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Belostotskii AM. Nanosecond-Scale Isomerization of the 4'-Carboxonium Cation Oxidatively Produced in Pyrimidine Units of DNA. J Org Chem 2018; 83:11604-11613. [PMID: 30153025 DOI: 10.1021/acs.joc.8b01580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The long-standing puzzle of the chemistry producing the Stubbe-Kozarich abasic site, which is the minor product in the oxidation of 2'-deoxycytidine units of DNA by Fe(II)-bleomycin, has been computationally solved in this study. Scrupulous DFT-based calculations that included extensive screening of the potential energy surface of model-solvated nucleotides and the elucidation of the chemical structure of the located nucleotide cations via natural bond orbital analysis demonstrated that the 2'-deoxycytidine unit bearing the 2'-deoxyribose ring 2e-oxidized at the 4'-position undergoes carboxonium ion- iminium ion (C═O+-C → C═N+) isomerization. This 1,2-elimination of the carbonyl group 4'-C═O from the carboxonium cation fragment is associated with minimal spatial reorganization of the molecule and appears to be an ultrafast reaction. The calculated barrier Δ G0# of 2.7 kcal mol-1 for this isomerization is lower than that reported for the addition of water to oxocarbenium ions. Thus, this unusual nucleotide transformation is the key chemical reaction that yields the Stubbe-Kozarich product. Such a product cannot be formed for purine nucleotide units in DNA. The isomerization of 4'-dehydro-2'-deoxyribose-4'-carboxonium cations formed in these DNA units is slower because it destroys the purine aromaticity, and the cations are intercepted by water molecules before they isomerize.
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Dizdaroglu M. Clemens von Sonntag and the early history of radiation-induced sugar damage in DNA. Int J Radiat Biol 2014; 90:446-58. [DOI: 10.3109/09553002.2014.894652] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Belostotskii AM, Genizi E, Hassner A. Essential reactive intermediates in nucleoside chemistry: cyclonucleoside cations. Org Biomol Chem 2012; 10:6624-8. [PMID: 22805739 DOI: 10.1039/c2ob25868d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DFT-based modeling as well as experimental examination of model keto nucleosides have revealed that high susceptibility of these compounds to acids is due to formation of intermediate cyclonucleoside cations of low energy. Theoretically established chemical structures of these previously overlooked intermediates explain the reaction courses for a cluster of nucleoside reactions.
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Abstract
Endogenous and exogenous sources cause free radical-induced DNA damage in living organisms by a variety of mechanisms. The highly reactive hydroxyl radical reacts with the heterocyclic DNA bases and the sugar moiety near or at diffusion-controlled rates. Hydrated electron and H atom also add to the heterocyclic bases. These reactions lead to adduct radicals, further reactions of which yield numerous products. These include DNA base and sugar products, single- and double-strand breaks, 8,5'-cyclopurine-2'-deoxynucleosides, tandem lesions, clustered sites and DNA-protein cross-links. Reaction conditions and the presence or absence of oxygen profoundly affect the types and yields of the products. There is mounting evidence for an important role of free radical-induced DNA damage in the etiology of numerous diseases including cancer. Further understanding of mechanisms of free radical-induced DNA damage, and cellular repair and biological consequences of DNA damage products will be of outmost importance for disease prevention and treatment.
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Affiliation(s)
- Miral Dizdaroglu
- Biochemical Science Division, National Institute of Standards and Technology, Gaithersburg, MD 20899, USA.
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Boussicault F, Kaloudis P, Caminal C, Mulazzani QG, Chatgilialoglu C. The Fate of C5′ Radicals of Purine Nucleosides under Oxidative Conditions. J Am Chem Soc 2008; 130:8377-85. [DOI: 10.1021/ja800763j] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Li MJ, Liu L, Wei K, Fu Y, Guo QX. Significant effects of phosphorylation on relative stabilities of DNA and RNA sugar radicals: remarkably high susceptibility of h-2' abstraction in RNA. J Phys Chem B 2007; 110:13582-9. [PMID: 16821885 DOI: 10.1021/jp060331j] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The roles of nucleic acid radicals in DNA and RNA damage cannot be properly understood in the absence of knowledge of the C-H bond strengths depicting the energy cost to generate each of these radicals. However, previous theoretical studies on the relative energies of different nucleic acid radicals are not fully convincing mainly because of the use of oversimplified model compounds. In the present study we chose nucleoside 3',5'-bisphosphates as model compounds for DNA and RNA, in which the effects of both the nucleobase and phosphorylation were taken into consideration. Using the newly developed ONIOM-G3B3 methods, we calculated the gas-phase bond dissociation enthalpies and solution-phase bond dissociation free energies of all the carbohydrate C-H bonds in the model compounds. It was found that the monoanionic phosphate group (OPO3H-) was a better radical stabilization group than the OH group by 1.3 kcal/mol, whereas the neutral phosphate group (OPO3H2) was a significantly worse radical stabilization group than OH by 4.4 kcal/mol. Due to these reasons, the relative thermodynamic susceptibility of H-abstraction from deoxyribonucleotides and ribonucleotides varied considerably depending on the phosphorylation state and the charge carried by the phosphate groups. Strikingly, the bond dissociation free energy of C2'-H in ribonucleotides was dramatically lower than that of all the other C-H bonds by 5-6 kcal/mol regardless of the phosphorylation state and the charge carried by the phosphate group. This explained the previous experimental finding that radiation damage of RNA occurs mainly via H-abstraction at H-2'. A model study suggested that the strength of the hydrogen bonding interaction between the 2'-OH and 3-phosphate groups should dramatically increase from ribonucleoside 3',5'-bisphosphate to its C2' radical. The strengthened hydrogen bonding stabilized the C2' radical, rendering the C2'-H bond of RNA extraordinarily vulnerable to H-abstraction.
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Affiliation(s)
- Min-Jie Li
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
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Hou R, Gu J, Xie Y, Yi X, Schaefer Iii HF. The 2'-deoxyadenosine-5'-phosphate anion, the analogous radical, and the different hydrogen-abstracted radical anions: molecular structures and effects on DNA damage. J Phys Chem B 2007; 109:22053-60. [PMID: 16853863 DOI: 10.1021/jp0524375] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The 2'-deoxyadenosine-5'-phosphate (5'-dAMP) anion and its related radicals have been studied by reliably calibrated theoretical approaches. This study reveals important physical characteristics of 5'-dAMP radical related processes. One-electron oxidation of the 5'-dAMP anion is found on both the phosphoryl group and the adenine base with electron detachment energies close to that of phosphate. Partial removal of electron density from the adenine fragment leads to an extended pi system which includes the amine group of the adenine. Although the radical-centered carbon increases the extent of bonding with its adjacent atoms, it usually weakens the chemical bonds between the atoms at the alpha- and beta-positions. This tendency should be important in predicting the reactivity of the sugar-based radicals. The overall stability sequence of the H-abstracted 5'-dAMP anionic radicals is consistent with the analogous results for the H-abstracted neutral radicals of the adenosine nucleoside: aliphatic radicals > aromatic radicals. The negatively charged phosphoryl group attached to atom C(5)' of the ribose does not change this energetic sequence. All the H-abstraction produced 5'-dAMP radical anions are distonic radical anions. Studies have shown that the charge-radical-separating feature of the distonic radical anions is biologically relevant. This result should be important in understanding the reactive properties of these H-abstraction-produced anion radicals.
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Affiliation(s)
- Ruobing Hou
- Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602-2525, USA
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Li MJ, Liu L, Fu Y, Guo QX. Development of an ONIOM-G3B3 method to accurately predict C-H and N-H bond dissociation enthalpies of ribonucleosides and deoxyribonucleosides. J Phys Chem B 2007; 109:13818-26. [PMID: 16852730 DOI: 10.1021/jp0508204] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The roles of ribonucleoside and deoxyribonucleoside radicals in DNA and RNA damage cannot be properly understood in the absence of knowledge of the C-H and N-H bond dissociation enthalpies (BDEs) depicting the energy cost to generate each of these radicals. However, because the nucleoside radicals tend to be extremely short-lived and it is very difficult to separate and identify different nucleoside radicals, experimental BDEs for nucleosides have remained elusive. Herein, we developed an ONIOM-G3B3 method in order to reliably predict the BDEs of nucleosides and we carefully benchmarked this new method against over 60 experimental BDEs of diverse sizable molecules. It was found that the accuracy of the ONIOM-G3B3 method was about 1.4 kcal/mol for BDE calculations. Using the ONIOM-G3B3 method, a full scale of C-H and N-H BDEs were obtained for the first time for ribonucleosides and deoxyribonucleosides with an estimated error bar of +/-1.4 kcal/mol. Discussions were then made about the interesting connections between these BDE values and previously reported experimental observations concerning radical-mediated DNA and RNA lesions. The significance of the work is twofold: (i) Nucleosides represent one of the most important groups of compounds in science. A full scale of reliable bond dissociation enthalpies for nucleosides is of fundamental importance. (ii) This work demonstrates the feasibility to accurately predict the bond strength of various sizable molecules ranging from nanosize molecular devices to biologically significant compounds.
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Affiliation(s)
- Min-Jie Li
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
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Melikyan GG, Villena F, Florut A, Sepanian S, Sarkissian H, Rowe A, Toure P, Mehta D, Christian N, Myer S, Miller D, Scanlon S, Porazik M, Gruselle M. Tetrahydrofuran-Mediated Stereoselective Radical C−C Bond Formation in Dicobalthexacarbonyl−Propargyl Complexes. Organometallics 2006. [DOI: 10.1021/om060579v] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gagik G. Melikyan
- Department of Chemistry and Biochemistry, California State University−Northridge, Northridge, California 91330-8262
| | - Ferdinand Villena
- Department of Chemistry and Biochemistry, California State University−Northridge, Northridge, California 91330-8262
| | - Arthur Florut
- Department of Chemistry and Biochemistry, California State University−Northridge, Northridge, California 91330-8262
| | - Steve Sepanian
- Department of Chemistry and Biochemistry, California State University−Northridge, Northridge, California 91330-8262
| | - Hagop Sarkissian
- Department of Chemistry and Biochemistry, California State University−Northridge, Northridge, California 91330-8262
| | - Aaron Rowe
- Department of Chemistry and Biochemistry, California State University−Northridge, Northridge, California 91330-8262
| | - Pogban Toure
- Department of Chemistry and Biochemistry, California State University−Northridge, Northridge, California 91330-8262
| | - Dutt Mehta
- Department of Chemistry and Biochemistry, California State University−Northridge, Northridge, California 91330-8262
| | - Nolan Christian
- Department of Chemistry and Biochemistry, California State University−Northridge, Northridge, California 91330-8262
| | - Steven Myer
- Department of Chemistry and Biochemistry, California State University−Northridge, Northridge, California 91330-8262
| | - David Miller
- Department of Chemistry and Biochemistry, California State University−Northridge, Northridge, California 91330-8262
| | - Stephanie Scanlon
- Department of Chemistry and Biochemistry, California State University−Northridge, Northridge, California 91330-8262
| | - Maria Porazik
- Department of Chemistry and Biochemistry, California State University−Northridge, Northridge, California 91330-8262
| | - Michel Gruselle
- Laboratoire de Chimie Inorganique et Materiaux Moleculaires UMR CNRS 7071, Universite Pierre et Marie Curie, Paris F, 75252 Cedex 05, France
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Evangelista FA, Schaefer HF. Structures and Energetics of Adenosine Radicals: (2‘-dAdo − H)•. J Phys Chem A 2004. [DOI: 10.1021/jp040361r] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Francesco A. Evangelista
- Scuola Normale Superiore di Pisa, 56126 Pisa, Italy, and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602-2525
| | - Henry F. Schaefer
- Scuola Normale Superiore di Pisa, 56126 Pisa, Italy, and Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602-2525
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The properties of DNA C4′-centered sugar radicals: the importance of the computational model. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.03.063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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12
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Nauser T, Schöneich C. Thiyl radical reaction with thymine: absolute rate constant for hydrogen abstraction and comparison to benzylic C-H bonds. Chem Res Toxicol 2003; 16:1056-61. [PMID: 12971792 DOI: 10.1021/tx034094c] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Free radical damage of DNA is a well-known process affecting biological tissue under conditions of oxidative stress. Thiols can repair DNA-derived radicals. However, the product thiyl radicals may also cause biological damage. To obtain quantitative information on the potential reactivity with DNA components, we measured the rate constant for hydrogen abstraction by cysteamine thiyl radicals from thymine C5-CH(3), k = (1.2 +/- 0.8) x 10(4) M(-1) s(-1), and thymidine-5'-monophosphate, k = (0.9 +/- 0.6) x 10(4) M(-1) s(-1). Hence, the hydrogen abstraction from C5-CH(3) occurs with rate constants similar to the hydrogen abstraction from the carbohydrate moieties. Especially at low oxygen concentration such as that found in skeletal muscle, such hydrogen abstraction processes by thiyl radicals may well compete against other dioxygen-dependent reactions. The rate constants for hydrogen abstraction at thymine C5-CH(3) were compared to those with benzylic substrates, toluenesulfonic acid, and benzyl alcohol.
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Affiliation(s)
- Thomas Nauser
- Department of Pharmaceutical Chemistry, University of Kansas, 2095 Constant Avenue, Lawrence, Kansas 66047, USA
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