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Chaturvedi R, Long EC. Mechanistic studies of dinucleotide and oligonucleotide model cyclobutane pyrimidine dimer (CPD) DNA lesions under alkaline conditions. Bioorg Med Chem 2021; 54:116499. [PMID: 34922308 DOI: 10.1016/j.bmc.2021.116499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/22/2021] [Accepted: 10/22/2021] [Indexed: 11/17/2022]
Abstract
Cyclobutane pyrimidine dimers (CPDs) are the most abundant mutagenic DNA lesions formed in mammalian cells upon exposure to UV-B radiation (280-315 nm) in sunlight. These lesions are thought to be chemically stable and to withstand high concentrations of acids and bases.While earlier investigations of DNA lesions containing saturated pyrimidines have shown that the C4 carbonyl is a potential target of nucleophilic attack, similar reactions with thymine nucleobase model CPDs clearly showed that the cis-syn CPD (major isomer) is stable in the presence of a high concentration of alkali at room temperature. Here is described the alkaline reactivity of these lesions when contained within a dinucleotide CPD model system. Results using cis-syn CPD formed from dinucleotide 5'-TpT-3' combined with [18O]-labelling indicated that CPD undergoes a water addition at the C4=O groups of these now saturated rings. The intermediate formed, however, completely reverts to the starting lesion. Along with confirming the target of water addition within CPD lesions, it was also determined that the two C4 carbonyls present on adjacent saturated pyrimidine rings of the photolesion undergo water exchange at different rates (3' > 5'). Moreover, the difference in reactivity exhibited by these two positions is not limited to a dinucleotide and was observed also in oligonucleotides. Overall, a full understanding of the chemistry of CPD lesions is crucial to our knowledge of naturally-occuring DNA modifications and may lead to further insight into their detection, modification, and biochemical recognition & repair.
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Affiliation(s)
- Ritu Chaturvedi
- Department of Chemistry & Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N. Blackford St., Indianapolis, IN 46202, United States.
| | - Eric C Long
- Department of Chemistry & Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 N. Blackford St., Indianapolis, IN 46202, United States.
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2
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Westwood MN, Ljunggren KD, Boyd B, Becker J, Dwyer TJ, Meints GA. Single-Base Lesions and Mismatches Alter the Backbone Conformational Dynamics in DNA. Biochemistry 2021; 60:873-885. [PMID: 33689312 DOI: 10.1021/acs.biochem.0c00784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
DNA damage has been implicated in numerous human diseases, particularly cancer, and the aging process. Single-base lesions and mismatches in DNA can be cytotoxic or mutagenic and are recognized by a DNA glycosylase during the process of base excision repair. Altered local dynamics and conformational properties in damaged DNAs have previously been suggested to assist in recognition and specificity. Herein, we use solution nuclear magnetic resonance to quantify changes in BI-BII backbone conformational dynamics due to the presence of single-base lesions in DNA, including uracil, dihydrouracil, 1,N6-ethenoadenine, and T:G mismatches. Stepwise changes to the %BII and ΔG of the BI-BII dynamic equilibrium compared to those of unmodified sequences were observed. Additionally, the equilibrium skews toward endothermicity for the phosphates nearest the lesion/mismatched base pair. Finally, the phosphates with the greatest alterations correlate with those most relevant to the repair of enzyme binding. All of these results suggest local conformational rearrangement of the DNA backbone may play a role in lesion recognition by repair enzymes.
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Affiliation(s)
- M N Westwood
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
| | - K D Ljunggren
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
| | - Benjamin Boyd
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
| | - Jaclyn Becker
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
| | - Tammy J Dwyer
- Department of Chemistry and Biochemistry, University of San Diego, San Diego, California 92110, United States
| | - Gary A Meints
- Department of Chemistry, Missouri State University, 901 South National Avenue, Springfield, Missouri 65897, United States
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Sarre A, Stelter M, Rollo F, De Bonis S, Seck A, Hognon C, Ravanat JL, Monari A, Dehez F, Moe E, Timmins J. The three Endonuclease III variants of Deinococcus radiodurans possess distinct and complementary DNA repair activities. DNA Repair (Amst) 2019; 78:45-59. [DOI: 10.1016/j.dnarep.2019.03.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 11/26/2022]
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4
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Jian Y, Lin G, Chomicz L, Li L. Reactivity of Damaged Pyrimidines: Formation of a Schiff Base Intermediate at the Glycosidic Bond of Saturated Dihydrouridine. J Am Chem Soc 2015; 137:3318-29. [DOI: 10.1021/ja512435j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yajun Jian
- Department
of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, United States
| | - Gengjie Lin
- Department
of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, United States
| | - Lidia Chomicz
- Department
of Chemistry, University of Gdansk, 80-308 Gdansk, Poland
| | - Lei Li
- Department
of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI), 402 North Blackford Street, Indianapolis, Indiana, 46202, United States
- Department
of Biochemistry and Molecular Biology and Department of Dermatology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, Indiana 46202, United States
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Lin G, Jian Y, Ouyang H, Li L. An unexpected deamination reaction after hydrolysis of the pyrimidine (6-4) pyrimidone photoproduct. Org Lett 2014; 16:5076-9. [PMID: 25250878 PMCID: PMC4184442 DOI: 10.1021/ol502433h] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Pyrimidine (6-4) pyrimidone photoproduct (6-4PP), a common DNA photolesion formed under solar irradiation, was indicated to hydrolyze under strong basic conditions, breaking the N3-C4 bond at the 5'-thymine. The reanalysis of this reaction revealed that the resulting water adduct may not be stable as previously proposed; it readily undergoes an esterification reaction induced by the 5-OH group at 6-4PP to form a five-membered ring, eliminating a molecule of ammonia.
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Affiliation(s)
- Gengjie Lin
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI) , 402 North Blackford Street, Indianapolis, Indiana 46202, United States
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6
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Lin G, Jian Y, Dria KJ, Long EC, Li L. Reactivity of damaged pyrimidines: DNA cleavage via hemiaminal formation at the C4 positions of the saturated thymine of spore photoproduct and dihydrouridine. J Am Chem Soc 2014; 136:12938-46. [PMID: 25127075 PMCID: PMC4183628 DOI: 10.1021/ja505407p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Described
here are mechanistic details of the chemical reactivities
of two modified/saturated pyrimidine residues that represent naturally
occurring forms of DNA damage: 5-thyminyl-5,6-dihydrothymine, commonly
referred to as the “spore photoproduct” (SP), and 5,6-dihydro-2′-deoxyuridine
(dHdU), formed via ionizing radiation damage to cytosine under anoxic
conditions and also serving as a general model of saturated pyrimidine
residues. It is shown that due to the loss of the pyrimidine C5–C6
double bond and consequent loss of ring aromaticity, the C4 position
of both these saturated pyrimidines is prone to the formation of a
hemiaminal intermediate via water addition. Water addition is facilitated
by basic conditions; however, it also occurs at physiological pH at
a slower rate. The hemiaminal species so-formed subsequently converts
to a ring-opened hydrolysis product through cleavage of the pyrimidine
N3–C4 bond. Further decomposition of this ring-opened product
above physiological pH leads to DNA strand break formation. Taken
together, these results suggest that once the aromaticity of a pyrimidine
residue is lost, the C4 position becomes a “hot spot”
for the formation of a tetrahedral intermediate, the decay of which
triggers a cascade of elimination reactions that can under certain
conditions convert a simple nucleobase modification into a DNA strand
break.
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Affiliation(s)
- Gengjie Lin
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis (IUPUI) , 402 North Blackford Street, Indianapolis, Indiana 46202, United States
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Tallman KA, Greenberg MM. Oxygen-dependent DNA damage amplification involving 5,6-dihydrothymidin-5-yl in a structurally minimal system. J Am Chem Soc 2001; 123:5181-7. [PMID: 11457379 DOI: 10.1021/ja010180s] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
5,6-Dihydrothymidin-5-yl (1) was independently generated in a dinucleotide from a phenyl selenide precursor (4). Under free radical chain propagation conditions, the products resulting from hydrogen atom donation and radical-pair reaction are the major observed products in the absence of O(2). The stereoselectivity of the trapping process is dependent on the structure of the hydrogen atom donor. No evidence for internucleotidyl hydrogen atom abstraction by 1 was detected. The tandem lesion (17) resulting from hydrogen atom abstraction from the C1' position of the adjacent 2'-deoxyuridine by the peroxyl radical derived from 1 (3) is observed under aerobic conditions. The structure of this product is confirmed by independent synthesis and its transformation into a second independently synthesized product (24). Internucleotidyl hydrogen atom abstraction is effected selectively by the 5S-diastereomer of the peroxyl radical. The formation of dinucleotide 17 provides further support for the novel O(2)-dependent DNA damage amplification mechanism involving 1 reported previously (Greenberg, M. M.; et al. J. Am. Chem. Soc. 1997, 119, 1828).
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Affiliation(s)
- K A Tallman
- Contribution from the Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523, USA
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