1
|
Grøsvik K, Tesfahun AN, Muruzábal-Lecumberri I, Haugland GT, Leiros I, Ruoff P, Kvaløy JT, Knævelsrud I, Ånensen H, Alexeeva M, Sato K, Matsuda A, Alseth I, Klungland A, Bjelland S. The Escherichia coli alkA Gene Is Activated to Alleviate Mutagenesis by an Oxidized Deoxynucleoside. Front Microbiol 2020; 11:263. [PMID: 32158436 PMCID: PMC7051996 DOI: 10.3389/fmicb.2020.00263] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 02/04/2020] [Indexed: 12/01/2022] Open
Abstract
The cellular methyl donor S-adenosylmethionine (SAM) and other endo/exogenous agents methylate DNA bases non-enzymatically into products interfering with replication and transcription. An important product is 3-methyladenine (m3A), which in Escherichia coli is removed by m3A-DNA glycosylase I (Tag) and II (AlkA). The tag gene is constitutively expressed, while alkA is induced by sub-lethal concentrations of methylating agents. We previously found that AlkA exhibits activity for the reactive oxygen-induced thymine (T) lesion 5-formyluracil (fU) in vitro. Here, we provide evidence for AlkA involvement in the repair of oxidized bases by showing that the adenine (A) ⋅ T → guanine (G) ⋅ cytosine (C) mutation rate increased 10-fold in E. coli wild-type and alkA– cells exposed to 0.1 mM 5-formyl-2′-deoxyuridine (fdU) compared to a wild-type specific reduction of the mutation rate at 0.2 mM fdU, which correlated with alkA gene induction. G⋅C → A⋅T alleviation occurred without alkA induction (at 0.1 mM fdU), correlating with a much higher AlkA efficiency for fU opposite to G than for that to A. The common keto form of fU is the AlkA substrate. Mispairing with G by ionized fU is favored by its exclusion from the AlkA active site.
Collapse
Affiliation(s)
- Kristin Grøsvik
- Department of Chemistry, Bioscience and Environmental Technology, Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Almaz Nigatu Tesfahun
- Department of Chemistry, Bioscience and Environmental Technology, Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Izaskun Muruzábal-Lecumberri
- Department of Chemistry, Bioscience and Environmental Technology, Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | | | - Ingar Leiros
- The Norwegian Structural Biology Centre, Department of Chemistry, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Peter Ruoff
- Department of Chemistry, Bioscience and Environmental Technology, Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Jan Terje Kvaløy
- Department of Mathematics and Physics, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Ingeborg Knævelsrud
- Department of Chemistry, Bioscience and Environmental Technology, Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Hilde Ånensen
- Department of Chemistry, Bioscience and Environmental Technology, Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Marina Alexeeva
- Department of Chemistry, Bioscience and Environmental Technology, Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| | - Kousuke Sato
- Faculty of Pharmaceutical Sciences, Health Sciences University of Hokkaido, Tobetsu, Japan
| | - Akira Matsuda
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Ingrun Alseth
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Arne Klungland
- Department of Microbiology, Oslo University Hospital, Oslo, Norway.,Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
| | - Svein Bjelland
- Department of Chemistry, Bioscience and Environmental Technology, Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, Norway
| |
Collapse
|
2
|
Kawasaki F, Murat P, Li Z, Santner T, Balasubramanian S. Synthesis and biophysical analysis of modified thymine-containing DNA oligonucleotides. Chem Commun (Camb) 2017; 53:1389-1392. [PMID: 28074944 PMCID: PMC5759927 DOI: 10.1039/c6cc08670e] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We report the synthesis of a 5-formyl-2'-deoxyuridine (5fU) phosphoramidite and the preparation of oligonucleotides comprising all known, naturally observed eukaryotic thymidine modifications. Biophysical characterization of the synthetic oligonucleotides indicates that 5fU, but not the other T-derivatives, can alter DNA structures.
Collapse
Affiliation(s)
- F Kawasaki
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - P Murat
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Z Li
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - T Santner
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - S Balasubramanian
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK. and Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK and School of Clinical Medicine, University of Cambridge, Cambridge CB2 0SP, UK
| |
Collapse
|
3
|
Wen J, Shen X, Shen H, Zhang FS. Hofmeister series and ionic effects of alkali metal ions on DNA conformation transition in normal and less polarised water solvent. Mol Phys 2014. [DOI: 10.1080/00268976.2014.906674] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
4
|
Tsunoda M, Sakaue T, Naito S, Sunami T, Abe N, Ueno Y, Matsuda A, Takénaka A. Insights into the structures of DNA damaged by hydroxyl radical: crystal structures of DNA duplexes containing 5-formyluracil. J Nucleic Acids 2010; 2010:107289. [PMID: 20976303 PMCID: PMC2952808 DOI: 10.4061/2010/107289] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2010] [Revised: 07/19/2010] [Accepted: 08/15/2010] [Indexed: 12/01/2022] Open
Abstract
Hydroxyl radicals are potent mutagens that attack DNA to form various base and ribose derivatives. One of the major damaged thymine derivatives is 5-formyluracil (fU), which induces pyrimidine transition during replication. In order to establish the structural basis for such mutagenesis, the crystal structures of two kinds of DNA d(CGCGRATfUCGCG) with R = A/G have been determined by X-ray crystallography. The fU residues form a Watson-Crick-type pair with A and two types of pairs (wobble and reversed wobble) with G, the latter being a new type of base pair between ionized thymine base and guanine base. In silico structural modeling suggests that the DNA polymerase can accept the reversed wobble pair with G, as well as the Watson-Crick pair with A.
Collapse
Affiliation(s)
- Masaru Tsunoda
- Faculty of Pharmacy, Iwaki Meisei University, Chuodai-Iino, Iwaki 970-8551, Japan
| | | | | | | | | | | | | | | |
Collapse
|
5
|
Knaevelsrud I, Slupphaug G, Leiros I, Matsuda A, Ruoff P, Bjelland S. Opposite-base dependent excision of 5-formyluracil from DNA by hSMUG1. Int J Radiat Biol 2009; 85:413-20. [PMID: 19365746 DOI: 10.1080/09553000902818915] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
PURPOSE The aim of this study was to determine the excision efficiency of hSMUG1 (human single-strand-selective monofunctional uracil-DNA glycosylase) for 5-formyluracil (fU), a major thymine lesion formed by ionizing radiation, opposite all normal bases in DNA, to possibly explain mutation induction by fU in the DNA of mammalian cells. MATERIALS AND METHODS An enzymatically [(32)P]labelled fU-containing 36 nucleotide DNA sequence plus its complementary sequence (with an A, C, G or T residue inserted opposite fU) was subjected to hSMUG1 in a pH 7.5-buffer, followed by NaOH-mediated cleavage of the resultant abasic sites. Cleaved and uncleaved DNA were separated by denaturing electrophoresis and quantified by autoradiography. RESULTS The hSMUG1 excised fU from DNA opposite all normal bases with the highest activity when opposite non-cognate C or T followed by G and cognate A. CONCLUSIONS The predominant T --> G and T --> A transversions induced by fU in mammalian cells may be explained by replicative incorporation of C and T, respectively, opposite the lesion and subsequent SMUG1-initiated repair of fU.
Collapse
Affiliation(s)
- Ingeborg Knaevelsrud
- Faculty of Science and Technology, Department of Mathematics and Natural Sciences, University of Stavanger, Stavanger, Norway
| | | | | | | | | | | |
Collapse
|
6
|
Wang F, Li F, Ganguly M, Marky LA, Gold B, Egli M, Stone MP. A bridging water anchors the tethered 5-(3-aminopropyl)-2'-deoxyuridine amine in the DNA major groove proximate to the N+2 C.G base pair: implications for formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards. Biochemistry 2008; 47:7147-57. [PMID: 18549246 DOI: 10.1021/bi800375m] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Site-specific insertion of 5-(3-aminopropyl)-2'-deoxyuridine (Z3dU) and 7-deaza-dG into the Dickerson-Drew dodecamers 5'-d(C (1)G (2)C (3)G (4)A (5)A (6)T (7)T (8)C (9) Z (10)C (11)G (12))-3'.5'-d(C (13)G (14)C (15)G (16)A (17)A (18)T (19)T (20)C (21) Z (22)C (23)G (24))-3' (named DDD (Z10)) and 5'-d(C (1)G (2)C (3)G (4)A (5)A (6)T (7) X (8)C (9) Z (10)C (11)G (12))-3'.5'-d(C (13)G (14)C (15)G (16)A (17)A (18)T (19) X (20)C (21) Z (22)C (23)G (24))-3' (named DDD (2+Z10)) (X = Z3dU; Z = 7-deaza-dG) suggests a mechanism underlying the formation of interstrand N+2 DNA cross-links by nitrogen mustards, e.g., melphalan and mechlorethamine. Analysis of the DDD (2+Z10) duplex reveals that the tethered cations at base pairs A (5).X (20) and X (8).A (17) extend within the major groove in the 3'-direction, toward conserved Mg (2+) binding sites located adjacent to N+2 base pairs C (3).Z (22) and Z (10).C (15). Bridging waters located between the tethered amines and either Z (10) or Z (22) O (6) stabilize the tethered cations and allow interactions with the N + 2 base pairs without DNA bending. Incorporation of 7-deaza-dG into the DDD (2+Z10) duplex weakens but does not eliminate electrostatic interactions between tethered amines and Z (10) O (6) and Z (22) O (6). The results suggest a mechanism by which tethered N7-dG aziridinium ions, the active species involved in formation of interstrand 5'-GNC-3' cross-links by nitrogen mustards, modify the electrostatics of the major groove and position the aziridinium ions proximate to the major groove edge of the N+2 C.G base pair, facilitating interstrand cross-linking.
Collapse
Affiliation(s)
- Feng Wang
- Department of Chemistry, Center in Molecular Toxicology, and Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, USA
| | | | | | | | | | | | | |
Collapse
|
7
|
Juan ECM, Kondo J, Kurihara T, Ito T, Ueno Y, Matsuda A, Takénaka A. Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules. Nucleic Acids Res 2007; 35:1969-77. [PMID: 17341465 PMCID: PMC1874594 DOI: 10.1093/nar/gkl821] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Oligonucleotides containing 5-(N-aminohexyl)carbamoyl-modified uracils have promising features for applications as antigene and antisense therapies. Relative to unmodified DNA, oligonucleotides containing 5-(N-aminohexyl)carbamoyl-2′-deoxyuridine (NU) or 5-(N-aminohexyl)carbamoyl-2′-O-methyluridine (NUm), respectively exhibit increased binding affinity for DNA and RNA, and enhanced nuclease resistance. To understand the structural implications of NU and NUm substitutions, we have determined the X-ray crystal structures of DNA:DNA duplexes containing either NU or NUm and of DNA:RNA hybrid duplexes containing NUm. The aminohexyl chains are fixed in the major groove through hydrogen bonds between the carbamoyl amino groups and the uracil O4 atoms. The terminal ammonium cations on these chains could interact with the phosphate oxygen anions of the residues in the target strands. These interactions partly account for the increased target binding affinity and nuclease resistance. In contrast to NU, NUm decreases DNA binding affinity. This could be explained by the drastic changes in sugar puckering and in the minor groove widths and hydration structures seen in the NUm containing DNA:DNA duplex structure. The conformation of NUm, however, is compatible with the preferred conformation in DNA:RNA hybrid duplexes. Furthermore, the ability of NUm to render the duplexes with altered minor grooves may increase nuclease resistance and elicit RNase H activity.
Collapse
Affiliation(s)
| | | | | | - Takanori Ito
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan, Graduate School of Pharmaceutical Sciences, Hokkaido Universitym, Sapporo 060-0812, Japan and Faculty of Engineering, Gifu University, Gifu 501-1193, Japan
| | - Yoshihito Ueno
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan, Graduate School of Pharmaceutical Sciences, Hokkaido Universitym, Sapporo 060-0812, Japan and Faculty of Engineering, Gifu University, Gifu 501-1193, Japan
| | - Akira Matsuda
- Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama 226-8501, Japan, Graduate School of Pharmaceutical Sciences, Hokkaido Universitym, Sapporo 060-0812, Japan and Faculty of Engineering, Gifu University, Gifu 501-1193, Japan
| | - Akio Takénaka
- *To whom correspondence should be addressed. +81 45 924 5709+81 45 924 5748
| |
Collapse
|
8
|
Abstract
Fifty years after the publication of the DNA double helix model by Watson and Crick, new nucleic acid structures keep emerging at an ever-increasing rate. The past three years have brought a flurry of new oligonucleotide structures, including those of a Hoogsteen-paired DNA duplex, Holliday junctions, DNA-drug complexes, quadruplexes, a host of RNA motifs and various nucleic acid analogues. Major advances were also made in terms of the structure and function of catalytic RNAs. These range from improved models of the phosphodiester cleavage reactions catalyzed by the hairpin and hepatitis delta virus ribozymes to the visualization of a complete active site of a group I self-splicing intron with bound 5'- and 3'-exons. These triumphs are complemented by a refined understanding of cation-nucleic-acid interactions and new routes to the generation of derivatives for phasing of DNA and RNA structures.
Collapse
Affiliation(s)
- Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA.
| |
Collapse
|
9
|
Kittaka A, Sugiyama T, Horii C, Tanaka H, Miyasaka T, T. Nakamura K, Kuroda R. Schiff Base Formation between 5-Formyl-2’-deoxyuridine and Lysine ε-Amino Group at Monomer and Oligomer Levels. HETEROCYCLES 2004. [DOI: 10.3987/com-04-s(p)38] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|