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Manderville RA, Wetmore SD. Understanding the Mutagenicity of O-Linked and C-Linked Guanine DNA Adducts: A Combined Experimental and Computational Approach. Chem Res Toxicol 2016; 30:177-188. [DOI: 10.1021/acs.chemrestox.6b00323] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Richard A. Manderville
- Departments
of Chemistry and Toxicology, University of Guelph, Guelph, ON, Canada N1G 2W1
| | - Stacey D. Wetmore
- Department of Chemistry & Biochemistry, University of Lethbridge, Lethbridge, AB, Canada T1K 3M4
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Manderville RA, Wetmore SD. C-Linked 8-aryl guanine nucleobase adducts: biological outcomes and utility as fluorescent probes. Chem Sci 2016; 7:3482-3493. [PMID: 29997840 PMCID: PMC6007177 DOI: 10.1039/c6sc00053c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 02/23/2016] [Indexed: 12/18/2022] Open
Abstract
Aryl radical species derived from enzymatic transformations of aromatic mutagens preferentially react at the 8-site of the guanine (G) nucleobase to afford carbon-linked 8arylG adducts. The resulting lesions possess altered biophysical and genetic coding properties compared to the precursor G nucleoside in B-form DNA. Unlike other adducts, these lesions also possess useful fluorescent properties, since direct attachment of the 8aryl ring extends the purine π-system to afford G mimics with red-shifted excitation maxima and emission that can be sensitive to the microenvironment of the 8arylG base within nucleic acid structures. In B-form DNA, 8arylG adducts are disruptive to duplex formation because they prefer to adopt the syn-conformation about the bond connecting the nucleobase to the deoxyribose backbone, which perturbs Watson-Crick (WC) H-bonding with the opposing cytosine (C). Thus, in a B-form duplex, the emissive properties of 8arylG adducts can be employed as a tool to provide insight into adduct conformation, which can be related to their biological outcomes. However, since Gs preferentially adopt the syn-conformation in left-handed Z-DNA and antiparallel G-quadruplex (GQ) structures, 8arylG lesions can be inserted into syn-G positions without disrupting H-bonding interactions. In fact, 8arylG lesions can serve as ideal fluorescent probes in an antiparallel GQ because their emission is sensitive to GQ folding. This perspective outlines recent developments in the biological implications of 8arylG formation together with their utility as fluorescent G analogs for use in DNA-based diagnostic systems.
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Affiliation(s)
- Richard A Manderville
- Department of Chemistry & Toxicology , University of Guelph , Guelph , ON , Canada N1G 2W1 .
| | - Stacey D Wetmore
- Department of Chemistry & Biochemistry , University of Lethbridge , Lethbridge , AB , Canada T1K 3M4 .
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Rankin KM, Sproviero M, Rankin K, Sharma P, Wetmore SD, Manderville RA. C8-heteroaryl-2'-deoxyguanosine adducts as conformational fluorescent probes in the NarI recognition sequence. J Org Chem 2012; 77:10498-508. [PMID: 23171213 DOI: 10.1021/jo302164c] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The optical, redox, and electronic properties of C(8)-heteroaryl-2'-deoxyguanosine (dG) adducts with C(8)-substituents consisting of furyl ((Fur)dG), pyrrolyl ((Pyr)dG), thienyl ((Th)dG), benzofuryl ((Bfur)dG), indolyl ((Ind)dG), and benzothienyl ((Bth)dG) are described. These adducts behave as fluorescent nucleobase probes with emission maxima from 379 to 419 nm and fluorescence quantum yields (Φ(fl)) in the 0.1-0.8 range in water at neutral pH. The probes exhibit quenched fluorescence with increased solvent viscosity and decreased solvent polarity. The (Fur)dG, (Bfur)dG, (Ind)dG, and (Bth)dG derivatives were incorporated into the G(3) position of the 12-mer oligonucleotide 5'-CTCG(1)G(2)CG(3)CCATC-3' that contains the recognition sequence of the NarI Type II restriction endonuclease. This sequence is widely used to study the biological activity (mutagenicity) of C(8)-arylamine-dG adducts with adduct conformation (anti vs syn) playing a critical role in the biological outcome. The modified NarI(X = (Fur)G, (Ind)G, (Bfur)G, or (Bth)G) oligonucleotides were hybridized to the complementary strand containing either C (NarI'(C)) or G (NarI'(G)) opposite the probe. The duplex structures were characterized by UV melting temperature analysis, fluorescence spectroscopy, collisional fluorescence quenching studies, and circular dichroism (CD). The emission of the probes showed sensitivity to the opposing base in the duplex, and suggested the utility of fluorescence spectroscopy to monitor probe conformation.
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Affiliation(s)
- Katherine M Rankin
- Department of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
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C8-linked bulky guanosine DNA adducts: experimental and computational insights into adduct conformational preferences and resulting mutagenicity. Future Med Chem 2012; 4:1981-2007. [PMID: 23088278 DOI: 10.4155/fmc.12.138] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Bulky DNA adducts are formed through the covalent attachment of aryl groups to the DNA nucleobases. Many of these adducts are known to possess conformational heterogeneity, which is responsible for the variety of mutagenic outcomes associated with these lesions. The present contribution reviews several conformational and mutagenic themes that are prevalent among the DNA adducts formed at the C8-site of the guanine nucleobase. The most important conclusions obtained (to date) from experiments are summarized including the anti/syn conformational preference of the adducts, their potential to inflict DNA mutations and mismatch stabilization, and their interactions with DNA polymerases and repair enzymes. Additionally, the unique role that computer calculations can play in understanding the structural properties of these adducts are highlighted.
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Witham AA, Beach DG, Gabryelski W, Manderville RA. Hydroxyl Radical-Induced Oxidation of a Phenolic C-Linked 2′-Deoxyguanosine Adduct Yields a Reactive Catechol. Chem Res Toxicol 2012; 25:315-25. [DOI: 10.1021/tx200365r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Aaron A. Witham
- Departments
of Chemistry and Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Daniel G. Beach
- Departments
of Chemistry and Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Wojciech Gabryelski
- Departments
of Chemistry and Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
| | - Richard A. Manderville
- Departments
of Chemistry and Toxicology, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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Omumi A, Millen AL, Wetmore SD, Manderville RA. Fluorescent properties and conformational preferences of C-linked phenolic-DNA adducts. Chem Res Toxicol 2011; 24:1694-709. [PMID: 21905681 DOI: 10.1021/tx200247f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Phenolic toxins and mutagenic diazoquinones generate C-linked adducts at the C8 site of 2'-deoxyguanosine (dG) through the intermediacy of radical species. We have previously reported the site-specific incorporation of these adducts into oligonucleotides using a postsynthetic palladium-catalyzed cross-coupling strategy [Omumi (2011 ) J. Am. Chem. Soc. 133 , 42 - 50 ]. We report here the structural impact of these lesions within two decanucleotide sequences containing either 5'- and 3'-flanking pyrimidines or purines. In the complementary strands, the base opposite (N) the C-linked adduct was varied to determine the possibility of mismatch stabilization by the modified nucleobases. The resulting adducted duplex structures were characterized using UV thermal denaturation studies, circular dichroism, fluorescence spectroscopy, and molecular dynamics (MD) simulations. The experimental data showed the C-linked adducts to destabilize the duplex when base paired with its normal partner C but to increase duplex stability within a G:G mismatch. The stabilization within the G:G mismatch was sequence dependent, with flanking purine bases playing a key role in the stabilizing influence of the adduct. MD simulations showed no large structural changes to the B form double helix, regardless of the (anti/syn) adduct preference. Consideration of H-bonding and stacking interactions derived from the MD simulations together with the thermal melting data and changes in fluorescent emission of the adducts upon hybridization to the complementary strands implied that the C-linked phenolic adducts preferentially adopt the syn-conformation within both duplexes regardless of the opposite base N. Given that biological outcome in terms of mutagenicity appears to be strongly correlated to the conformational preference of the corresponding N-linked C8-dG adducts, the potential biological implications of phenolic C-linked adducts are discussed.
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Affiliation(s)
- Alireza Omumi
- Departments of Chemistry and Toxicology, University of Guelph, Guelph, Ontario, Canada
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Fleming AM, Kannan A, Muller JG, Liao Y, Burrows CJ. Copper/H2O2-Mediated Oxidation of 2′-Deoxyguanosine in the Presence of 2-Naphthol Leads to the Formation of Two Distinct Isomeric Adducts. J Org Chem 2011; 76:7953-63. [DOI: 10.1021/jo201423n] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Aaron M. Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Arunkumar Kannan
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - James G. Muller
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Yi Liao
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0850, United States
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Schlitt KM, Millen AL, Wetmore SD, Manderville RA. An indole-linked C8-deoxyguanosine nucleoside acts as a fluorescent reporter of Watson-Crick versus Hoogsteen base pairing. Org Biomol Chem 2011; 9:1565-71. [PMID: 21240404 DOI: 10.1039/c0ob00883d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Pyrrole- and indole-linked C(8)-deoxyguanosine nucleosides act as fluorescent reporters of H-bonding specificity. Their fluorescence is quenched upon Watson-Crick H-bonding to dC, while Hoogsteen H-bonding to G enhances emission intensity. The indole-linked probe is ∼ 10-fold brighter and shows promise as a fluorescent reporter of Hoogsteen base pairing.
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Affiliation(s)
- Katherine M Schlitt
- Department of Chemistry, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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Sagoo S, Beach DG, Manderville RA, Gabryelski W. Tautomerization in gas-phase ion chemistry of isomeric C-8 deoxyguanosine adducts from phenol-induced DNA damage. JOURNAL OF MASS SPECTROMETRY : JMS 2011; 46:41-9. [PMID: 21184435 DOI: 10.1002/jms.1869] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Collision-induced dissociation (CID) of 8-(4''-hydroxyphenyl)-2'-deoxyguanosine and 8-(2''-hydroxyphenyl)-2'-deoxyguanosine was investigated using sequential tandem mass spectrometry. These adducts represent biomarkers of DNA damage linked to phenolic radicals and were investigated to gain insight into the effects of chemical structure of a C-8 modification on fragmentation pathways of modified 2'-deoxyguanosine (dG). CID in MS(2) of the deprotonated molecules of both the isomers generated the same product ion having the same m/z values. CID in MS(3) of the product ion at m/z 242 and CID in MS(4) experiments carried out on the selected product ions at m/z 225 and m/z 218 afford distinct fragmentation patterns. The conformational properties of isomeric product ions from CID showed that the ortho-isomers possess the unique ability to tautomerize through an intramolecular proton transfer between the phenolic OH group and the imine nitrogen (N7). Tautomerization of ortho-isomers to their keto-tautomers led to differences in their system of conjugated double bonds compared with either their enol-tautomer or the para-isomer. The charge redistribution through the N-7 site on the imidazole ring is a critical step in guanosine adduct fragmentation which is disrupted by the formation of the keto-tautomer. For this reason, different reaction pathways are observed for 8-(4''-hydroxyphenyl)-2'-deoxyguanosine and 8-(2''-hydroxyphenyl)-2'-deoxyguanosine. We present herein the dissociation and the gas-phase ion-molecule reactions for highly conjugated ions involved in the CID ion chemistry of the investigated adducts. These will be useful for those using tandem mass spectrometry for structural elucidation of C-8 modified dG adducts. This study demonstrates that the modification at the C-8 site of dG has the potential to significantly alter the reactivity of adducts. We also show the ability of tandem mass spectrometry to completely differentiate between the isomeric dG adducts investigated.
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Affiliation(s)
- Sandeep Sagoo
- Department of Chemistry, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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Omumi A, Beach DG, Baker M, Gabryelski W, Manderville RA. Postsynthetic guanine arylation of DNA by Suzuki-Miyaura cross-coupling. J Am Chem Soc 2010; 133:42-50. [PMID: 21067186 DOI: 10.1021/ja106158b] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Direct radical addition reactions at the C(8)-site of 2'-deoxyguanosine (dG) can afford C(8)-Ar-dG adducts that are produced by carcinogenic arylhydrazines, polycyclic aromatic hydrocarbons, and certain phenolic toxins. Such modified nucleobases are also highly fluorescent for sensing applications and possess useful electron transfer properties. The site-specific synthesis of oligonucleotides containing the C(8)-Ar-G adduct can be problematic. These lesions are sensitive to acids and oxidants that are commonly used in solid-phase DNA synthesis and are too bulky to be accepted as substrates for enzymatic synthesis by DNA polymerases. Using the Suzuki-Miyaura cross-coupling reaction, we have synthesized a number of C(8)-Ar-G-modified oligonucleotides (dimers, trimers, decamers, and a 15-mer) using a range of arylboronic acids. Good to excellent yields were obtained, and the reaction is insensitive to the nature of the bases flanking the convertible 8-Br-G nucleobase, as both pyrimidines and purines are tolerated. The impact of the C(8)-Ar-G lesion was also characterized by electrospray ionization tandem mass spectrometry, UV melting temperature analysis, circular dichroism, and fluorescence spectroscopy. The C(8)-Ar-G-modified oligonucleotides are expected to be useful substrates for diagnostic applications and understanding the biological impact of the C(8)-Ar-G lesion.
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Affiliation(s)
- Alireza Omumi
- Department of Chemistry, University of Guelph, Guelph, Ontario, Canada N1G 2W1
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Millen AL, Churchill CDM, Manderville RA, Wetmore SD. Effect of Watson−Crick and Hoogsteen Base Pairing on the Conformational Stability of C8-Phenoxyl-2′-deoxyguanosine Adducts. J Phys Chem B 2010; 114:12995-3004. [DOI: 10.1021/jp105817p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Andrea L. Millen
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, and Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Cassandra D. M. Churchill
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, and Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Richard A. Manderville
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, and Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Stacey D. Wetmore
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, and Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
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Millen AL, Manderville RA, Wetmore SD. Conformational Flexibility of C8-Phenoxyl-2′-deoxyguanosine Nucleotide Adducts. J Phys Chem B 2010; 114:4373-82. [DOI: 10.1021/jp911993f] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Andrea L. Millen
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Richard A. Manderville
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
| | - Stacey D. Wetmore
- Department of Chemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada, T1K 3M4, Department of Chemistry, University of Guelph, Guelph, Ontario, Canada, N1G 2W1
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Structural and biological impact of radical addition reactions with DNA nucleobases. ADVANCES IN PHYSICAL ORGANIC CHEMISTRY 2009. [DOI: 10.1016/s0065-3160(08)00005-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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