1
|
Abdu K, Aiertza MK, Wilkinson OJ, Senthong P, Craggs TD, Povey AC, Margison GP, Williams DM. Synthesis of oligodeoxyribonucleotides containing a tricyclic thio analogue of O6-methylguanine and their recognition by MGMT and Atl1. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2020; 39:1108-1121. [PMID: 32449465 DOI: 10.1080/15257770.2020.1764971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Promutagenic O6-alkylguanine adducts in DNA are repaired in humans by O6-methylguanine-DNA-methyltransferase (MGMT) in an irreversible reaction. Here we describe the synthesis of a phosphoramidite that allows the preparation of oligodeoxyribonucleotides (ODNs) containing a novel tricyclic thio analogue of O6-methylguanine in which the third ring bridges the 6-thio group and C7 of a 7-deazapurine. These ODNs are very poor substrates for MGMT and poorly recognised by the alkyltransferase-like protein, Atl1. Examination of the active sites of both MGMT and Atl1 suggest large steric clashes hindering binding of the analogue. Such analogues, if mutagenic, are likely to be highly toxic.
Collapse
Affiliation(s)
- Kabir Abdu
- Department of Pure and Industrial Chemistry, Faculty of Physical Sciences, Bayero University, Kano, Nigeria
| | - Miren K Aiertza
- Centre for Chemical Biology, Department of Chemistry, Sheffield Institute for Nucleic Acids, University of Sheffield, Sheffield, UK
| | - Oliver J Wilkinson
- Centre for Chemical Biology, Department of Chemistry, Sheffield Institute for Nucleic Acids, University of Sheffield, Sheffield, UK
| | | | - Timothy D Craggs
- Centre for Chemical Biology, Department of Chemistry, Sheffield Institute for Nucleic Acids, University of Sheffield, Sheffield, UK
| | - Andrew C Povey
- Centre of Epidemiology, Faculty of Biology, Medicine and Health
| | | | - David M Williams
- Centre for Chemical Biology, Department of Chemistry, Sheffield Institute for Nucleic Acids, University of Sheffield, Sheffield, UK
| |
Collapse
|
2
|
O'Flaherty DK, Wilds CJ. Site-specific covalent capture of human O 6-alkylguanine-DNA-alkyltransferase using single-stranded intrastrand cross-linked DNA. Org Biomol Chem 2018; 15:189-196. [PMID: 27886318 DOI: 10.1039/c6ob02246d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
A methodology is reported to conjugate human O6-alkylguanine-DNA-alkyltransferase (hAGT) to the 3'-end of DNA in excellent yields with short reaction times by using intrastrand cross-linked (IaCL) DNA probes. This strategy exploited the substrate specificity of hAGT to generate the desired DNA-protein covalent complex. IaCL DNA linking two thymidine residues, or linking a thymidine residue to a 2'-deoxyguanosine residue (either in a 5'→3' or 3'→5' fashion), lacking a phosphodiester linkage at the cross-linked site, were prepared using a phosphoramidite strategy followed by solid-phase synthesis. All duplexes containing the model IaCL displayed a reduction in thermal stability relative to unmodified control duplexes. The O4-thymidine-alkylene-O4-thymidine and the (5'→3') O6-2'-deoxyguanosine-alkylene-O4-thymidine IaCL DNA adducts were not repaired by any of the AGTs evaluated (human AGT and Escherichia coli homologues, OGT and Ada-C). The (5'→3') O4-thymidine-alkylene-O6-2'-deoxyguanosine IaCL DNA containing a butylene or heptylene tethers were efficiently repaired by the human variant, whereas Ada-C was capable of modestly repairing the heptylene IaCL adduct. The IaCL strategy has expanded the toolbox for hAGT conjugation to DNA strands, without requiring the presence of a complementary DNA sequence. Finally, hAGT was functionalized with a fluorescently-labelled DNA sequence to demonstrate the applicability of this conjugation method.
Collapse
Affiliation(s)
- D K O'Flaherty
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B1R6, Canada.
| | - C J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B1R6, Canada.
| |
Collapse
|
3
|
Denisov AY, McManus FP, O'Flaherty DK, Noronha AM, Wilds CJ. Structural basis of interstrand cross-link repair by O6-alkylguanine DNA alkyltransferase. Org Biomol Chem 2017; 15:8361-8370. [DOI: 10.1039/c7ob02093g] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Conformation of the alkylene lesion may play a role in interstrand cross-link repair by O6-alkylguanine DNA alkyltransferases.
Collapse
Affiliation(s)
- Alexey Y. Denisov
- Department of Chemistry and Biochemistry
- Concordia University
- Montréal
- Canada
| | - Francis P. McManus
- Department of Chemistry and Biochemistry
- Concordia University
- Montréal
- Canada
| | | | - Anne M. Noronha
- Department of Chemistry and Biochemistry
- Concordia University
- Montréal
- Canada
| | | |
Collapse
|
4
|
Geigle SN, Wyss LA, Sturla SJ, Gillingham DG. Copper carbenes alkylate guanine chemoselectively through a substrate directed reaction. Chem Sci 2017; 8:499-506. [PMID: 28451197 PMCID: PMC5341205 DOI: 10.1039/c6sc03502g] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 09/02/2016] [Indexed: 12/19/2022] Open
Abstract
Cu(i) carbenes derived from α-diazocarbonyl compounds lead to selective alkylation of the O6 position in guanine (O6-G) in mono- and oligonucleotides. Only purine-type lactam oxygens are targeted - other types of amides or lactams are poorly reactive under conditions that give smooth alkylation of guanine. Mechanistic studies point to N7G as a directing group that controls selectivity. Given the importance of O6-G adducts in biology and biotechnology we expect that Cu(i)-catalyzed O6-G alkylation will be a broadly used synthetic tool. While the propensity for transition metals to increase redox damage is well-appreciated, our results suggest that transition metals might also increase the vulnerability of nucleic acids to alkylation damage.
Collapse
Affiliation(s)
- Stefanie N Geigle
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , CH-4056 , Basel , Switzerland .
| | - Laura A Wyss
- Department of Health Sciences and Technology , ETH Zurich , Schmelzbergstrasse 9 , CH-8092 Zurich , Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology , ETH Zurich , Schmelzbergstrasse 9 , CH-8092 Zurich , Switzerland
| | - Dennis G Gillingham
- Department of Chemistry , University of Basel , St. Johanns-Ring 19 , CH-4056 , Basel , Switzerland .
| |
Collapse
|
5
|
Räz MH, Dexter HR, Millington CL, van Loon B, Williams DM, Sturla SJ. Bypass of Mutagenic O(6)-Carboxymethylguanine DNA Adducts by Human Y- and B-Family Polymerases. Chem Res Toxicol 2016; 29:1493-503. [PMID: 27404553 DOI: 10.1021/acs.chemrestox.6b00168] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The generation of chemical alkylating agents from nitrosation of glycine and bile acid conjugates in the gastrointestinal tract is hypothesized to initiate carcinogenesis. O(6)-carboxymethylguanine (O(6)-CMG) is a product of DNA alkylation derived from nitrosated glycine. Although the tendency of the structurally related adduct O(6)-methylguanine to code for the misincoporation of TTP during DNA replication is well-established, the impact of the presence of the O(6)-CMG adduct in a DNA template on the efficiency and fidelity of translesion DNA synthesis (TLS) by human DNA polymerases (Pols) has hitherto not been described. Herein, we characterize the ability of the four human TLS Pols η, ι, κ, and ζ and the replicative Pol δ to bypass O(6)-CMG in a prevalent mutational hot-spot for colon cancer. The results indicate that Pol η replicates past O(6)-CMG, incorporating dCMP or dAMP, whereas Pol κ incorporates dCMP only, and Pol ι incorporates primarily dTMP. Additionally, the subsequent extension step was carried out with high efficiency by TLS Pols η, κ, and ζ, while Pol ι was unable to extend from a terminal mismatch. These results provide a first basis of O(6)-CMG-promoted base misincorporation by Y- and B-family polymerases potentially leading to mutational signatures associated with colon cancer.
Collapse
Affiliation(s)
- Michael H Räz
- Department of Health Sciences and Technology, ETH Zürich , Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| | - Hannah R Dexter
- Center for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield , Sheffield S3 7HF, United Kingdom
| | - Christopher L Millington
- Center for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield , Sheffield S3 7HF, United Kingdom
| | - Barbara van Loon
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU) , Erling Skjalgssons gate 1, 7491 Trondheim, Norway
| | - David M Williams
- Center for Chemical Biology, Department of Chemistry, Krebs Institute, University of Sheffield , Sheffield S3 7HF, United Kingdom
| | - Shana J Sturla
- Department of Health Sciences and Technology, ETH Zürich , Schmelzbergstrasse 9, 8092 Zürich, Switzerland
| |
Collapse
|
6
|
O'Flaherty DK, Patra A, Su Y, Guengerich FP, Egli M, Wilds CJ. Lesion Orientation of O4-Alkylthymidine Influences Replication by Human DNA Polymerase η. Chem Sci 2016; 7:4896-4904. [PMID: 27574558 PMCID: PMC5001687 DOI: 10.1039/c6sc00666c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Conformation of the α-carbon of O4-alkylthymidine was shown to exert an influence on human DNA polymerase η (hPol η) bypass. Crystal structures of hPol η·DNA·dNTP ternary complexes reveal a unique conformation adopted by O4-methylthymidine, where the nucleobase resides nestled at the active site ceiling where hydrogen-bonding with the incoming nucleotide is prevented.
DNA lesions that elude repair may undergo translesion synthesis catalyzed by Y-family DNA polymerases. O4-Alkylthymidines, persistent adducts that can result from carcinogenic agents, may be encountered by DNA polymerases. The influence of lesion orientation around the C4–O4 bond on processing by human DNA polymerase η (hPol η) was studied for oligonucleotides containing O4-methylthymidine (O4MedT), O4-ethylthymidine (O4EtdT), and analogs restricting the O4-methylene group in an anti-orientation. Primer extension assays revealed that the O4-alkyl orientation influences hPol η bypass. Crystal structures of hPol η·DNA·dNTP ternary complexes with O4MedT or O4EtdT in the template strand showed the nucleobase of the former lodged near the ceiling of the active site, with the syn-O4-methyl group engaged in extensive hydrophobic interactions. This unique arrangement for O4-methylthymidine with hPol η, inaccessible for the other analogs due to steric/conformational restriction, is consistent with differences observed for nucleotide incorporation and supports the concept that lesion conformation influences extension across DNA damage. Together, these results provide mechanistic insights on the mutagenicity of O4MedT and O4EtdT when acted upon by hPol η.
Collapse
Affiliation(s)
- D K O'Flaherty
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B1R6, Canada
| | - A Patra
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Y Su
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - F P Guengerich
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - M Egli
- Department of Biochemistry, Vanderbilt Institute of Chemical Biology, and Center for Structural Biology, School of Medicine, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - C J Wilds
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec H4B1R6, Canada
| |
Collapse
|
7
|
O'Flaherty DK, Wilds CJ. O
6
-Alkylguanine DNA Alkyltransferase Repair Activity Towards Intrastrand Cross-Linked DNA is Influenced by the Internucleotide Linkage. Chem Asian J 2016; 11:576-83. [PMID: 26692563 DOI: 10.1002/asia.201501253] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Indexed: 01/12/2023]
Affiliation(s)
- Derek K. O'Flaherty
- Department of Chemistry&Biochemistry; Concordia University; 7141 Sherbrooke St. West Montréal Québec (Canada
| | - Christopher J. Wilds
- Department of Chemistry&Biochemistry; Concordia University; 7141 Sherbrooke St. West Montréal Québec (Canada
| |
Collapse
|