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Huang SR, Tureček F. Noncanonical Isomers of Nucleoside Cation Radicals: An Ab Initio Study of the Dark Matter of DNA Ionization. J Phys Chem A 2022; 126:2480-2497. [PMID: 35439003 DOI: 10.1021/acs.jpca.2c00894] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cation radicals of DNA nucleosides, 2'-deoxyadenosine, 2'-deoxyguanosine, 2'-deoxycytidine, and 2'-deoxythymidine, can exist in standard canonical forms or as noncanonical isomers in which the charge is introduced by protonation of the nucleobase, whereas the radical predominantly resides in the deoxyribose moiety. Density functional theory as well as correlated ab initio calculations with coupled clusters (CCSD(T)) that were extrapolated to the complete basis set limit showed that noncanonical nucleoside ion isomers were thermodynamically more stable than their canonical forms in both the gas phase and as water-solvated ions. This indicated the possibility of exothermic conversion of canonical to noncanonical forms. The noncanonical isomers were calculated to have very low adiabatic ion-electron recombination energies (REad) for the lowest-energy isomers 2'-deoxy-(N-3H)adenos-1'-yl (4.74 eV), 2'-deoxy-(N-7H)guanos-1'-yl (4.66 eV), 2'-deoxy-(N-3H)cytid-1'-yl (5.12 eV), and 2'-deoxy-5-methylene-(O-2H)uridine (5.24 eV). These were substantially lower than the REad value calculated for the canonical 2'-deoxyadenosine, 2'-deoxy guanosine, 2'-deoxy cytidine, and 2'-deoxy thymidine cation radicals, which were 7.82, 7.46, 8.14, and 8.20 eV, respectively, for the lowest-energy ion conformers of each type. Charge and spin distributions in noncovalent cation-radical dA⊂dT and dG⊂dC nucleoside pairs and dAT, dCT, dTC, and dGC dinucleotides were analyzed to elucidate the electronic structure of the cation radicals. Born-Oppenheimer molecular dynamics trajectory calculations of the dinucleotides and nucleoside pairs indicated rapid exothermic proton transfer from noncanonical T+· to A in both dAT+· and dA⊂dT+·, leading to charge and radical separation. Noncanonical T+· in dCT+· and dTC+· initiated rapid proton transfer to cytosine, whereas the canonical dCT+· dinucleotide ion retained the cation radical structure without isomerization. No spontaneous proton transfer was found in dGC+· and dG⊂dC+· containing canonical neutral and noncanonical ionized deoxycytidine.
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Affiliation(s)
- Shu R Huang
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
| | - František Tureček
- Department of Chemistry, University of Washington, Bagley Hall, Box 351700, Seattle, Washington 98195-1700, United States
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The Two Faces of the Guanyl Radical: Molecular Context and Behavior. Molecules 2021; 26:molecules26123511. [PMID: 34207639 PMCID: PMC8227002 DOI: 10.3390/molecules26123511] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/29/2021] [Accepted: 06/01/2021] [Indexed: 12/16/2022] Open
Abstract
The guanyl radical or neutral guanine radical G(-H)• results from the loss of a hydrogen atom (H•) or an electron/proton (e–/H+) couple from the guanine structures (G). The guanyl radical exists in two tautomeric forms. As the modes of formation of the two tautomers, their relationship and reactivity at the nucleoside level are subjects of intense research and are discussed in a holistic manner, including time-resolved spectroscopies, product studies, and relevant theoretical calculations. Particular attention is given to the one-electron oxidation of the GC pair and the complex mechanism of the deprotonation vs. hydration step of GC•+ pair. The role of the two G(-H)• tautomers in single- and double-stranded oligonucleotides and the G-quadruplex, the supramolecular arrangement that attracts interest for its biological consequences, are considered. The importance of biomarkers of guanine DNA damage is also addressed.
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Cercola R, Uleanya KO, Dessent CEH. Electron detachment dynamics of the iodide-guanine cluster: does ionization occur from the iodide or from guanine? Mol Phys 2019. [DOI: 10.1080/00268976.2019.1679402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Affiliation(s)
- Kazuo Kobayashi
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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Liu Y, Korn JA, Dang A, Tureček F. Hydrogen-Rich Cation Radicals of DNA Dinucleotides: Generation and Structure Elucidation by UV-Vis Action Spectroscopy. J Phys Chem B 2018; 122:9665-9680. [PMID: 30269486 DOI: 10.1021/acs.jpcb.8b07925] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Hydrogen-rich DNA dinucleotide cation radicals (dGG + 2H)+•, (dCG + 2H)+•, and (dGC + 2H)+• represent transient species comprising protonated and hydrogen atom adducted nucleobase rings that serve as models for proton and radical migrations in ionized DNA. These DNA cation radicals were generated in the gas phase by electron-transfer dissociation of dinucleotide dication-crown-ether complexes and characterized by UV-vis photodissociation action spectra, ab initio calculations of structures and relative energies, and time-dependent density functional theory calculations of UV-vis absorption spectra. Theoretical calculations indicate that (dGG + 2H)+• cation radicals formed by electron transfer underwent an exothermic conformational collapse that was accompanied by guanine ring stacking and facile internucleobase hydrogen atom transfer, forming 3'-guanine C-8-H radicals. In contrast, exothermic hydrogen transfer from the 5'-cytosine radical onto the guanine ring in (dCG + 2H)+• was kinetically hampered, resulting in the formation of a mixture of 5'-cytosine and 3'-guanine radicals. Conformational folding and nucleobase stacking were energetically unfavorable in (dGC + 2H)+• that retained its structure of a 3'-cytosine radical, as formed by one-electron reduction of the dication. Hydrogen-rich guanine (G + H)• and cytosine (C + H)• radicals were calculated to have vastly different basicities in water, as illustrated by the respective p Ka values of 20.0 and 4.6, which is pertinent to their different abilities to undergo proton-transfer reactions in solution.
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Affiliation(s)
- Yang Liu
- Department of Chemistry, Bagley Hall , University of Washington , P.O. Box 351700, Seattle , Washington 98195-1700 , United States
| | - Joseph A Korn
- Department of Chemistry, Bagley Hall , University of Washington , P.O. Box 351700, Seattle , Washington 98195-1700 , United States
| | - Andy Dang
- Department of Chemistry, Bagley Hall , University of Washington , P.O. Box 351700, Seattle , Washington 98195-1700 , United States
| | - František Tureček
- Department of Chemistry, Bagley Hall , University of Washington , P.O. Box 351700, Seattle , Washington 98195-1700 , United States
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Raczyńska ED, Makowski M. Effects of Positive and Negative Ionization on Prototropy in Pyrimidine Bases: An Unusual Case of Isocytosine. J Phys Chem A 2018; 122:7863-7879. [PMID: 30192141 DOI: 10.1021/acs.jpca.8b07539] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Intramolecular proton-transfers (prototropic conversions) have been studied for the guanine building block isocytosine (iC), and effects of positive ionization, called one-electron oxidation (iC - e → iC+•), and negative ionization, called one-electron reduction (iC + e → iC-•), on tautomeric conversions when proceeding from neutral to ionized isocytosine have been discussed. Although radical cations and radical anions are very short-lived species, the ionization effects could be investigated by quantum-chemical methods. Such kind of studies gives some information about the labile protons and the most basic positions in the neutral and radical forms of the tautomeric system. For investigations, the complete isomeric mixture of isocytosine has been considered and calculations performed in two extreme environments, apolar {DFT(B3LYP)/6-311+G(d,p)} and polar {PCM(water)//DFT(B3LYP)/6-311+G(d,p)}. For selected isomers, the G4 theory has also been applied. There are no good relations for energetic parameters of neutral and ionized forms. Ionization energies depend on localization of labile protons. Tautomeric equilibria for neutral and ionized isocytosine, favored sites of protonation and deprotonation, and favored structures of protonated and deprotonated forms strongly depend on environment. Acidity of iC+• is close to that of the iC conjugate acid, and basicity of iC-• is close to that of the iC conjugate base. This increase of acid-base properties of charged radicals explains the proton-transfer in ionized pairs of nucleobases. When compared to other pyrimidine bases such as uracil (U) and cytosine (C), which exhibit analogous tautomeric equilibria between nine prototropic tautomers as isocytosine, the tautomeric preferences for iC, iC+•, iC-•, U, U+•, U-•, C, C+•, and C-• are completely different. The differences suggest that acid-base properties of functional groups, their stabilities, and ionization energies play a principal role in proton-transfers for pyrimidine bases and influence compositions of tautomeric mixtures.
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Affiliation(s)
- Ewa D Raczyńska
- Department of Chemistry , Warsaw University of Life Sciences (SGGW) , ul. Nowoursynowska 159c , 02-776 Warszawa , Poland
| | - Mariusz Makowski
- Faculty of Chemistry , University of Gdańsk , ul. Wita Stwosza 63 , 80-308 Gdańsk , Poland
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Ma J, Marignier JL, Pernot P, Houée-Levin C, Kumar A, Sevilla MD, Adhikary A, Mostafavi M. Direct observation of the oxidation of DNA bases by phosphate radicals formed under radiation: a model of the backbone-to-base hole transfer. Phys Chem Chem Phys 2018; 20:14927-14937. [PMID: 29786710 DOI: 10.1039/c8cp00352a] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In irradiated DNA, by the base-to-base and backbone-to-base hole transfer processes, the hole (i.e., the unpaired spin) localizes on the most electropositive base, guanine. Phosphate radicals formed via ionization events in the DNA-backbone must play an important role in the backbone-to-base hole transfer process. However, earlier studies on irradiated hydrated DNA, on irradiated DNA-models in frozen aqueous solution and in neat dimethyl phosphate showed the formation of carbon-centered radicals and not phosphate radicals. Therefore, to model the backbone-to-base hole transfer process, we report picosecond pulse radiolysis studies of the reactions between H2PO4˙ with the DNA bases - G, A, T, and C in 6 M H3PO4 at 22 °C. The time-resolved observations show that in 6 M H3PO4, H2PO4˙ causes the one-electron oxidation of adenine, guanine and thymine, by forming the cation radicals via a single electron transfer (SET) process; however, the rate constant of the reaction of H2PO4˙ with cytosine is too low (<107 L mol-1 s-1) to be measured. The rates of these reactions are influenced by the protonation states and the reorganization energies of the base radicals and of the phosphate radical in 6 M H3PO4.
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Affiliation(s)
- Jun Ma
- Laboratoire de Chimie Physique, CNRS/Université Paris-Sud 11, Bâtiment 349, 91405 Orsay, France.
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Morozova OB, Fishman NN, Yurkovskaya AV. Kinetics of Reversible Protonation of Transient Neutral Guanine Radical in Neutral Aqueous Solution. Chemphyschem 2018; 19:2696-2702. [PMID: 29978943 DOI: 10.1002/cphc.201800539] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Indexed: 11/11/2022]
Abstract
Time-resolved chemically induced dynamic nuclear polarization (TR-CIDNP) is applied to follow transformation of the short-lived neutral guanine radical into a secondary guanine radical by its protonation, presumably at position N7. In the initial step the photoreaction of guanosine-5'-monophosphate (GMP) with triplet excited 3,3',4,4'-tetracarboxy benzophenone (TCBP) leads to formation of the neutral radical G(-H). . The evidence of the radical conversion is based on the inversion of CIDNP sign for TCBP and GMP protons on the microsecond timescale as a result of the change in magnetic resonance parameters in the pairs of TCBP and GMP radicals due to structural changes of the GMP radical. Acceleration of the CIDNP sign change upon addition of phosphate (proton donor) confirms that the radical transformation responsible for the observed CIDNP kinetics is protonation of the neutral guanine radical with formation of the newly characterized cation radical, (G.+ )'. From the full analysis of the pH-dependent CIDNP kinetics, the protonation and deprotonation behaviour is quantitatively characterized, giving pKa =8.0±0.2 of the cation radical (G.+ )'.
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Affiliation(s)
- Olga B Morozova
- International Tomography Center, Institutskaya 3a, 630090, Novosibirsk, Russia.,Novosibirsk State University, Pirogova 2, 630090, Novosibirsk, Russia
| | - Natalya N Fishman
- International Tomography Center, Institutskaya 3a, 630090, Novosibirsk, Russia.,Novosibirsk State University, Pirogova 2, 630090, Novosibirsk, Russia
| | - Alexandra V Yurkovskaya
- International Tomography Center, Institutskaya 3a, 630090, Novosibirsk, Russia.,Novosibirsk State University, Pirogova 2, 630090, Novosibirsk, Russia
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Morozova OB, Fishman NN, Yurkovskaya AV. Indirect NMR detection of transient guanosyl radical protonation in neutral aqueous solution. Phys Chem Chem Phys 2018; 19:21262-21266. [PMID: 28759067 DOI: 10.1039/c7cp03797j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By using the time-resolved chemically induced dynamic nuclear polarization technique, we show that the neutral guanosyl radical, G(-H)˙, formed in the reaction of guanosine-5'-monophosphate with a triplet-excited 3,3',4,4'-tetracarboxy benzophenone in neutral aqueous solution, protonates readily at the N7 position with the formation of a new guanosyl cation radical (G˙+)'.
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Affiliation(s)
- O B Morozova
- International Tomography Center, Institutskaya 3a, 630090 Novosibirsk, Russia. and Novosibirsk State University, Pirogova 2, 630090 Novosibirsk, Russia
| | - N N Fishman
- International Tomography Center, Institutskaya 3a, 630090 Novosibirsk, Russia. and Novosibirsk State University, Pirogova 2, 630090 Novosibirsk, Russia
| | - A V Yurkovskaya
- International Tomography Center, Institutskaya 3a, 630090 Novosibirsk, Russia. and Novosibirsk State University, Pirogova 2, 630090 Novosibirsk, Russia
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Mishra AK, Harris MA, Young RM, Wasielewski MR, Lewis FD. Dynamics of Charge Injection and Charge Recombination in DNA Mini-Hairpins. J Phys Chem B 2017. [DOI: 10.1021/acs.jpcb.7b03084] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ashutosh Kumar Mishra
- Department
of Chemistry, ‡Argonne−Northwestern Solar Energy Research (ANSER) Center, and §Institute for
Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michelle A. Harris
- Department
of Chemistry, ‡Argonne−Northwestern Solar Energy Research (ANSER) Center, and §Institute for
Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ryan M. Young
- Department
of Chemistry, ‡Argonne−Northwestern Solar Energy Research (ANSER) Center, and §Institute for
Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department
of Chemistry, ‡Argonne−Northwestern Solar Energy Research (ANSER) Center, and §Institute for
Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Frederick D. Lewis
- Department
of Chemistry, ‡Argonne−Northwestern Solar Energy Research (ANSER) Center, and §Institute for
Sustainability and Energy at Northwestern, Northwestern University, Evanston, Illinois 60208-3113, United States
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11
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Effects of ionization on stability of 1-methylcytosine - DFT and PCM studies. J Mol Model 2016; 22:146. [PMID: 27259531 PMCID: PMC4893064 DOI: 10.1007/s00894-016-3020-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/26/2016] [Indexed: 01/01/2023]
Abstract
Consequences of ionization were studied by quantum-chemical methods (DFT and PCM) for 1-methylcytosine (MC)—a model of the nucleobase cytosine (C) connected with sugar in DNA. For calculations, three prototropic tautomers (one amino and two imino forms) and two imino zwitterions were considered, including conformational or configurational isomerism of exo heterogroups. Ionization and interactions between neighboring groups affect intramolecular proton-transfers, geometric and thermodynamic parameters, and electron delocalization for individual isomers. We discovered that an imino isomer is present in the isomeric mixture in the highest amount for positively ionized MC. Its contribution in neutral and negatively ionized MC is considerably smaller. Acid-base parameters for selected radical ions were estimated in the gas phase and compared to those of neutral MC. Gas-phase acidity of radical cations is close to that of the conjugate acid of MC, and gas-phase basicity of radical anions is close to that of the conjugate base of MC. Various routes of amino-imino conversion between neutral and ionized isomers were considered. Energetic-barrier for intramolecular proton-transfer in MC is close to that in the parent system—formamidine.
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Harris MA, Mishra AK, Young RM, Brown KE, Wasielewski MR, Lewis FD. Direct Observation of the Hole Carriers in DNA Photoinduced Charge Transport. J Am Chem Soc 2016; 138:5491-4. [DOI: 10.1021/jacs.6b00702] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Michelle A. Harris
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ashutosh Kumar Mishra
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Ryan M. Young
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Kristen E. Brown
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Frederick D. Lewis
- Department of Chemistry and
Argonne-Northwestern Solar Energy Research (ANSER) Center, Northwestern University, Evanston, Illinois 60208-3113, United States
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