28916762 PMCID: PMC5601431 DOI: 10.1038/s41598-017-12010-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/30/2017] [Indexed: 11/08/2022] Open
Abstract
Interactions between DNA and proteins are mainly studied through chemical procedures involving bi-functional reagents, mostly formaldehyde. Chromatin immunoprecipitation is used to identify the binding between transcription factors (TFs) and chromatin, and to evaluate the occurrence and impact of histone/DNA modifications. The current bottleneck in probing DNA-protein interactions using these approaches is caused by the fact that chemical crosslinkers do not discriminate direct and indirect bindings or short-lived chromatin occupancy. Here, we describe a novel application of UV laser-induced (L-) crosslinking and demonstrate that a combination of chemical and L-crosslinking is able to distinguish between direct and indirect DNA-protein interactions in a small number of living cells. The spatial and temporal dynamics of TF bindings to chromatin and their role in gene expression regulation may thus be assessed. The combination of chemical and L-crosslinking offers an exciting and unprecedented tool for biomedical applications.
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8
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Dina NE, Muntean CM, Leopold N, Fălămaș A, Halmagyi A, Coste A. Structural Changes Induced in Grapevine (Vitis vinifera L.) DNA by Femtosecond IR Laser Pulses: A Surface-Enhanced Raman Spectroscopic Study. NANOMATERIALS 2016; 6:nano6060096. [PMID: 28335224 PMCID: PMC5302626 DOI: 10.3390/nano6060096] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 04/25/2016] [Accepted: 05/17/2016] [Indexed: 11/25/2022]
Abstract
In this work, surface-enhanced Raman spectra of ten genomic DNAs extracted from leaf tissues of different grapevine (Vitis vinifera L.) varieties, respectively, are analyzed in the wavenumber range 300–1800 cm−1. Furthermore, structural changes induced in grapevine genomic nucleic acids upon femtosecond (170 fs) infrared (IR) laser pulse irradiation (λ = 1100 nm) are discussed in detail for seven genomic DNAs, respectively. Surface-enhanced Raman spectroscopy (SERS) signatures, vibrational band assignments and structural characterization of genomic DNAs are reported for each case. As a general observation, the wavenumber range between 1500 and 1660 cm−1 of the spectra seems to be modified upon laser treatment. This finding could reflect changes in the base-stacking interactions in DNA. Spectral shifts are mainly attributed to purines (dA, dG) and deoxyribose. Pyrimidine residues seem to be less affected by IR femtosecond laser pulse irradiation. Furthermore, changes in the conformational properties of nucleic acid segments are observed after laser treatment. We have found that DNA isolated from Feteasca Neagra grapevine leaf tissues is the most structurally-responsive system to the femtosecond IR laser irradiation process. In addition, using unbiased computational resources by means of principal component analysis (PCA), eight different grapevine varieties were discriminated.
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Affiliation(s)
- Nicoleta E Dina
- National Institute for Research & Development of Isotopic and Molecular Technologies, Donat 67-103, 400293 Cluj-Napoca, Romania.
| | - Cristina M Muntean
- National Institute for Research & Development of Isotopic and Molecular Technologies, Donat 67-103, 400293 Cluj-Napoca, Romania.
| | - Nicolae Leopold
- Babeş-Bolyai University, Faculty of Physics, Kogălniceanu 1, 400084 Cluj-Napoca, Romania.
| | - Alexandra Fălămaș
- National Institute for Research & Development of Isotopic and Molecular Technologies, Donat 67-103, 400293 Cluj-Napoca, Romania.
| | - Adela Halmagyi
- National Institute of Research and Development for Biological Sciences, branch Institute of Biological Research, Republicii Street 48, 400015 Cluj-Napoca, Romania.
| | - Ana Coste
- National Institute of Research and Development for Biological Sciences, branch Institute of Biological Research, Republicii Street 48, 400015 Cluj-Napoca, Romania.
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9
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Micciarelli M, Altucci C, Della Ventura B, Velotta R, Toşa V, Pérez ABG, Rodríguez MP, de Lera AR, Bende A. Low-lying excited-states of 5-benzyluracil. Phys Chem Chem Phys 2013; 15:7161-73. [PMID: 23558515 DOI: 10.1039/c3cp50343g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A numerical study is reported concerning the first and second singlet excited-states of 5-benzyluracil using the multireference self-consistent field (state-averaged CASSCF) method. The vertical excitation energies of low-lying excited-states were characterized using the SA-CASSCF method, as well as using higher-level methods, such as CASPT2, MRCI and EOM-CCSD. The local minima and conical intersections found on the potential energy surfaces (PESs) were characterized in terms of molecular geometry and natural population analysis. Different relaxation pathways on the PESs are identified and discussed by comparing with the similar pathways found for the individual monomers of uracil and benzene. The molecule can be thought of as a model system for the study of crosslink reaction between DNA and proteins induced by UV light.
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Affiliation(s)
- Marco Micciarelli
- Dipartimento di Scienze Fisiche, Università di Napoli Federico II, Napoli, Italy
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10
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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: 2.0] [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.
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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
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11
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Fischer F, Volkmer B, Puschmann S, Greinert R, Breitbart E, Kiefer J, Wepf R. Assessing the risk of skin damage due to femtosecond laser irradiation. JOURNAL OF BIOPHOTONICS 2008; 1:470-7. [PMID: 19343673 DOI: 10.1002/jbio.200810050] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
We irradiated freshly excised skin biopsies with four irradiation regimes usually taken for multiphoton imaging. If there is any skin damaging, it is mainly an effect similar to the damaging effects of UV-irradiation. Using fluorescent antibodies against cyclobutane-pyrimidin-dimers (CPDs) in combination with immuno-fluorescence image analysis we quantitatively compared fs-irradiation effects with UV-irradiation (solar simulator). Based on these results we are giving a risk assessment. The results show that multi photon imaging using the parameters described here is in the ballpark of damaging occurring from every day sun exposure.
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Affiliation(s)
- Frank Fischer
- Beiersdorf AG, Unnastrasse 48, 20245 Hamburg, Germany.
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12
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Fischer F, Volkmer B, Puschmann S, Greinert R, Breitbart W, Kiefer J, Wepf R. Risk estimation of skin damage due to ultrashort pulsed, focused near-infrared laser irradiation at 800 nm. JOURNAL OF BIOMEDICAL OPTICS 2008; 13:041320. [PMID: 19021328 DOI: 10.1117/1.2960016] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
New imaging techniques using near-infrared (NIR) femtosecond lasers (fs-lasers) in multiphoton laser scanning microscopy (MPLSM) have great potential for in vivo applications, particularly in human skin. However, little is known about possible risks. In order to evaluate the risk, a "biological dosimeter" was used. We irradiated fresh human skin samples with both an fs-laser and a solar simulator UV source (SSU). DNA damage introduced in the epidermis was evaluated using fluorescent antibodies against cyclobutane-pyrimidin-dimers (CPDs) in combination with immunofluorescence image analysis. Four fs-irradiation regimes (at 800-nm wavelength) were evaluated differing in laser power and step width of horizontal scans. Fs-irradiation did not give CPDs at 15-mW or 30-mW irradiation power using 10 horizontal scans every 5 microns. CPDs could be seen at 60-mW laser power and 5-microm step size and at 35-mW using 1-micron step width. Quantitative comparison of SSU-induced CPDs showed that the 60-mW laser irradiation regime is comparable to UV-irradiation, giving 0.6 minimal erythemal dose (MED). The 1-micron irradiation regime was comparable to 0.45 MED. Under these experimental conditions, the risk of DNA damage due to fs-laser irradiation on skin is in the range of natural UV-exposure.
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Affiliation(s)
- Frank Fischer
- Research Microscopy, Beiersdorf AG, Unnastrasse 48, D-20245 Hamburg, Germany.
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13
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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: 1.4] [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.
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Affiliation(s)
- Christopher J Fecko
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY, USA
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14
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Wilds CJ, Palus E, Noronha AM. An approach for the synthesis of duplexes containing N3T-butyl-N3T interstrand cross-links via a bisphosphoramidite strategy. CAN J CHEM 2007. [DOI: 10.1139/v07-015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA duplexes containing an interstrand cross-link have been synthesized utilizing a bis-3′-O-phosphoramidite deoxythymidine dimer where the N3 atoms are bridged by a butyl linker. With this approach sufficient quantities of high purity cross-linked duplexes are obtained that will enable various biochemical and structural studies to aid in research directed towards understanding the mechanism of interstrand cross-linked DNA repair. This methodology has advantages over a previously reported method to synthesize cross-linked DNA duplexes involving a monophosphoramidite of the same cross-linked thymidine dimer including circumventing the use of costly 5′-O-deoxyphosphoramidites in the assembly of the cross-linked duplex by solid-phase synthesis. This strategy can be employed to produce cross-linked duplexes in which the lesions are engineered to have a directly opposed (1–1) or staggered (1–2 or 2–1) orientations. Biophysical studies of duplexes containing this N3T-butyl-N3T cross-link in staggered 1–2 and 2–1 orientations reveal that both duplexes have a higher Tm than a non-cross-linked duplex suggesting that these linkages do not result in the destabilization of duplex DNA. Circular dichroism spectra of the 1–2 and 2–1 cross-linked duplexes exhibit minor differences from B-form structure, which correlates with molecular modeling studies.Key words: chemically modified oligonucleotides, interstrand cross-link, DNA adduct, DNA repair.
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15
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Abdurashidova G, Radulescu S, Sandoval O, Zahariev S, Danailov MB, Demidovich A, Santamaria L, Biamonti G, Riva S, Falaschi A. Functional interactions of DNA topoisomerases with a human replication origin. EMBO J 2007; 26:998-1009. [PMID: 17290216 PMCID: PMC1852844 DOI: 10.1038/sj.emboj.7601578] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2006] [Accepted: 01/04/2007] [Indexed: 01/22/2023] Open
Abstract
The human DNA replication origin, located in the lamin B2 gene, interacts with the DNA topoisomerases I and II in a cell cycle-modulated manner. The topoisomerases interact in vivo and in vitro with precise bonds ahead of the start sites of bidirectional replication, within the pre-replicative complex region; topoisomerase I is bound in M, early G1 and G1/S border and topoisomerase II in M and the middle of G1. The Orc2 protein competes for the same sites of the origin bound by either topoisomerase in different moments of the cell cycle; furthermore, it interacts on the DNA with topoisomerase II during the assembly of the pre-replicative complex and with DNA-bound topoisomerase I at the G1/S border. Inhibition of topoisomerase I activity abolishes origin firing. Thus, the two topoisomerases are closely associated with the replicative complexes, and DNA topology plays an essential functional role in origin activation.
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Affiliation(s)
- Gulnara Abdurashidova
- Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Sorina Radulescu
- Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Oscar Sandoval
- Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Sotir Zahariev
- Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | | | | | - Laura Santamaria
- Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
| | - Giuseppe Biamonti
- Molecular Biology Section, Istituto di Genetica Molecolare, CNR, Pavia, Italy
| | - Silvano Riva
- Molecular Biology Section, Istituto di Genetica Molecolare, CNR, Pavia, Italy
| | - Arturo Falaschi
- Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Trieste, Italy
- Molecular Biology Laboratory, Scuola Normale Superiore, Pisa, Italy
- Laboratory of Gene and Molecular Therapy, Istituto di Fisiologia Clinica, CNR, Pisa, Italy
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16
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Vindigni A. Biochemical, biophysical, and proteomic approaches to study DNA helicases. MOLECULAR BIOSYSTEMS 2007; 3:266-74. [PMID: 17372655 DOI: 10.1039/b616145f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Helicases are a family of enzymes that play an essential role in nearly all DNA metabolic processes, catalyzing the transient opening of DNA duplexes. These motor proteins couple the chemical energy of ATP binding and hydrolysis to the separation of the complementary strands of a DNA or RNA duplex substrate. A full understanding of their mechanism of DNA unwinding can be achieved only through careful investigation of the thermodynamic and kinetic parameters that control this ATP-driven process, as well as through analysis of the helicases' tertiary and quaternary structures associated with nucleic acids and/or nucleotide recognition. This review describes the various biochemical, biophysical, and, more recently, proteomic techniques that have been developed to shed light on the still controversial, and in some aspects elusive, helicase-catalyzed mechanism of DNA unwinding.
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Affiliation(s)
- Alessandro Vindigni
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34012 Trieste, Italy.
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17
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Flickinger DA, Coffee RN, Gibson GN, Weinacht TC. Bichromatic, phase compensating interferometer based on prism pair compressors. APPLIED OPTICS 2006; 45:6187-91. [PMID: 16892122 DOI: 10.1364/ao.45.006187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We present a bichromatic prism pair interferometer (BPPI) for controlling the delay between laser pulses of two different frequencies propagating collinearly in a single beam. The BPPI is especially useful when working with ultrafast laser pulses because it intrinsically allows for independent control over the second-order dispersion experienced by the differently colored pulses. We use this control to demonstrate successful precompensation for blue (lambda approximately 390 nm) and UV (lambda approximately 260 nm) pulses that pass through 2.2 cm of dispersive material after the interferometer. The BPPI is extremely flexible and works with all frequencies from the UV to the near-infrared. We demonstrate this by describing measurements made with BPPIs configured for three different combinations of central frequencies.
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Affiliation(s)
- Daniel A Flickinger
- Department of Physics and Astronomy, Stony Brook University, New York 11794-3800, USA.
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18
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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: 1.7] [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.
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Affiliation(s)
- Guangxing Sun
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
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19
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Keene LT, Fiero T, Clayton CR, Halada GP, Cardoza D, Weinacht T. On the use of femtosecond laser ablation to facilitate spectroscopic depth profiling of heterogeneous polymeric coatings. Polym Degrad Stab 2005. [DOI: 10.1016/j.polymdegradstab.2005.01.033] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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20
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Zhang L, Zhang K, Prändl R, Schöffl F. Detecting DNA-binding of proteins in vivo by UV-crosslinking and immunoprecipitation. Biochem Biophys Res Commun 2004; 322:705-11. [PMID: 15336521 DOI: 10.1016/j.bbrc.2004.07.202] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2004] [Indexed: 10/26/2022]
Abstract
The temporal and spatial binding of proteins on DNA is important to the regulation of genome expression and maintenance. However, examining how the protein-DNA complexes assemble in living cells is challenging. The development of UV-crosslinking/immunoprecipitation (UV-X-ChIP) technique and the progress of its applications show the powerful potential of this method in detecting such binding behavior in vivo. UV light is a zero length crosslinker and is believed to produce less perturbation of the complex than chemical crosslinker. The use of UV laser as UV light source allows the number of photons required for crosslinking to be delivered in nano- or pico- or femtosecond intervals, extremely shortening the irradiation time and achieving higher crosslinking efficiency than conventional UV lamp, thus being well suitable for kinetic studies. UV-X-ChIP technique has been successfully applied on the study of DNA replication, transcription, chromatin structure, and genome-wide location of DNA-binding proteins.
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Affiliation(s)
- Lemin Zhang
- Laboratory for Conservation and Utilization of Bio-resource, Yunnan University, Kunming, Yunnan 650091, PR China.
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21
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Nagaich AK, Hager GL. UV laser cross-linking: a real-time assay to study dynamic protein/DNA interactions during chromatin remodeling. Sci Signal 2004; 2004:pl13. [PMID: 15507594 DOI: 10.1126/stke.2562004pl13] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
We describe the use of laser ultraviolet (UV) cross-linking to study the interaction of transcription factors with in vitro assembled chromatinized DNA templates in real time. Because the laser source delivers a high density of photons in a single ns pulse, the cross-linking reaction is completed in less than 1 microseconds, allowing the investigator to freeze rapid dynamic changes in protein-DNA interactions. Using this approach, we have sampled the dynamic equilibrium of the glucocorticoid receptor (GR) and the chromatin remodeling complex (SWI/SNF) during adenosine triphosphate (ATP)-dependent chromatin remodeling on a chromatinized mouse mammary tumor virus promoter in vitro. UV laser cross-linking shows that the GR and SWI/SNF complex undergoes a periodic binding and displacement event during the process of chromatin remodeling. The assay provides unique information regarding the equilibrium of protein-DNA interactions in real time and can be easily adapted to study the dynamic events in the assembly and disassembly of other multiprotein complexes on chromatin or DNA templates.
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Affiliation(s)
- Akhilesh K Nagaich
- Laboratory of Receptor Biology and Gene Expression, Bldg 41 Room B602, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892-5055, USA
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22
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Abdurashidova G, Danailov MB, Ochem A, Triolo G, Djeliova V, Radulescu S, Vindigni A, Riva S, Falaschi A. Localization of proteins bound to a replication origin of human DNA along the cell cycle. EMBO J 2003; 22:4294-303. [PMID: 12912926 PMCID: PMC175794 DOI: 10.1093/emboj/cdg404] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2002] [Revised: 05/19/2003] [Accepted: 06/27/2003] [Indexed: 12/17/2022] Open
Abstract
The proteins bound in vivo at the human lamin B2 DNA replication origin and their precise sites of binding were investigated along the cell cycle utilizing two novel procedures based on immunoprecipitation following UV irradiation with a pulsed laser light source. In G(1), the pre-replicative complex contains CDC6, MCM3, ORC1 and ORC2 proteins; of these, the post-replicative complex in S phase contains only ORC2; in M phase none of them are bound. The precise nucleotide of binding was identified for the two ORC and the CDC6 proteins near the start sites for leading-strand synthesis; the transition from the pre- to the post-replicative complex is accompanied by a 17 bp displacement of the ORC2 protein towards the start site.
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Affiliation(s)
- Gulnara Abdurashidova
- International Centre for Genetic Engineering and Biotechnology, Padriciano 99, I-34012 Trieste, Italy
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23
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Lejnine S, Durfee G, Murnane M, Kapteyn HC, Makarov VL, Langmore JP. Crosslinking of proteins to DNA in human nuclei using a 60 femtosecond 266 nm laser. Nucleic Acids Res 1999; 27:3676-84. [PMID: 10471736 PMCID: PMC148622 DOI: 10.1093/nar/27.18.3676] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We developed appropriate conditions to use a laser with 60 femtosecond pulses, a frequency of 1 KHz and a wavelength of 266 nm to efficiently crosslink proteins to DNA in human nuclei for the purpose of using immunoprecipitation to study the binding of specific proteins to specific sequences of DNA under native conditions. Irradiation of nuclei for 30 min with 1-3 GW/cm(2)pulses crosslinked 10-12% of total protein to DNA. The efficiency of crosslinking was dose and protein specific. Histones H1 and H3 were crosslinked by 15 min of irradiation with 20-25% efficiency, at least 10 times more strongly than the other histones, consistent with experiments using conventional UV light. Irradiation for 15 min did not damage proteins, as assayed by SDS-PAGE of Ku-70 and histones. Although the same level of irradiation did not cause double-strand breaks, it did make the DNA partially insensitive to Eco RI restriction enzyme, probably through formation of thymidine dimers. Immuno-analysis of crosslinked nucleoprotein showed that Ku crosslinking to nuclear DNA is detectable only in the presence of breaks in the DNA, and that nucleosomes are bound to a significant fraction of the telomeric repeat (TTAGGG) (n).
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Affiliation(s)
- S Lejnine
- Biophysics Research Division, University of Michigan, Ann Arbor 48109-1055, USA
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