1
|
Tashiro R, Sugiyama H. Photoreaction of DNA Containing 5-Halouracil and its Products. Photochem Photobiol 2022; 98:532-545. [PMID: 34543451 PMCID: PMC9197447 DOI: 10.1111/php.13521] [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] [Received: 07/15/2021] [Accepted: 09/13/2021] [Indexed: 11/30/2022]
Abstract
5-Halouracil, which is a DNA base analog in which the methyl group at the C5 position of thymine is replaced with a halogen atom, has been used in studies of DNA damage. In DNA strands, the uracil radical generated from 5-halouracil causes DNA damage via a hydrogen-abstraction reaction. We analyzed the photoreaction of 5-halouracil in various DNA structures and revealed that the reaction is DNA structure-dependent. In this review, we summarize the results of the analysis of the reactivity of 5-halouracil in various DNA local structures. Among the 5-halouracil molecules, 5-bromouracil has been used as a probe in the analysis of photoinduced electron transfer through DNA. The analysis of groove-binder/DNA and protein/DNA complexes using a 5-bromouracil-based electron transfer system is also described.
Collapse
Affiliation(s)
- Ryu Tashiro
- Faculty of Pharmaceutical Sciences, Suzuka University of Medical Science, 3500-3 Minamitamagaki-Cyo, Suzuka, Mie, 513-8670, Japan
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
- Institute for Integrated Cell-Material Science (WPI-iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan
| |
Collapse
|
2
|
Saha A, Bombard S, Granzhan A, Teulade-Fichou MP. Probing of G-Quadruplex Structures via Ligand-Sensitized Photochemical Reactions in BrU-Substituted DNA. Sci Rep 2018; 8:15814. [PMID: 30361545 PMCID: PMC6202380 DOI: 10.1038/s41598-018-34141-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/12/2018] [Indexed: 01/18/2023] Open
Abstract
We studied photochemical reactions of BrU-substituted G-quadruplex (G4) DNA substrates with two pyrene-substituted polyazamacrocyclic ligands, M-1PY and M-2PY. Both ligands bind to and stabilize G4-DNA structures without altering their folding topology, as demonstrated by FRET-melting experiments, fluorimetric titrations and CD spectroscopy. Notably, the bis-pyrene derivative (M-2PY) behaves as a significantly more affine and selective G4 ligand, compared with its mono-pyrene counterpart (M-1PY) and control compounds. Upon short UVA irradiation (365 nm) both ligands, in particular M-2PY, efficiently sensitize photoreactions at BrU residues incorporated in G4 structures and give rise to two kinds of photoproducts, namely DNA strand cleavage and covalent ligand-DNA photoadducts. Remarkably, the photoinduced strand cleavage is observed exclusively with G4 structures presenting BrU residues in lateral or diagonal loops, but not with parallel G4-DNA structures presenting only propeller loops. In contrast, the formation of fluorescent photoadducts is observed with all BrU-substituted G4-DNA substrates, with M-2PY giving significantly higher yields (up to 27%) than M-1PY. Both ligand-sensitized photoreactions are specific to BrU-modified G4-DNA structures with respect to double-stranded or stem-loop substrates. Thus, ligand-sensitized photoreactions with BrU-substituted G4-DNA may be exploited (i) as a photochemical probe, allowing "photofootprinting" of G4 folding topologies in vitro and (ii) for covalent trapping of G4 structures as photoadducts with pyrene-substituted ligands.
Collapse
Affiliation(s)
- Abhijit Saha
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405, Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405, Orsay, France
| | - Sophie Bombard
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405, Orsay, France.,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405, Orsay, France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405, Orsay, France. .,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405, Orsay, France.
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405, Orsay, France. .,CNRS UMR9187, INSERM U1196, Université Paris Sud, Université Paris Saclay, 91405, Orsay, France.
| |
Collapse
|
3
|
Kawamoto Y, Bando T, Sugiyama H. Sequence-specific DNA binding Pyrrole-imidazole polyamides and their applications. Bioorg Med Chem 2018; 26:1393-1411. [PMID: 29439914 DOI: 10.1016/j.bmc.2018.01.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/25/2018] [Accepted: 01/28/2018] [Indexed: 12/25/2022]
Abstract
Pyrrole-imidazole polyamides (Py-Im polyamides) are cell-permeable compounds that bind to the minor groove of double-stranded DNA in a sequence-specific manner without causing denaturation of the DNA. These compounds can be used to control gene expression and to stain specific sequences in cells. Here, we review the history, structural variations, and functional investigations of Py-Im polyamides.
Collapse
Affiliation(s)
- Yusuke Kawamoto
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan
| | - Toshikazu Bando
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8502, Japan; Institute for Integrated Cell-Material Science (iCeMS), Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| |
Collapse
|
4
|
Saha A, Kizaki S, Han JH, Yu Z, Sugiyama H. UVA irradiation of BrU-substituted DNA in the presence of Hoechst 33258. Bioorg Med Chem 2018; 26:37-40. [PMID: 29170027 DOI: 10.1016/j.bmc.2017.11.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 11/02/2017] [Accepted: 11/04/2017] [Indexed: 01/15/2023]
Abstract
Given that our knowledge of DNA repair is limited because of the complexity of the DNA system, a technique called UVA micro-irradiation has been developed that can be used to visualize the recruitment of DNA repair proteins at double-strand break (DSB) sites. Interestingly, Hoechst 33258 was used under micro-irradiation to sensitize 5-bromouracil (BrU)-labelled DNA, causing efficient DSBs. However, the molecular basis of DSB formation under UVA micro-irradiation remains unknown. Herein, we investigated the mechanism of DSB formation under UVA micro-irradiation conditions. Our results suggest that the generation of a uracil-5-yl radical through electron transfer from Hoechst 33258 to BrU caused DNA cleavage preferentially at self-complementary 5'-AABrUBrU-3' sequences to induce DSB. We also investigated the DNA cleavage in the context of the nucleosome to gain a better understanding of UVA micro-irradiation in a cell-like model. We found that DNA cleavage occurred in both core and linker DNA regions although its efficiency reduced in core DNA.
Collapse
Affiliation(s)
- Abhijit Saha
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Seiichiro Kizaki
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Ji Hoon Han
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Zutao Yu
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Hiroshi Sugiyama
- Department of Science, Graduate School of Science, Kyoto University, Sakyo, Kyoto 606-8501, Japan; Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida Ushinomiya-cho, Sakyo, Kyoto 606-8502, Japan.
| |
Collapse
|
5
|
Cerón-Carrasco JP, Ruiz J, Vicente C, de Haro C, Bautista D, Zúñiga J, Requena A. DFT Simulation of Structural and Optical Properties of 9-Aminoacridine Half-Sandwich Ru(II), Rh(III), and Ir(III) Antitumoral Complexes and Their Interaction with DNA. J Chem Theory Comput 2017. [DOI: 10.1021/acs.jctc.7b00139] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- José Pedro Cerón-Carrasco
- Bioinformatics
and High Performance Computing Research Group (BIO-HPC), Universidad Católica San Antonio de Murcia (UCAM), Campus de los
Jerónimos, 30107 Murcia, Spain
| | | | | | | | | | | | | |
Collapse
|
6
|
Fujimoto K, Furusawa M, Nakamura S, Sakamoto T. UVA-responsive Anticancer Prodrugs Based on Photoinduced Electron Injection into Oligonucleotide Having 5-Halouracils. CHEM LETT 2016. [DOI: 10.1246/cl.160492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
|
7
|
Pandian GN, Sugiyama H. Nature-Inspired Design of Smart Biomaterials Using the Chemical Biology of Nucleic Acids. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2016. [DOI: 10.1246/bcsj.20160062] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
8
|
Han YW, Sugiyama H, Harada Y. The application of fluorescence-conjugated pyrrole/imidazole polyamides in the characterization of protein–DNA complex formation. Biomater Sci 2016; 4:391-9. [DOI: 10.1039/c5bm00214a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Fluorescent conjugates of Py–Im polyamides are used as sequence-specific fluorescent probes and applied to the characterisation of protein–DNA complex dynamics.
Collapse
Affiliation(s)
- Yong-Woon Han
- Institute for Integrated Cell-Materials Science (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Hiroshi Sugiyama
- Institute for Integrated Cell-Materials Science (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501
- Japan
- Department of Chemistry
| | - Yoshie Harada
- Institute for Integrated Cell-Materials Science (WPI-iCeMS)
- Kyoto University
- Kyoto 606-8501
- Japan
- Graduate School of Biostudies
| |
Collapse
|
9
|
Bätzner E, Liang Y, Schweigert C, Unterreiner AN, Wagenknecht HA. Acceleration of Long-Range Photoinduced Electron Transfer through DNA by Hydroxyquinolines as Artificial Base Pairs. Chemphyschem 2015; 16:1607-12. [PMID: 25784385 DOI: 10.1002/cphc.201500062] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Indexed: 02/05/2023]
Abstract
The C-nucleoside based on the hydroxyquinoline ligand (Hq) is complementary to itself and forms stable Hq-Hq pairs in double-stranded DNA. These artificial Hq-Hq pairs may serve as artificial electron carriers for long-range photoinduced electron transfer in DNA, as elucidated by a combination of gel electrophoretic analysis of irradiated samples and time-resolved transient absorption spectroscopy. For this study, the Hq-Hq pair was combined with a DNA-based donor-acceptor system consisting of 6-N,N-dimethylaminopyrene conjugated to 2'-deoxyuridine as photoinducible electron donor, and methyl viologen attached to the 2'-position of uridine as electron acceptor. The Hq radical anion was identified in the time-resolved measurements and strand cleavage products support its role as an intermediate charge carrier. Hence, the Hq-Hq pair significantly enhances the electron hopping capability of DNA compared to natural DNA bases over long distances while keeping the self-assembly properties as the most attractive feature of DNA as a supramolecular architecture.
Collapse
Affiliation(s)
- Effi Bätzner
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany)
| | - Yu Liang
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe (Germany)
| | - Caroline Schweigert
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe (Germany)
| | - Andreas-Neil Unterreiner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe (Germany).
| | - Hans-Achim Wagenknecht
- Institute of Organic Chemistry, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 6, 76131 Karlsruhe (Germany).
| |
Collapse
|
10
|
Saha A, Hashiya F, Kizaki S, Asamitsu S, Hashiya K, Bando T, Sugiyama H. A novel detection technique of polyamide binding sites by photo-induced electron transfer in BrU substituted DNA. Chem Commun (Camb) 2015; 51:14485-8. [DOI: 10.1039/c5cc05104e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate a highly sensitive detection technique of polyamide binding sites using the photochemistry of BrU labeled DNA.
Collapse
Affiliation(s)
- Abhijit Saha
- Department of Science
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Fumitaka Hashiya
- Department of Science
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Seiichiro Kizaki
- Department of Science
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Sefan Asamitsu
- Department of Science
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Kaori Hashiya
- Department of Science
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Toshikazu Bando
- Department of Science
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501
- Japan
| | - Hiroshi Sugiyama
- Department of Science
- Graduate School of Science
- Kyoto University
- Kyoto 606-8501
- Japan
| |
Collapse
|