1
|
Saintomé C, Monfret O, Doisneau G, Guianvarc'h D. Oligonucleotide-Based Photoaffinity Probes: Chemical Tools and Applications for Protein Labeling. Chembiochem 2024:e202400097. [PMID: 38703401 DOI: 10.1002/cbic.202400097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 04/30/2024] [Accepted: 05/03/2024] [Indexed: 05/06/2024]
Abstract
A variety of proteins interact with DNA and RNA, including polymerases, histones, ribosomes, transcription factors, and repair enzymes. However, the transient non-covalent nature of these interactions poses challenges for analysis. Introducing a covalent bond between proteins and DNA via photochemical activation of a photosensitive functional group introduced onto nucleic acids offers a means to stabilize these often weak interactions without significantly altering the binding interface. Consequently, photoactivatable oligonucleotides are powerful tools for investigating nucleic acid-protein interactions involved in numerous biological and pathological processes. In this review, we provide a comprehensive overview of the chemical tools developed so far and the different strategies used for incorporating the most commonly used photoreactive reagents into oligonucleotide probes or nucleic acids. Furthermore, we illustrate their application with several examples including protein binding site mapping, identification of protein binding partners, and in cell studies.
Collapse
Affiliation(s)
- Carole Saintomé
- Sorbonne Université, UFR 927, MNHN CNRS UMR 7196, INSERM U1154, 43 rue Cuvier, 75005, Paris, France
| | - Océane Monfret
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR CNRS 8182, 91405, Orsay, France
| | - Gilles Doisneau
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR CNRS 8182, 91405, Orsay, France
| | - Dominique Guianvarc'h
- Université Paris-Saclay, CNRS, Institut de Chimie Moléculaire et des Matériaux d'Orsay, UMR CNRS 8182, 91405, Orsay, France
| |
Collapse
|
2
|
Wu X, Kim M, Wang LJ, Veetil AK, Wang Y. Programming sp 3 Quantum Defects along Carbon Nanotubes with Halogenated DNA. J Am Chem Soc 2024; 146:8826-8831. [PMID: 38526163 DOI: 10.1021/jacs.3c14784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Atomic defect color centers in solid-state systems hold immense potential to advance various quantum technologies. However, the fabrication of high-quality, densely packed defects presents a significant challenge. Herein we introduce a DNA-programmable photochemical approach for creating organic color-center quantum defects on semiconducting single-walled carbon nanotubes (SWCNTs). Key to this precision defect chemistry is the strategic substitution of thymine with halogenated uracil in DNA strands that are orderly wrapped around the nanotube. Photochemical activation of the reactive uracil initiates the formation of sp3 defects along the nanotube as deep exciton traps, with a pronounced photoluminescence shift from the nanotube band gap emission (by 191 meV for (6,5)-SWCNTs). Furthermore, by altering the DNA spacers, we achieve systematic control over the defect placements along the nanotube. This method, bridging advanced molecular chemistry with quantum materials science, marks a crucial step in crafting quantum defects for critical applications in quantum information science, imaging, and sensing.
Collapse
Affiliation(s)
- Xiaojian Wu
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Mijin Kim
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Lucy J Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - Abhindev Kizhakke Veetil
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
| | - YuHuang Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland 20742, United States
- Maryland NanoCenter, University of Maryland, College Park, Maryland 20742, United States
| |
Collapse
|
3
|
Leone D, Pohl R, Hubálek M, Kadeřábková M, Krömer M, Sýkorová V, Hocek M. Glyoxal‐Linked Nucleotides and DNA for Bioconjugations and Crosslinking with Arginine‐Containing Peptides and Proteins. Chemistry 2022; 28:e202104208. [DOI: 10.1002/chem.202104208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Indexed: 12/16/2022]
Affiliation(s)
- Denise‐Liu' Leone
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Marta Kadeřábková
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Matouš Krömer
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| |
Collapse
|
4
|
Leone D, Hubálek M, Pohl R, Sýkorová V, Hocek M. 1,3-Diketone-Modified Nucleotides and DNA for Cross-Linking with Arginine-Containing Peptides and Proteins. Angew Chem Int Ed Engl 2021; 60:17383-17387. [PMID: 34107150 PMCID: PMC8362068 DOI: 10.1002/anie.202105126] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/27/2021] [Indexed: 12/28/2022]
Abstract
Linear or branched 1,3-diketone-linked thymidine 5'-O-mono- and triphosphate were synthesized through CuAAC click reaction of diketone-alkynes with 5-azidomethyl-dUMP or -dUTP. The triphosphates were good substrates for KOD XL DNA polymerase in primer extension synthesis of modified DNA. The nucleotide bearing linear 3,5-dioxohexyl group (HDO) efficiently reacted with arginine-containing peptides to form stable pyrimidine-linked conjugates, whereas the branched 2-acetyl-3-oxo-butyl (PDO) group was not reactive. Reaction with Lys or a terminal amino group formed enamine adducts that were prone to hydrolysis. This reactive HDO modification in DNA was used for bioconjugations and cross-linking with Arg-containing peptides or proteins (e.g. histones).
Collapse
Affiliation(s)
- Denise‐Liu' Leone
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 812843Prague 2Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and BiochemistryCzech Academy of SciencesFlemingovo nam. 216610Prague 6Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in PragueHlavova 812843Prague 2Czech Republic
| |
Collapse
|
5
|
Leone D, Hubálek M, Pohl R, Sýkorová V, Hocek M. 1,3‐Diketone‐Modified Nucleotides and DNA for Cross‐Linking with Arginine‐Containing Peptides and Proteins. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202105126] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Denise‐Liu' Leone
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Veronika Sýkorová
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic Chemistry Faculty of Science Charles University in Prague Hlavova 8 12843 Prague 2 Czech Republic
| |
Collapse
|
6
|
Ivancová I, Pohl R, Hubálek M, Hocek M. Squaramate-Modified Nucleotides and DNA for Specific Cross-Linking with Lysine-Containing Peptides and Proteins. Angew Chem Int Ed Engl 2019; 58:13345-13348. [PMID: 31328344 PMCID: PMC6771961 DOI: 10.1002/anie.201906737] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 07/12/2019] [Indexed: 01/31/2023]
Abstract
Squaramate‐linked 2′‐deoxycytidine 5′‐O‐triphosphate was synthesized and found to be good substrate for KOD XL DNA polymerase in primer extension or PCR synthesis of modified DNA. The resulting squaramate‐linked DNA reacts with primary amines to form a stable diamide linkage. This reaction was used for bioconjugations of DNA with Cy5 and Lys‐containing peptides. Squaramate‐linked DNA formed covalent cross‐links with histone proteins. This reactive nucleotide has potential for other bioconjugations of nucleic acids with amines, peptides or proteins without need of any external reagent.
Collapse
Affiliation(s)
- Ivana Ivancová
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843, Prague 2, Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam. 2, 16610, Prague 6, Czech Republic.,Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843, Prague 2, Czech Republic
| |
Collapse
|
7
|
Ivancová I, Pohl R, Hubálek M, Hocek M. Squaramate‐Modified Nucleotides and DNA for Specific Cross‐Linking with Lysine‐Containing Peptides and Proteins. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201906737] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ivana Ivancová
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in Prague Hlavova 8 CZ-12843 Prague 2 Czech Republic
| | - Radek Pohl
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and BiochemistryCzech Academy of Sciences Flemingovo nam. 2 16610 Prague 6 Czech Republic
- Department of Organic ChemistryFaculty of ScienceCharles University in Prague Hlavova 8 CZ-12843 Prague 2 Czech Republic
| |
Collapse
|
8
|
Flett FJ, Ruksenaite E, Armstrong LA, Bharati S, Carloni R, Morris ER, Mackay CL, Interthal H, Richardson JM. Structural basis for DNA 3'-end processing by human tyrosyl-DNA phosphodiesterase 1. Nat Commun 2018; 9:24. [PMID: 29295983 PMCID: PMC5750209 DOI: 10.1038/s41467-017-02530-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Accepted: 12/06/2017] [Indexed: 11/15/2022] Open
Abstract
Tyrosyl-DNA phosphodiesterase (Tdp1) is a DNA 3'-end processing enzyme that repairs topoisomerase 1B-induced DNA damage. We use a new tool combining site-specific DNA-protein cross-linking with mass spectrometry to identify Tdp1 interactions with DNA. A conserved phenylalanine (F259) of Tdp1, required for efficient DNA processing in biochemical assays, cross-links to defined positions in DNA substrates. Crystal structures of Tdp1-DNA complexes capture the DNA repair machinery after 3'-end cleavage; these reveal how Tdp1 coordinates the 3'-phosphorylated product of nucleosidase activity and accommodates duplex DNA. A hydrophobic wedge splits the DNA ends, directing the scissile strand through a channel towards the active site. The F259 side-chain stacks against the -3 base pair, delimiting the junction of duplexed and melted DNA, and fixes the scissile strand in the channel. Our results explain why Tdp1 cleavage is non-processive and provide a molecular basis for DNA 3'-end processing by Tdp1.
Collapse
Affiliation(s)
- Fiona J Flett
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Roger Land Building, Alexander Crum Brown Road, Edinburgh, EH9 3FF, UK
| | - Emilija Ruksenaite
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Lee A Armstrong
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Shipra Bharati
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - Roberta Carloni
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Roger Land Building, Alexander Crum Brown Road, Edinburgh, EH9 3FF, UK
| | - Elizabeth R Morris
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK
| | - C Logan Mackay
- EaStCHEM School of Chemistry, University of Edinburgh, The King's Buildings, David Brewster Road, Edinburgh, EH9 3FJ, UK
| | - Heidrun Interthal
- Institute of Cell Biology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Roger Land Building, Alexander Crum Brown Road, Edinburgh, EH9 3FF, UK.
| | - Julia M Richardson
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, The King's Buildings, Max Born Crescent, Edinburgh, EH9 3BF, UK.
| |
Collapse
|
9
|
Dai X, Song D, Liu K, Su H. Photoinduced C—I bond homolysis of 5-iodouracil: A singlet predissociation pathway. J Chem Phys 2017; 146:025103. [DOI: 10.1063/1.4973650] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Xiaojuan Dai
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Di Song
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Kunhui Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Hongmei Su
- Beijing National Laboratory for Molecular Sciences (BNLMS), Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- College of Chemistry, Beijing Normal University, Beijing 100875, China
| |
Collapse
|
10
|
Kim Y, Liu C, Tan W. Aptamers generated by Cell SELEX for biomarker discovery. Biomark Med 2010; 3:193-202. [PMID: 20477510 DOI: 10.2217/bmm.09.5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Biomarker discovery is essential to the advancement of our knowledge about diseases and to the development of new strategies for treatment and therapy. Among the newest technologies in this rapidly growing field is a process termed Cell SELEX by which a panel of aptamers can be generated to specifically target disease cells. Thus, Cell SELEX, together with the in vitro selection of aptamers, brings a promising approach to accelerate the progress of biomarker discovery. In this review, the Cell SELEX method and potential uses of selected aptamers are discussed. In addition, identification of potential biomarkers by using cell-binding aptamers is addressed. We believe that using the Cell SELEX strategy represents a significant improvement over current approaches to biomarker identification by the simplicity, efficiency and specificity of its application.
Collapse
Affiliation(s)
- Youngmi Kim
- Department of Chemistry & Department of Physiology & Functional Genomics, Department of Pathology & Laboratory Medicine, Shands Cancer Center & Center for Research at the Bio/nano Interface, UF Genetics Institute & McKnight Brain Institute, University of Florida, Gainesville, FL 32611-37200, USA
| | | | | |
Collapse
|
11
|
Rastogi V, Alcolea Palafox M, Guerrero-Martínez A, Tardajos G, Vats J, Kostova I, Schlucker S, Kiefer W. FT-IR and FT-Raman spectra, ab initio and density functional computations of the vibrational spectra, molecular geometry, atomic charges and some molecular properties of the biomolecule 5-iodouracil. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.10.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
12
|
Dahdah DB, Morin I, Moreau MJJ, Dixon NE, Schaeffer PM. Site-specific covalent attachment of DNA to proteins using a photoactivatable Tus-Ter complex. Chem Commun (Camb) 2009:3050-2. [PMID: 19462083 DOI: 10.1039/b900905a] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Investigations into the photocrosslinking kinetics of the protein Tus with various bromodeoxyuridine-substituted Ter DNA variants highlight the potential use of this complex as a photoactivatable connector between proteins of interest and specific DNA sequences.
Collapse
Affiliation(s)
- Dahdah B Dahdah
- Comparative Genomics Centre, School of Pharmacy & Molecular Sciences, James Cook University, Townsville, QLD 4811, Australia
| | | | | | | | | |
Collapse
|
13
|
Phillips JA, Lopez-Colon D, Zhu Z, Xu Y, Tan W. Applications of aptamers in cancer cell biology. Anal Chim Acta 2008; 621:101-8. [PMID: 18573375 DOI: 10.1016/j.aca.2008.05.031] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2008] [Revised: 05/05/2008] [Accepted: 05/06/2008] [Indexed: 01/10/2023]
Abstract
Identifying cells associated with specific disease states is critically important for the early detection and diagnosis of cancer. To facilitate this task, molecular probes, which bind biomarkers that are either specifically or differentially expressed in diseased cells relative to healthy cells, provide a simple and effective method. This review focuses on the use of DNA aptamers as molecular probes for cancer cells. These aptamers are created by means of the cell-based Systematic Evolution of Ligands by EXponential enrichment (SELEX) process, which uses whole disease cells as targets. We describe at length the steps of the cell-SELEX process and discuss several applications for the aptamers, including profiling leukemia patient samples and discovering cell-surface cancer biomarkers. We conclude with a discussion of an aptamer-conjugated nanoparticle enrichment and detection scheme.
Collapse
Affiliation(s)
- Joseph A Phillips
- Center for Research at the Bio/Nano Interface, Department of Chemistry, Shands Cancer Center, University of Florida Genetics Institute, and McKnight Brain Institute, University of Florida, Gainesville, FL 32611-7200, USA
| | | | | | | | | |
Collapse
|
14
|
Norris CL, Meisenheimer KM, Koch TH. Mechanistic Studies Relevant to Bromouridine-Enhanced Nucleoprotein Photocrosslinking: Possible Involvement of an Excited Tyrosine Residue of the Protein. Photochem Photobiol 2008. [DOI: 10.1111/j.1751-1097.1997.tb08546.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
15
|
Nordhoff E, Lehrach H. Identification and characterization of DNA-binding proteins by mass spectrometry. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2006; 104:111-95. [PMID: 17290821 DOI: 10.1007/10_2006_037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Mass spectrometry is the most sensitive and specific analytical technique available for protein identification and quantification. Over the past 10 years, by the use of mass spectrometric techniques hundreds of previously unknown proteins have been identified as DNA-binding proteins that are involved in the regulation of gene expression, replication, or DNA repair. Beyond this task, the applications of mass spectrometry cover all aspects from sequence and modification analysis to protein structure, dynamics, and interactions. In particular, two new, complementary ionization techniques have made this possible: matrix-assisted laser desorption/ionization and electrospray ionization. Their combination with different mass-over-charge analyzers and ion fragmentation techniques, as well as specific enzymatic or chemical reactions and other analytical techniques, has led to the development of a broad repertoire of mass spectrometric methods that are now available for the identification and detailed characterization of DNA-binding proteins. These techniques, how they work, what their requirements and limitations are, and selected examples that document their performance are described and discussed in this chapter.
Collapse
Affiliation(s)
- Eckhard Nordhoff
- Department Lehrach, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.
| | | |
Collapse
|
16
|
Kühn-Hölsken E, Lenz C, Sander B, Lührmann R, Urlaub H. Complete MALDI-ToF MS analysis of cross-linked peptide-RNA oligonucleotides derived from nonlabeled UV-irradiated ribonucleoprotein particles. RNA (NEW YORK, N.Y.) 2005; 11:1915-30. [PMID: 16314460 PMCID: PMC1370879 DOI: 10.1261/rna.2176605] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Accepted: 09/12/2005] [Indexed: 05/05/2023]
Abstract
Protein-RNA cross-linking combined with mass spectrometry is a powerful tool to elucidate hitherto non-characterized protein-RNA contacts in ribonucleoprotein particles, as, for example, within spliceosomes. Here, we describe an improved methodology for the sequence analysis of purified peptide-RNA oligonucleotide cross-links that is based solely on MALDI-ToF mass spectrometry. The utility of this methodology is demonstrated on cross-links isolated from UV-irradiated spliceosomal particles; these were (1) [15.5K-61 K-U4 atac] small nuclear ribonucleoprotein (snRNP) particles prepared by reconstitution in vitro, and (2) U1 snRNP particles purified from HeLa cells. We show that the use of 2',4',6'-trihydroxyacetophenone (THAP) as MALDI matrix allows analysis of cross-linked peptide-RNA oligonucleotides in the reflectron mode at high resolution, enabling sufficient accuracy to assign unambiguously cross-linked RNA sequences. Most important, post-source decay (PSD) analysis under these conditions was successfully applied to obtain sequence information about the cross-linked peptide and RNA moieties within a single spectrum, including the identification of the actual cross-linking site. Thus, in U4 atac snRNA we identified His 270 in the spliceosomal U4/U6 snRNP-specific protein 61 K (hPrp31p) cross-linked to U 44; in the U1 snRNP we show that Leu175 of the U1 snRNP-specific 70K protein is cross-linked to U 30 of U1 snRNA. This type of analysis is applicable to any type of RNP complex and may be expected to pave the way for the further analysis of protein-RNA complexes in much lower abundance and/or of cross-links that are obtained in low yield.
Collapse
MESH Headings
- Amino Acid Sequence
- Cross-Linking Reagents/pharmacology
- Crystallography, X-Ray
- HeLa Cells
- Humans
- Models, Chemical
- Models, Molecular
- Molecular Sequence Data
- Oligonucleotides/analysis
- Peptides
- RNA/chemistry
- Ribonucleoprotein, U1 Small Nuclear/chemistry
- Ribonucleoprotein, U1 Small Nuclear/metabolism
- Ribonucleoprotein, U4-U6 Small Nuclear/chemistry
- Ribonucleoprotein, U4-U6 Small Nuclear/metabolism
- Sequence Homology, Amino Acid
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
- Ultraviolet Rays
Collapse
Affiliation(s)
- Eva Kühn-Hölsken
- Bioanalytical Mass Spectrometry Group, Max Planck institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | | | | | | | | |
Collapse
|
17
|
Tiss A, Barre O, Michaud-Soret I, Forest E. Characterization of the DNA-binding site in the ferric uptake regulator protein from Escherichia coli by UV crosslinking and mass spectrometry. FEBS Lett 2005; 579:5454-60. [PMID: 16212958 DOI: 10.1016/j.febslet.2005.08.067] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 06/27/2005] [Accepted: 08/02/2005] [Indexed: 10/25/2022]
Abstract
Ferric uptake regulator protein (Fur) is activated by its cofactor iron to a state that binds to a specific DNA sequence called 'Fur box'. Using mass spectrometry-based methods, we showed that Tyr 55 of Escherichia coli Fur, as well as the two thymines in positions 18 and 19 of the consensus Fur Box, are involved with binding. A conformational model of the Fur-DNA complex is proposed, in which DNA is in contact with each H4 [A52-A64] Fur helix. We propose that this interaction is a common feature for the Fur-like proteins, such as Zur and PerR, and their respective DNA boxes.
Collapse
Affiliation(s)
- Ali Tiss
- Laboratoire de Spectrométrie de Masse des Protéines, Institut de Biologie Structurale (UMR 5075 CEA-CNRS-UJF), Grenoble, France
| | | | | | | |
Collapse
|
18
|
Pingoud V, Geyer H, Geyer R, Kubareva E, Bujnicki JM, Pingoud A. Identification of base-specific contacts in protein-DNA complexes by photocrosslinking and mass spectrometry: a case study using the restriction endonuclease SsoII. MOLECULAR BIOSYSTEMS 2005; 1:135-41. [PMID: 16880975 DOI: 10.1039/b503091a] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Specific protein-nucleic acid interactions are of paramount importance for the propagation, maintenance and expression of genetic information. Restriction endonucleases serve as model systems to study the mechanisms of DNA recognition by proteins. SsoII is a Type II restriction endonuclease that recognizes the double stranded sequence downward arrow CCNGG and cleaves it in the presence of Mg(2+)-ions, as indicated. SsoII shows sequence similarity over a stretch of approximately 70 amino acid residues with several other restriction endonucleases that recognize a similar sequence as SsoII (Cfr10I, EcoRII, NgoMIV, PspGI). In NgoMIV this stretch is involved in DNA recognition and cleavage, as shown by the crystal structure analysis of an enzyme-product complex. To find out whether the presumptive DNA recognition region in SsoII is indeed in contact with DNA we have photocrosslinked SsoII with an oligodeoxyribonucleotide in which the first guanine of the recognition sequence was replaced by 5-iodouracil. Following digestion by trypsin, the peptide-oligodeoxyribonucleotide conjugate was purified by Fe(3+)-IMAC and then incubated with hydrogen fluoride, which hydrolyzes the oligodeoxyribonucleotide to yield the peptide-deoxyuridine conjugate. The site of photocrosslinking was identified by MALDI-TOF-MS and MALDI-TOF-MS/MS to be Trp189, adjacent to Arg188, which aligns with Arg194 in NgoMIV, involved in recognition of the second guanine in the NgoMIV recognition sequence G downward arrow CCGGC. This result confirms previously published conclusions drawn on the basis of a mutational analysis of SsoII. The methodology that was employed here can be used in principle to identify the DNA binding site of any protein.
Collapse
Affiliation(s)
- Vera Pingoud
- Institut für Biochemie (FB 08), Justus-Liebig-Universität, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany.
| | | | | | | | | | | |
Collapse
|
19
|
Abstract
An assay based on photoinduced reaction and subsequent cleavage of duplex DNA containing a bromodeoxyuridine ((Br)U) residue and an abasic site was developed to screen aromatic amines for their ability to initiate charge transfer by reductive electron donation. Two candidates, N,N,N',N'-tetramethyl-1,5-diaminonaphthalene (TMDN) and 1,5-diaminonaphthalene (DAN), expressed the desired activity, and an oligodeoxynucleotide-TMDN conjugate was subsequently prepared to identify additional variables affecting the efficiency of electron injection and transfer into DNA. This system demonstrated only mild sensitivity to molecular oxygen but was strongly inhibited by high concentrations of 2-mercaptoethanol. The nucleobase counter to the attached TMDN strongly modulated charge transfer as evident by a 60-fold decrease in reduction of the distal (Br)U when the counterbase A was substituted for C. An inverse relationship between this reduction and quenching of TMDN fluorescence by the counterbase was also discovered and is consistent with a competition between radical recombination and electron migration away from the initial site of its injection into DNA.
Collapse
Affiliation(s)
- Takeo Ito
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
| | | |
Collapse
|
20
|
Wenska G, Taras-Goślińska K, Skalski B, Hug GL, Carmichael I, Marciniak B. Generation of Thiyl Radicals by the Photolysis of 5-Iodo-4-thiouridine. J Org Chem 2005; 70:982-8. [PMID: 15675858 DOI: 10.1021/jo048496g] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The photochemistry of 2',3',5'-tri-O-acetyl-5-iodo-4-thiouridine (3) in deoxygenated 1:1 CH(3)CN-H(2)O pH 5.8 (phosphate buffer) solution has been studied by means of steady-state and nanosecond laser flash photolysis methods. Under steady-state irradiation (lambda > or = 334 nm), the stable photoproducts were iodide ion, 2',3',5'-tri-O-acetyl-4-thiouridine (4), and two disulfides. The disulfides were the symmetrical bis-(2',3',5'-tri-O-acetyl-5-iodo-4-thiouridine) (5) and unsymmetrical 6, which contains both 4-thiouridine and 5-iodo-4-thiouridine residues. The formation of the dehalogenated photoproduct suggests that C(5)-I bond cleavage is a primary photochemical step. Attempts to scavenge the resulting C(5)-centered radical by suitable addends, bis-(N-alpha-acetyl)cystine-bis-N-ethylamide or benzene, were unsuccessful. Analysis of the photoproducts formed under these conditions showed that the S-atom is the reactive center. The photoproduct 4, obtained by irradiation of 3 in CD(3)CN-H(2)O, followed by reversed-phase HPLC isolation using nonlabeled eluents, did not contain deuterium. An analogous experiment performed in CH(3)CN-D(2)O gave deuterated product 4-d with 88% of the deuterium incorporated at C(5). Transient absorption observed upon laser excitation (lambda= 308 nm) of 3 was assigned to the 4-uridinylthiyl radical on the basis of the similarity of this spectrum with that obtained upon laser photolysis of the disulfide: bis-(2',3',5'-tri-O-acetyl-4-thiouridine) 14. On the basis of the results of steady-state and laser photolysis studies, a mechanism of the photochemical reaction of 3 is proposed. The key mechanistic step is a transformation of the C(5)-centered radical formed initially by C(5)-I bond cleavage into a long-lived S-centered radical via a 1,3-hydrogen shift. Theoretical calculations confirmed that the long-lived S-centered radical is the most stable radical derived from the 4-thiouracil residue.
Collapse
Affiliation(s)
- Grazyna Wenska
- Faculty of Chemistry, A. Mickiewicz University, Grunwaldzka 6, 60-780 Poznań, Poland.
| | | | | | | | | | | |
Collapse
|
21
|
Ryan DE, Kim CH, Murray JB, Adams CJ, Stockley PG, Abelson J. New tertiary constraints between the RNA components of active yeast spliceosomes: a photo-crosslinking study. RNA (NEW YORK, N.Y.) 2004; 10:1251-65. [PMID: 15272121 PMCID: PMC1370615 DOI: 10.1261/rna.7060404] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2004] [Accepted: 04/30/2004] [Indexed: 05/24/2023]
Abstract
Elucidation of the three-dimensional (3D) structures of the two sequential active sites in spliceosomes is essential for understanding the mechanism of premessenger RNA splicing. The mechanism is predicted to be catalyzed by the small nuclear RNA (snRNA) components of spliceosomes. To obtain new tertiary constraints between the RNA components, we produced and mapped crosslinks between U6 snRNA and the proximal RNAs of active yeast spliceosomes ("yeast" in this report is Saccharomyces cerevisiae). Thus, specific sites in U6, when substituted with a photoreactive 4-thiouridine or 5-iodouridine, produced spliceosome-dependent crosslinks to U2 snRNA, or in one case, to the pre-mRNA substrate. One set of U2-U6 crosslinks formed before the Prp2p-dependent step of spliceosome assembly, whereas another set formed during or after this step but before the first chemical step of splicing. This latter set of crosslinks formed across U2-U6 helix I. Importantly, this set provides new tertiary constraints for developing 3D models of fully assembled yeast spliceosomes, which are poised for the first chemical step of splicing.
Collapse
Affiliation(s)
- Daniel E Ryan
- Division of Biology 147-75, California Institute of Technology, Pasedena 91125, USA.
| | | | | | | | | | | |
Collapse
|
22
|
Koch TH, Smith D, Tabacman E, Zichi DA. Kinetic analysis of site-specific photoaptamer-protein cross-linking. J Mol Biol 2004; 336:1159-73. [PMID: 15037076 DOI: 10.1016/j.jmb.2004.01.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2003] [Revised: 12/29/2003] [Accepted: 01/05/2004] [Indexed: 10/26/2022]
Abstract
ssDNA oligonucleotides containing bromodeoxyuridine, BrdU-photoaptamers, are rapidly emerging as specific protein capture reagents in protein microarray technologies. A mathematical model for the kinetic analysis of photoaptamer-protein photocross-linking reactions is presented. The model is based on specific aptamer/protein binding followed by laser excitation that can lead to either covalent cross-linking of the photoaptamer and protein in the complex or irreversible photodamage to the aptamer. Two distinct kinetic regimes, (1) frozen and (2) rapid equilibrium, are developed analytically to model binding kinetics between laser pulses. The models are used to characterize the photocross-linking between three photoaptamers and their cognate protein targets; photoaptamers 0650 and 0615 cross-link human basic fibroblast growth factor and 0518 cross-links HIV MN envelope glycoprotein. Data for cross-linking reaction yields as a function of both laser energy dose and target protein concentration are analyzed for affinity constants and cross-link reaction rates. The binding dissociation constants derived from the cross-linking data are in good accord with independent measurements; the rapid equilibrium model appears to produce results more consistent with the experimental observations, although there is significant overlap between the two models for most conditions explored here. The rate of photodamage for 0615 and 0518 is 3.5 and 2.5 times that of the specific cross-link, giving low maximum reaction yields of approximately 20% and approximately 30%, whereas 0650 cross-links with a rate over five times higher than its photodamage rate and has a maximum reaction yield exceeding 80%. Quantum yields for the three systems are estimated from the data; photoaptamer 0650 has a reasonably high quantum yield of approximately 0.2 for protein cross-linking, while 0518 and 0615 have quantum yields of 0.07 and 0.02. The work presented here provides a useful set of metrics that allow for refinement of photoaptamer properties.
Collapse
Affiliation(s)
- Tad H Koch
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA
| | | | | | | |
Collapse
|
23
|
Sanderson JM, Whelan EJ. Characterisation of the interactions of aromatic amino acids with diacetyl phosphatidylcholine. Phys Chem Chem Phys 2004. [DOI: 10.1039/b312184d] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
24
|
Steen H, Jensen ON. Analysis of protein-nucleic acid interactions by photochemical cross-linking and mass spectrometry. MASS SPECTROMETRY REVIEWS 2002; 21:163-182. [PMID: 12476441 DOI: 10.1002/mas.10024] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Photochemical cross-linking is a commonly used method for studying the molecular details of protein-nucleic acid interactions. Photochemical cross-linking aids in defining nucleic acid binding sites of proteins via subsequent identification of cross-linked protein domains and amino acid residues. Mass spectrometry (MS) has emerged as a sensitive and efficient analytical technique for determination of such cross-linking sites in proteins. The present review of the field describes a number of MS-based approaches for the characterization of cross-linked protein-nucleic acid complexes and for sequencing of peptide-nucleic acid heteroconjugates. The combination of photochemical cross-linking and MS provides a fast screening method to gain insights into the overall structure and formation of protein-oligonucleotide complexes. Because the analytical methods are continuously refined and protein structural data are rapidly accumulating in databases, we envision that many protein-nucleic acid assemblies will be initially characterized by combinations of cross-linking methods, MS, and computational molecular modeling.
Collapse
Affiliation(s)
- Hanno Steen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark
| | | |
Collapse
|
25
|
Pieper U, Groll DH, Wünsch S, Gast FU, Speck C, Mücke N, Pingoud A. The GTP-dependent restriction enzyme McrBC from Escherichia coli forms high-molecular mass complexes with DNA and produces a cleavage pattern with a characteristic 10-base pair repeat. Biochemistry 2002; 41:5245-54. [PMID: 11955074 DOI: 10.1021/bi015687u] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The GTP-dependent restriction enzyme McrBC consists of two polypeptides: one (McrB) that is responsible for GTP binding and hydrolysis as well as DNA binding and another (McrC) that is responsible for DNA cleavage. It recognizes two methylated or hemimethylated RC sites (R(m)C) at a distance of approximately 30 to more than 2000 base pairs and cleaves the DNA close to one of the two R(m)C sites. This process is strictly coupled to GTP hydrolysis and involves the formation of high-molecular mass complexes. We show here using footprinting techniques, surface plasmon resonance, and scanning force microscopy experiments that in the absence of McrC, McrB binds to a single R(m)C site. If a second R(m)C site is present on the DNA, it is occupied independently by McrB. Whereas the DNA-binding domain of McrB forms 1:1 complexes with each R(m)C site and shows a clear footprint on both R(m)C sites, full-length McrB forms complexes with a stoichiometry of at least 4:1 at each R(m)C site, resulting in a slightly more extended footprint. In the presence of McrC, McrB forms high-molecular mass complexes of unknown stoichiometry, which are considerably larger than the complexes formed with McrB alone. In these complexes and when GTP is present, the DNA is cleaved next to one of the R(m)C sites at distances differing by one to five helical turns, suggesting that in the McrBC-DNA complex only a few topologically well-defined phosphodiester bonds of the DNA are accessible for the nucleolytic center of McrC.
Collapse
Affiliation(s)
- Uwe Pieper
- Institut für Biochemie (FB 08), Justus-Liebig-Universität, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | | | | | | | | | | | | |
Collapse
|
26
|
Steen H, Petersen J, Mann M, Jensen ON. Mass spectrometric analysis of a UV-cross-linked protein-DNA complex: tryptophans 54 and 88 of E. coli SSB cross-link to DNA. Protein Sci 2001; 10:1989-2001. [PMID: 11567090 PMCID: PMC2374209 DOI: 10.1110/ps.07601] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Protein-nucleic acid complexes are commonly studied by photochemical cross-linking. UV-induced cross-linking of protein to nucleic acid may be followed by structural analysis of the conjugated protein to localize the cross-linked amino acids and thereby identify the nucleic acid binding site. Mass spectrometry is becoming increasingly popular for characterization of purified peptide-nucleic acid heteroconjugates derived from UV cross-linked protein-nucleic acid complexes. The efficiency of mass spectrometry-based methods is, however, hampered by the contrasting physico-chemical properties of nucleic acid and peptide entities present in such heteroconjugates. Sample preparation of the peptide-nucleic acid heteroconjugates is, therefore, a crucial step in any mass spectrometry-based analytical procedure. This study demonstrates the performance of four different MS-based strategies to characterize E. coli single-stranded DNA binding protein (SSB) that was UV-cross-linked to a 5-iodouracil containing DNA oligomer. Two methods were optimized to circumvent the need for standard liquid chromatography and gel electrophoresis, thereby dramatically increasing the overall sensitivity of the analysis. Enzymatic degradation of protein and oligonucleotide was combined with miniaturized sample preparation methods for enrichment and desalting of cross-linked peptide-nucleic acid heteroconjugates from complex mixtures prior to mass spectrometric analysis. Detailed characterization of the peptidic component of two different peptide-DNA heteroconjugates was accomplished by matrix-assisted laser desorption/ionization mass spectrometry and allowed assignment of tryptophan-54 and tryptophan-88 as candidate cross-linked residues. Sequencing of those peptide-DNA heteroconjugates by nanoelectrospray quadrupole time-of-flight tandem mass spectrometry identified tryptophan-54 and tryptophan-88 as the sites of cross-linking. Although the UV-cross-linking yield of the protein-DNA complex did not exceed 15%, less than 100 pmole of SSB protein was required for detailed structural analysis by mass spectrometry.
Collapse
Affiliation(s)
- H Steen
- Center for Experimental BioInformatics, Department of Biochemistry and Molecular Biology, University of Southern Denmark/Odense University, DK-5230 Odense M, Denmark
| | | | | | | |
Collapse
|
27
|
Mikata Y, He Q, Lippard SJ. Laser-induced photo-cross-linking of cisplatin-modified DNA to HMG-domain proteins. Biochemistry 2001; 40:7533-41. [PMID: 11412107 DOI: 10.1021/bi010318j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Laser-induced photo-cross-linking was investigated for DNA, modified with cisplatin at specific sites, bound to structure-specific recognition domains of proteins in the high-mobility group (HMG) class. The efficiency of photo-cross-linking depends on the wavelength and power of the laser, the nature of the protein domain, and the oligodeoxyribonucleotide sequences flanking the platinated site. Introduction of 5-iodouridine at thymine sites of the oligodeoxyribonucleotide as an additional photoreactive group did not increase the photo-cross-linking yield. Formation of platinum-mediated DNA-DNA interstrand cross-linking observed previously upon irradiation with 302 nm light [Kane, S. A., and Lippard, S. J. (1996) Biochemistry 35, 2180-2188] was significantly reduced with laser irradiation. HMG1 domain B is superior to domain A for platinum-mediated photo-cross-linking, a result attributed to the different positioning of the proteins with respect to the platinum adduct and the greater ability of domain B to access photolabilized platinum in the major groove. Studies with proteins containing specifically mutated amino acids, and with DNA probes in which the sequences flanking the platinum cross-link site were varied, suggest that the most effective photo-cross-linking occurs for protein domains bound symmetrically and flexibly to cisplatin-modified DNA. The thermodynamic equilibrium between the protein-platinated DNA complex and its components, revealed in gel electrophoretic mobility shift assays (EMSAs), is significantly shifted to the right upon irreversible photo-cross-linking. Thus, only upon photo-cross-linking can the interaction of cisplatin-DNA 1,3-intrastrand d(GpTpG) or interstrand cross-links with HMG1 domain B protein be detected. Photo-cross-linking is thus an effective tool for investigating the interaction of cisplatin-modified DNA with damage-recognition proteins under heterogeneous conditions such those in cell extracts or living cells.
Collapse
Affiliation(s)
- Y Mikata
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139-4307, USA
| | | | | |
Collapse
|
28
|
Meisenheimer KM, Meisenheimer PL, Koch TH. Nucleoprotein photo-cross-linking using halopyrimidine-substituted RNAs. Methods Enzymol 2001; 318:88-104. [PMID: 10889982 DOI: 10.1016/s0076-6879(00)18046-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- K M Meisenheimer
- Department of Chemistry, Angelo State University, San Angelo, Texas 76909, USA
| | | | | |
Collapse
|
29
|
Wada T, Sugahara N, Kawano M, Inoue Y. First Asymmetric Photochemistry with Nucleosides and DNA: EnantiodifferentiatingZ–EPhotoisomerization of Cyclooctene. CHEM LETT 2000. [DOI: 10.1246/cl.2000.1174] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
|
30
|
Abstract
High sensitivity and specificity of two modified ssDNA aptamers capable of photocross-linking recombinant human basic fibroblast growth factor (bFGF((155))) were demonstrated. The aptamers were identified through a novel, covalent, in vitro selection methodology called photochemical systematic evolution of ligands by exponential enrichment (PhotoSELEX). The aptamers exhibited high sensitivity for bFGF((155)) comparable with commercially available ELISA monoclonal antibodies with an absolute sensitivity of at least 0.058 ppt bFGF((155)) under prevailing test conditions. The aptamers exquisitely distinguished bFGF((155)) from consanguine proteins, vascular endothelial growth factor (VEGF) and platelet derived growth factor (PDGF). A commercially viable diagnostic system incorporating PhotoSELEX-evolved aptamers capable of simultaneous quantification of a large number of analyte molecules is also described. Such a system benefits from covalent bonding of aptamer to target protein allowing vigorous washing with denaturants to improve signal to noise.
Collapse
Affiliation(s)
- M C Golden
- Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA
| | | | | | | |
Collapse
|
31
|
Chen T, Cook GP, Koppisch AT, Greenberg MM. Investigation of the Origin of the Sequence Selectivity for the 5-Halo-2‘-deoxyuridine Sensitization of DNA to Damage by UV-Irradiation. J Am Chem Soc 2000. [DOI: 10.1021/ja994357i] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tongqian Chen
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Gary P. Cook
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Andrew T. Koppisch
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Marc M. Greenberg
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| |
Collapse
|
32
|
Ioele M, Bazzanini R, Chatgilialoglu C, Mulazzani QG. Chemical Radiation Studies of 8-Bromoguanosine in Aqueous Solutions. J Am Chem Soc 2000. [DOI: 10.1021/ja991785f] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Marcella Ioele
- Contribution from the I.Co.C.E.A. and F.R.A.E., Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Rita Bazzanini
- Contribution from the I.Co.C.E.A. and F.R.A.E., Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Chryssostomos Chatgilialoglu
- Contribution from the I.Co.C.E.A. and F.R.A.E., Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Quinto G. Mulazzani
- Contribution from the I.Co.C.E.A. and F.R.A.E., Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| |
Collapse
|
33
|
Schweizer U, Hey T, Lipps G, Krauss G. Photocrosslinking locates a binding site for the large subunit of human replication protein A to the damaged strand of cisplatin-modified DNA. Nucleic Acids Res 1999; 27:3183-9. [PMID: 10454616 PMCID: PMC148546 DOI: 10.1093/nar/27.15.3183] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The repair proteins XPA, XPC and replication protein A (RPA) have been implicated in the primary recognition of damaged DNA sites during nucleotide excision repair. Detailed structural information on the binding of these proteins to DNA lesions is however lacking. We have studied the binding of human RPA (hRPA) and hRPA-XPA-complexes to model oligonucleo-tides containing a single 1, 3-d(GTG)-cisplatin-modification by photocrosslinking and electrophoretic mobility shift experiments. The 70 kDa subunit of hRPA can be crosslinked with high efficiency to cisplatin-modified DNA probes carrying 5-iodo-2"-deoxyuridin (5-IdU) as crosslinking chromophore. High efficiency crosslinking is dependent on the presence of the DNA lesion and occurs preferentially at its 5"-side. Examination of the crosslinking efficiency in dependence on the position of the 5-IdU chromophore indicates a specific positioning of hRPA with respect to the platination site. When hRPA and XPA are both present mainly hRPA is crosslinked to the DNA. Our mobility shift experiments directly show the formation of a stable ternary complex of hRPA, XPA and the damaged DNA. The affinity of the XPA-hRPA complex to the damaged DNA is increased by more than one order of magnitude as compared to hRPA alone.
Collapse
Affiliation(s)
- U Schweizer
- Lehrstuhl für Biochemie, Universität Bayreuth, Universitätsstrasse 30, D-95447 Bayreuth, Germany
| | | | | | | |
Collapse
|
34
|
Kawai K, Saito I, Sugiyama H. Photochemical halogen-exchange reaction of 5-iodouracil-containing oligonucleotides. Tetrahedron Lett 1999. [DOI: 10.1016/s0040-4039(99)01082-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
35
|
Holz B, Dank N, Eickhoff JE, Lipps G, Krauss G, Weinhold E. Identification of the binding site for the extrahelical target base in N6-adenine DNA methyltransferases by photo-cross-linking with duplex oligodeoxyribonucleotides containing 5-iodouracil at the target position. J Biol Chem 1999; 274:15066-72. [PMID: 10329711 DOI: 10.1074/jbc.274.21.15066] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
DNA methyltransferases flip their target bases out of the DNA double helix for catalysis. Base flipping of C5-cytosine DNA methyltransferases was directly observed in the protein-DNA cocrystal structures of M.HhaI and M.HaeIII. Indirect structural evidence for base flipping of N6-adenine and N4-cytosine DNA methyltransferases was obtained by modeling DNA into the three-dimensional structures of M.TaqI and M.PvuII in complex with the cofactor. In addition, biochemical evidence of base flipping was reported for different N6-adenine DNA methyltransferases. As no protein-DNA cocrystal structure for the related N6-adenine and N4-cytosine DNA methyltransferases is available, we used light-induced photochemical cross-linking to identify the binding site of the extrahelical target bases. The N6-adenine DNA methyltransferases M.TaqI and M.CviBIII, which both methylate adenine within the double-stranded 5'-TCGA-3' DNA sequence, were photo-cross-linked to duplex oligodeoxyribonucleotides containing 5-iodouracil at the target position in 50-60% and almost quantitative yield, respectively. Proteolytic fragmentation of the M. CviBIII-DNA complex followed by Edman degradation and electrospray ionization mass spectrometry indicates photo-cross-linking to tyrosine 122. In addition, the mutant methyltransferases M. TaqI/Y108A and M.TaqI/F196A were photo-cross-linked with 6-fold and 2-fold reduced efficiency, respectively, which suggests that tyrosine 108 is the primary site of modification in M.TaqI. Our results indicate a close proximity between the extrahelical target base and tyrosine 122 in M.CviBIII or tyrosine 108 in M.TaqI. As both residues belong to the conserved motif IV ((N/D/S)(P/I)P(Y/F/W)) found in all N6-adenine and N4-cytosine DNA as well as in N6-adenine RNA methyltransferases, a similar spatial relationship between the target bases and the aromatic amino acid residue within motif IV is expected for all these methyltransferases.
Collapse
Affiliation(s)
- B Holz
- Max-Planck-Institut für molekulare Physiologie, Abteilung Physikalische Biochemie, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany
| | | | | | | | | | | |
Collapse
|
36
|
Abstract
Transcription is the fundamental process by which RNA is synthesized by RNA polymerases on double-stranded DNA templates. One structurally simple RNA polymerase is encoded by bacteriophage T7. T7 RNA polymerase is an excellent candidate for studying structural aspects of transcription, because unlike the eucaryotic and bacterial RNA polymerases, it is a single subunit enzyme and does not require additional factors to carry out the entire process of transcription from start to finish. An important advantage of studying transcription using this enzyme is that the high-resolution crystal structure of T7 RNA polymerase has been solved. However, a cocrystal structure of the polymerase complexed with promoter has not yet been published. Here, we have used cross-linking techniques to understand the interaction of promoter with T7 RNA polymerase. We constructed promoters that were substituted with the photo-cross-linkable nucleotide 5-iodo uracil at every dT in the promoter from -17 to -1. This substitution replaces the 5-methyl in dT with an iodine atom. The substituted promoters were photo-cross-linked to T7 RNAP, and the efficiency of cross-linking was quantitated at every position. In the melting domain, the strongest contacts occurred at -3 and at -1 on the template strand while very weak cross-linking was seen at -2 and at -4 on the nontemplate strand. In the binding domain, the strongest contacts were seen at -16, -15, and -13 and at -10 on the template strand while at -17 and -14 on the nontemplate strand very weak cross-linking was observed. Cross-linking was poor in the intervening region between the binding and the melting domains. These results suggested that, in the T7 RNA polymerase-promoter complex, the polymerase molecule mainly contacts the template bases in the TATA box while the upstream contacts are used as an anchor for DNA binding. For a systematic study designed to probe the nature of base-specific interactions in the polymerase-promoter complex, we used neutral salts from the Hofmeister series. In general, the order of perturbation was sulfate > citrate > acetate for anions and ammonium > magnesium > potassium for cations. Using acrylamide, a neutral hydrophobic agent to probe for nonionic contacts, we observed that at -2, -4, and -17 the contacts had a hydrophobic component, while at many other positions there was no significant effect, suggesting that the contacts in the promoter-polymerase complexes were predominantly ionic but at certain positions nonionic interactions also existed. To localize a specific interaction in the melting domain, we proteolyzed the cross-linked T7 RNAP and analyzed the fragments using gel electrophoresis, mass spectrometry, and amino acid composition. High-resolution mapping indicated that amino acid residues 614-627 may be in the vicinity of the melting domain. Specifically, Y623 may contact -3 on the template strand.
Collapse
Affiliation(s)
- S Sastry
- Laboratory of Molecular Genetics, The Rockefeller University, New York 10021, USA.
| | | |
Collapse
|
37
|
Pingoud V, Thole H, Christ F, Grindl W, Wende W, Pingoud A. Photocross-linking of the homing endonuclease PI-SceI to its recognition sequence. J Biol Chem 1999; 274:10235-43. [PMID: 10187809 DOI: 10.1074/jbc.274.15.10235] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
PI-SceI is an intein-encoded protein that belongs to the LAGLIDADG family of homing endonucleases. According to the crystal structure and mutational studies, this endonuclease consists of two domains, one responsible for protein splicing, the other for DNA cleavage, and both presumably for DNA binding. To define the DNA binding site of PI-SceI, photocross-linking was used to identify amino acid residues in contact with DNA. Sixty-three double-stranded oligodeoxynucleotides comprising the minimal recognition sequence and containing single 5-iodopyrimidine substitutions in almost all positions of the recognition sequence were synthesized and irradiated in the presence of PI-SceI with a helium/cadmium laser (325 nm). The best cross-linking yield (approximately 30%) was obtained with an oligodeoxynucleotide with a 5-iododeoxyuridine at position +9 in the bottom strand. The subsequent analysis showed that cross-linking had occurred with amino acid His-333, 6 amino acids after the second LAGLIDADG motif. With the H333A variant of PI-SceI or in the presence of excess unmodified oligodeoxynucleotide, no cross-linking was observed, indicating the specificity of the cross-linking reaction. Chemical modification of His residues in PI-SceI by diethylpyrocarbonate leads to a substantial reduction in the binding and cleavage activity of PI-SceI. This inactivation can be suppressed by substrate binding. This result further supports the finding that at least one His residue is in close contact to the DNA. Based on these and published results, conclusions are drawn regarding the DNA binding site of PI-SceI.
Collapse
Affiliation(s)
- V Pingoud
- Institut für Biochemie, Fachbereich Biologie, Justus-Liebig-Universität, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany.
| | | | | | | | | | | |
Collapse
|
38
|
Jeltsch A, Roth M, Friedrich T. Mutational analysis of target base flipping by the EcoRV adenine-N6 DNA methyltransferase. J Mol Biol 1999; 285:1121-30. [PMID: 9918720 DOI: 10.1006/jmbi.1998.2389] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA methyltransferases flip their target base out of the DNA helix. Here, we have investigated base flipping by wild-type EcoRV DNA methyltransferase (M.EcoRV) and five M.EcoRV variants (D193A, Y196A, S229A, W231R and Y258A). These variants bind to DNA and S-adenosylmethionine but have a severely reduced catalytic efficiency or are catalytically inactive. To measure base flipping three different assays were used, viz. analysis of the yields of photocrosslinking reactions between the enzymes and a substrate in which the target base is replaced by 5-iodouracil, analysis of the binding constants to substrates containing a mismatch base-pair at the target position and analysis of the salt dependence of specific complex formation. Our data show that the Y196A, W231R and Y258A variants are not able to stabilize a flipped target base, suggesting that the aromatic amino acid residues (Tyr196, Trp231 and Tyr258) are involved in hydrophobic interactions with the flipped base. The D193A variant behaves like wild-type M.EcoRV with respect to base flipping. The fact that this variant is catalytically inactive indicates that Asp193 has a function in chemical catalysis. The S229A variant can better flip modified bases but does not tightly lock the flipped base into the adenine-binding pocket, suggesting that Ser229 could form a contact to the flipped adenine.
Collapse
Affiliation(s)
- A Jeltsch
- Institut für Biochemie, Fachbereich Biologie, Heinrich-Buff-Ring 58, Giessen, 35392, Germany.
| | | | | |
Collapse
|
39
|
Ruckman J, Green LS, Beeson J, Waugh S, Gillette WL, Henninger DD, Claesson-Welsh L, Janjić N. 2'-Fluoropyrimidine RNA-based aptamers to the 165-amino acid form of vascular endothelial growth factor (VEGF165). Inhibition of receptor binding and VEGF-induced vascular permeability through interactions requiring the exon 7-encoded domain. J Biol Chem 1998; 273:20556-67. [PMID: 9685413 DOI: 10.1074/jbc.273.32.20556] [Citation(s) in RCA: 502] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Vascular endothelial growth factor (VEGF) has been implicated in the pathological induction of new blood vessel growth in a variety of proliferative disorders. Using the SELEX process (systematic evolution of ligands by exponential enrichment), we have isolated 2'-F-pyrimidine RNA oligonucleotide ligands (aptamers) to human VEGF165. Representative aptamers from three distinct sequence families were truncated to the minimal sequence capable of high affinity binding to VEGF (23-29 nucleotides) and were further modified by replacement of 2'-O-methyl for 2'-OH at all ribopurine positions where the substitution was tolerated. Equilibrium dissociation constants for the interaction of VEGF with the truncated, 2'-O-methyl-modified aptamers range between 49 and 130 pM. These aptamers bind equally well to murine VEGF164, do not bind to VEGF121 or the smaller isoform of placenta growth factor (PlGF129), and show reduced, but significant affinity for the VEGF165/PlGF129 heterodimer. Cysteine 137 in the exon 7-encoded domain of VEGF165 forms a photo-inducible cross-link to a single uridine residue in each of the three aptamers. The aptamers potently inhibit the binding of VEGF to the human VEGF receptors, KDR and Flt-1, expressed by transfected porcine aortic endothelial cells. Furthermore, one of the aptamers is able to significantly reduce intradermal VEGF-induced vascular permeability in vivo.
Collapse
Affiliation(s)
- J Ruckman
- NeXstar Pharmaceuticals, Inc., Boulder, Colorado 80301, USA
| | | | | | | | | | | | | | | |
Collapse
|
40
|
Raschke U, Werner G, Wilde H, Stottmeister U. Photodecomposition of 4-amino-1,2,4-triazin-3,5-diones and -thiones in oxygenated aqueous solutions. J Photochem Photobiol A Chem 1998. [DOI: 10.1016/s1010-6030(98)00265-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
41
|
Fujimoto K, Sugiyama H, Saito I. Sequence dependent photoreduction of 5-bromouracil-contaning oligonucleotides via electron transfer. Tetrahedron Lett 1998. [DOI: 10.1016/s0040-4039(98)00079-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
|
42
|
Wong DL, Pavlovich JG, Reich NO. Electrospray ionization mass spectrometric characterization of photocrosslinked DNA-EcoRI DNA methyltransferase complexes. Nucleic Acids Res 1998; 26:645-9. [PMID: 9421528 PMCID: PMC147290 DOI: 10.1093/nar/26.2.645] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
We describe a novel strategy combining photocrosslinking and HPLC-based electrospray ionization mass spectrometry to identify UV crosslinked DNA-protein complexes. Eco RI DNA methyltransferase modifies the second adenine within the recognition sequence GAATTC. Substitution of 5-iodouracil for the thymine adjacent to the target base (GAATTC) does not detectably alter the DNA-protein complex. Irradiation of the 5-iodouracil-substituted DNA-protein complex at various wavelengths was optimized, with a crosslinking yield >60% at 313 nm after 1 min. No protein degradation was observed under these conditions. The crosslinked DNA-protein complex was further analyzed by electrospray ionization mass spectrometry. The total mass is consistent with irradiation-dependent covalent bond formation between one strand of DNA and the protein. These preliminary results support the possibility of identifying picomole quantities of crosslinked peptides by similar strategies.
Collapse
Affiliation(s)
- D L Wong
- Department of Chemistry and Program in Biochemistry and Molecular Biology, University of California, Santa Barbara, CA 93106, USA
| | | | | |
Collapse
|
43
|
Bromination of pyrimidines using bromide and monoperoxysulfate: A competition study between cytidine, uridine and thymidine. Tetrahedron Lett 1997. [DOI: 10.1016/s0040-4039(97)00512-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
44
|
Meisenheimer KM, Koch TH. Photocross-linking of nucleic acids to associated proteins. Crit Rev Biochem Mol Biol 1997; 32:101-40. [PMID: 9145285 DOI: 10.3109/10409239709108550] [Citation(s) in RCA: 213] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Photocross-linking is a useful technique for the partial definition of the nucleic acid-protein interface of nucleoprotein complexes. It can be accomplished by one or two photon excitations of wild-type nucleoprotein complexes or by one photon excitation of nucleoprotein complexes bearing one or more substitutions with photoreactive chromophores. Chromophores that have been incorporated into nucleic acids for this purpose include aryl azides, 5-azidouracil, 8-azidoadenine, 8-azidoguanine, 4-thiouracil, 5-bromouracil, 5-iodouracil, and 5-iodocytosine. The various techniques and chromophores are described and compared, with attention to the photochemical mechanism.
Collapse
Affiliation(s)
- K M Meisenheimer
- Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA
| | | |
Collapse
|