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Narayanan S J J, Tripathi D, Verma P, Adhikary A, Dutta AK. Secondary Electron Attachment-Induced Radiation Damage to Genetic Materials. ACS OMEGA 2023; 8:10669-10689. [PMID: 37008102 PMCID: PMC10061531 DOI: 10.1021/acsomega.2c06776] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Accepted: 02/20/2023] [Indexed: 06/19/2023]
Abstract
Reactions of radiation-produced secondary electrons (SEs) with biomacromolecules (e.g., DNA) are considered one of the primary causes of radiation-induced cell death. In this Review, we summarize the latest developments in the modeling of SE attachment-induced radiation damage. The initial attachment of electrons to genetic materials has traditionally been attributed to the temporary bound or resonance states. Recent studies have, however, indicated an alternative possibility with two steps. First, the dipole-bound states act as a doorway for electron capture. Subsequently, the electron gets transferred to the valence-bound state, in which the electron is localized on the nucleobase. The transfer from the dipole-bound to valence-bound state happens through a mixing of electronic and nuclear degrees of freedom. In the presence of aqueous media, the water-bound states act as the doorway state, which is similar to that of the presolvated electron. Electron transfer from the initial doorway state to the nucleobase-bound state in the presence of bulk aqueous media happens on an ultrafast time scale, and it can account for the decrease in DNA strand breaks in aqueous environments. Analyses of the theoretically obtained results along with experimental data have also been discussed.
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Affiliation(s)
- Jishnu Narayanan S J
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
| | - Divya Tripathi
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
| | - Pooja Verma
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
| | - Amitava Adhikary
- Department
of Chemistry, Oakland University, 146 Library Drive, Rochester, Michigan 48309, United States
| | - Achintya Kumar Dutta
- Department
of Chemistry, Indian Institute of Technology
Bombay, Powai, Mumbai 400076, India
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2
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Denisov SA, Ward S, Shcherbakov V, Stark AD, Kaczmarek R, Radzikowska-Cieciura E, Debnath D, Jacobs T, Kumar A, Sevilla MD, Pernot P, Dembinski R, Mostafavi M, Adhikary A. Modulation of the Directionality of Hole Transfer between the Base and the Sugar-Phosphate Backbone in DNA with the Number of Sulfur Atoms in the Phosphate Group. J Phys Chem B 2022; 126:430-442. [PMID: 34990129 PMCID: PMC8776618 DOI: 10.1021/acs.jpcb.1c09068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
This work shows that S atom substitution in phosphate controls the directionality of hole transfer processes between the base and sugar-phosphate backbone in DNA systems. The investigation combines synthesis, electron spin resonance (ESR) studies in supercooled homogeneous solution, pulse radiolysis in aqueous solution at ambient temperature, and density functional theory (DFT) calculations of in-house synthesized model compound dimethylphosphorothioate (DMTP(O-)═S) and nucleotide (5'-O-methoxyphosphorothioyl-2'-deoxyguanosine (G-P(O-)═S)). ESR investigations show that DMTP(O-)═S reacts with Cl2•- to form the σ2σ*1 adduct radical -P-S[Formula: see text]Cl, which subsequently reacts with DMTP(O-)═S to produce [-P-S[Formula: see text]S-P-]-. -P-S[Formula: see text]Cl in G-P(O-)═S undergoes hole transfer to Gua, forming the cation radical (G•+) via thermally activated hopping. However, pulse radiolysis measurements show that DMTP(O-)═S forms the thiyl radical (-P-S•) by one-electron oxidation, which did not produce [-P-S[Formula: see text]S-P-]-. Gua in G-P(O-)═S is oxidized unimolecularly by the -P-S• intermediate in the sub-picosecond range. DFT thermochemical calculations explain the differences in ESR and pulse radiolysis results obtained at different temperatures.
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Affiliation(s)
- Sergey A. Denisov
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Samuel Ward
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Viacheslav Shcherbakov
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Alexander D. Stark
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Renata Kaczmarek
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Ewa Radzikowska-Cieciura
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Dipra Debnath
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Taisiya Jacobs
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Anil Kumar
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Michael D. Sevilla
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
| | - Pascal Pernot
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Roman Dembinski
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA,Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Łódź, Poland
| | - Mehran Mostafavi
- Institut de Chimie Physique, UMR 8000 CNRS/Université Paris-Saclay, Bât. 349, Orsay 91405 Cedex, France
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, 146 Library Drive, Rochester, MI 48309-4479, USA
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Magliulo M, Manoli K, Macchia E, Palazzo G, Torsi L. Tailoring Functional Interlayers in Organic Field-Effect Transistor Biosensors. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2015; 27:7528-51. [PMID: 25429859 DOI: 10.1002/adma.201403477] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/24/2014] [Indexed: 05/18/2023]
Abstract
This review aims to provide an update on the development involving dielectric/organic semiconductor (OSC) interfaces for the realization of biofunctional organic field-effect transistors (OFETs). Specific focus is given on biointerfaces and recent technological approaches where biological materials serve as interlayers in back-gated OFETs for biosensing applications. Initially, to better understand the effects produced by the presence of biomolecules deposited at the dielectric/OSC interfacial region, the tuning of the dielectric surface properties by means of self-assembled monolayers is discussed. Afterward, emphasis is given to the modification of solid-state dielectric surfaces, in particular inorganic dielectrics, with biological molecules such as peptides and proteins. Special attention is paid on how the presence of an interlayer of biomolecules and bioreceptors underneath the OSC impacts on the charge transport and sensing performance of the device. Moreover, naturally occurring materials, such as carbohydrates and DNA, used directly as bulk gating materials in OFETs are reviewed. The role of metal contact/OSC interface in the overall performance of OFET-based sensors is also discussed.
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Affiliation(s)
- Maria Magliulo
- Università degli Studi di Bari "Aldo Moro", Via Orabona, 470125, Bari, Italy
| | - Kyriaki Manoli
- Università degli Studi di Bari "Aldo Moro", Via Orabona, 470125, Bari, Italy
| | - Eleonora Macchia
- Università degli Studi di Bari "Aldo Moro", Via Orabona, 470125, Bari, Italy
- Dipartimento Interateneo di Fisica "M. Merlin", Università degli Studi di Bari "A. Moro", Via Orabona, 470125, Bari, Italy
| | - Gerardo Palazzo
- Università degli Studi di Bari "Aldo Moro", Via Orabona, 470125, Bari, Italy
| | - Luisa Torsi
- Università degli Studi di Bari "Aldo Moro", Via Orabona, 470125, Bari, Italy
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Adhikary A, Kumar A, Bishop CT, Wiegand TJ, Hindi RM, Adhikary A, Sevilla MD. π-Radical to σ-Radical Tautomerization in One-Electron-Oxidized 1-Methylcytosine and Its Analogs. J Phys Chem B 2015; 119:11496-505. [PMID: 26237072 DOI: 10.1021/acs.jpcb.5b05162] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
In this work, iminyl σ-radical formation in several one-electron-oxidized cytosine analogs, including 1-MeC, cidofovir, 2'-deoxycytidine (dCyd), and 2'-deoxycytidine 5'-monophosphate (5'-dCMP), were investigated in homogeneous, aqueous (D2O or H2O) glassy solutions at low temperatures by employing electron spin resonance (ESR) spectroscopy. Upon employing density functional theory (DFT) (DFT/B3LYP/6-31G* method), the calculated hyperfine coupling constant (HFCC) values of iminyl σ-radical agree quite well with the experimentally observed ones, thus confirming its assignment. ESR and DFT studies show that the cytosine iminyl σ-radical is a tautomer of the deprotonated cytosine π-cation radical [cytosine π-aminyl radical, C(N4-H)(•)]. Employing 1-MeC samples at various pHs ranging from ca. 8 to 11, ESR studies show that the tautomeric equilibrium between C(N4-H)(•) and the iminyl σ-radical at low temperature is too slow to be established without added base. ESR and DFT studies agree that, in the iminyl σ-radical, the unpaired spin is localized on the exocyclic nitrogen (N4) in an in-plane pure p-orbital. This gives rise to an anisotropic nitrogen hyperfine coupling (Azz = 40 G) from N4 and a near isotropic β-nitrogen coupling of 9.7 G from the cytosine ring nitrogen at N3. Iminyl σ-radical should exist in its N3-protonated form, as the N3-protonated iminyl σ-radical is stabilized in solution by over 30 kcal/mol (ΔG = -32 kcal/mol) over its conjugate base, the N3-deprotonated form. This is the first observation of an isotropic β-hyperfine ring nitrogen coupling in an N-centered DNA radical. Our theoretical calculations predict that the cytosine iminyl σ-radical can be formed in double-stranded DNA by a radiation-induced ionization-deprotonation process that is only 10 kcal/mol above the lowest energy path.
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Affiliation(s)
- Amitava Adhikary
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Anil Kumar
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Casandra T Bishop
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Tyler J Wiegand
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Ragda M Hindi
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Ananya Adhikary
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Michael D Sevilla
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
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Adhikary A, Kumar A, Palmer BJ, Todd AD, Heizer AN, Sevilla MD. Reactions of 5-methylcytosine cation radicals in DNA and model systems: thermal deprotonation from the 5-methyl group vs. excited state deprotonation from sugar. Int J Radiat Biol 2014; 90:433-45. [PMID: 24428230 DOI: 10.3109/09553002.2014.884293] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
PURPOSE To study the formation and subsequent reactions of the 5-methyl-2'-deoxycytidine cation radical (5-Me-2'-dC•(+)) in nucleosides and DNA-oligomers and compare to one-electron oxidized thymidine. MATERIALS AND METHODS Employing electron spin resonance (ESR), cation radical formation and its reactions were investigated in 5-Me-2'-dC, thymidine (Thd) and their derivatives, in fully double-stranded (ds) d[GC*GC*GC*GC*](2) and in the 5-Me-C/A mismatched, d[GGAC*AAGC:CCTAATCG], where C* = 5-Me-C. RESULTS We report 5-Me-2'-dC•(+) production by one-electron oxidation of 5-Me-2'-dC by Cl(2)•- via annealing in the dark at 155 K. Progressive annealing of 5-Me-2'-dC•(+) at 155 K produces the allylic radical (C-CH(2)•). However, photoexcitation of 5-Me-2'-dC•(+) by 405 nm laser or by photoflood lamp leads to only C3'• formation. Photoexcitation of N3-deprotonated thyminyl radical in Thd and its 5'-nucleotides leads to C3'• formation but not in 3'-TMP which resulted in the allylic radical (U-CH(2)•) and C5'• production. For excited 5-Me-2',3'-ddC•(+), absence of the 3'-OH group does not prevent C3'• formation. For d[GC*GC*GC*GC*](2) and d[GGAC*AAGC:CCTAATCG], intra-base paired proton transferred form of G cation radical (G(N1-H)•: C(+ H(+))) is found with no observable 5-Me-2'-dC•(+) formation. Photoexcitation of (G(N1-H)•:C(+ H(+))) in d[GC*GC*GC*GC*](2) produced only C1'• and not the expected photoproducts from 5-Me-2'-dC•(+). However, photoexcitation of (G(N1-H)•:C(+ H(+))) in d[GGAC*AAGC:CCTAATCG] led to C5'• and C1'• formation. CONCLUSIONS C-CH(2)• formation from 5-Me-2'-dC•(+) occurs via ground state deprotonation from C5-methyl group on the base. In the excited 5-Me-2'-dC•(+) and 5-Me-2',3'-ddC•(+), spin and charge localization at C3' followed by deprotonation leads to C3'• formation. Thus, deprotonation from C3' in the excited cation radical is kinetically controlled and sugar C-H bond energies are not the only controlling factors in these deprotonations.
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Affiliation(s)
- Amitava Adhikary
- Department of Chemistry, Oakland University , Rochester, MI , USA
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6
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Staniforth M, Stavros VG. Recent advances in experimental techniques to probe fast excited-state dynamics in biological molecules in the gas phase: dynamics in nucleotides, amino acids and beyond. Proc Math Phys Eng Sci 2013; 469:20130458. [PMID: 24204191 PMCID: PMC3780818 DOI: 10.1098/rspa.2013.0458] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 08/07/2013] [Indexed: 11/23/2022] Open
Abstract
In many chemical reactions, an activation barrier must be overcome before a chemical transformation can occur. As such, understanding the behaviour of molecules in energetically excited states is critical to understanding the chemical changes that these molecules undergo. Among the most prominent reactions for mankind to understand are chemical changes that occur in our own biological molecules. A notable example is the focus towards understanding the interaction of DNA with ultraviolet radiation and the subsequent chemical changes. However, the interaction of radiation with large biological structures is highly complex, and thus the photochemistry of these systems as a whole is poorly understood. Studying the gas-phase spectroscopy and ultrafast dynamics of the building blocks of these more complex biomolecules offers the tantalizing prospect of providing a scientifically intuitive bottom-up approach, beginning with the study of the subunits of large polymeric biomolecules and monitoring the evolution in photochemistry as the complexity of the molecules is increased. While highly attractive, one of the main challenges of this approach is in transferring large, and in many cases, thermally labile molecules into vacuum. This review discusses the recent advances in cutting-edge experimental methodologies, emerging as excellent candidates for progressing this bottom-up approach.
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Affiliation(s)
| | - Vasilios G. Stavros
- Department of Chemistry, University of Warwick, Library Road, Coventry CV4 7AL, UK
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7
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Kumar A, Sevilla MD. π- vs σ-radical states of one-electron-oxidized DNA/RNA bases: a density functional theory study. J Phys Chem B 2013; 117:11623-32. [PMID: 24000793 DOI: 10.1021/jp407897n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As a result of their inherent planarity, DNA base radicals generated by one-electron oxidation/reduction or bond cleavage form π- or σ-radicals. While most DNA base systems form π-radicals, there are a number of nucleobase analogues such as one-electron-oxidized 6-azauraci1, 6-azacytosine, and 2-thiothymine or one-electron reduced 5-bromouracil that form more reactive σ-radicals. Elucidating the availability of these states within DNA, base radical electronic structure is important to the understanding of the reactivity of DNA base radicals in different environments. In this work, we address this question by the calculation of the relative energies of π- and σ-radical states in DNA/RNA bases and their analogues. We used density functional theory B3LYP/6-31++G** method to optimize the geometries of π- and σ-radicals in Cs symmetry (i.e., planar) in the gas phase and in solution using the polarized continuum model (PCM). The calculations predict that σ- and π-radical states in one-electron-oxidized bases of thymine, T(N3-H)(•), and uracil, U(N3-H)(•), are very close in energy; i.e., the π-radical is only ca. 4 kcal/mol more stable than the σ-radical. For the one-electron-oxidized radicals of cytosine, C(•+), C(N4-H)(•), adenine, A(•+), A(N6-H)(•), and guanine, G(•+), G(N2-H)(•), G(N1-H)(•), the π-radicals are ca. 16-41 kcal/mol more stable than their corresponding σ-radicals. Inclusion of solvent (PCM) is found to stabilize the π- over σ-radical of each of the systems. U(N3-H)(•) with three discrete water molecules in the gas phase is found to form a three-electron σ bond between the N3 atom of uracil and the O atom of a water molecule, but on inclusion of full solvation and discrete hydration, the π-radical remains most stable.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
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Duffy MJ, Kelly O, Calvert CR, King RB, Belshaw L, Kelly TJ, Costello JT, Timson DJ, Bryan WA, Kierspel T, Turcu ICE, Cacho CM, Springate E, Williams ID, Greenwood JB. Fragmentation of neutral amino acids and small peptides by intense, femtosecond laser pulses. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:1366-1375. [PMID: 23817831 DOI: 10.1007/s13361-013-0653-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 04/15/2013] [Accepted: 04/16/2013] [Indexed: 06/02/2023]
Abstract
High power femtosecond laser pulses have unique properties that could lead to their application as ionization or activation sources in mass spectrometry. By concentrating many photons into pulse lengths approaching the timescales associated with atomic motion, very strong electric field strengths are generated, which can efficiently ionize and fragment molecules without the need for resonant absorption. However, the complex interaction between these pulses and biomolecular species is not well understood. To address this issue, we have studied the interaction of intense, femtosecond pulses with a number of amino acids and small peptides. Unlike previous studies, we have used neutral forms of these molecular targets, which allowed us to investigate dissociation of radical cations without the spectra being complicated by the action of mobile protons. We found fragmentation was dominated by fast, radical-initiated dissociation close to the charge site generated by the initial ionization or from subsequent ultrafast migration of this charge. Fragments with lower yields, which are useful for structural determinations, were also observed and attributed to radical migration caused by hydrogen atom transfer within the molecule.
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Affiliation(s)
- Martin J Duffy
- Centre for Plasma Physics, School of Mathematics and Physics, Queen's University Belfast, Belfast, UK
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Belshaw L, Calegari F, Duffy MJ, Trabattoni A, Poletto L, Nisoli M, Greenwood JB. Observation of Ultrafast Charge Migration in an Amino Acid. J Phys Chem Lett 2012; 3:3751-3754. [PMID: 26291106 DOI: 10.1021/jz3016028] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We present the first direct measurement of ultrafast charge migration in a biomolecular building block - the amino acid phenylalanine. Using an extreme ultraviolet pulse of 1.5 fs duration to ionize molecules isolated in the gas phase, the location of the resulting hole was probed by a 6 fs visible/near-infrared pulse. By measuring the yield of a doubly charged ion as a function of the delay between the two pulses, the positive hole was observed to migrate to one end of the cation within 30 fs. This process is likely to originate from even faster coherent charge oscillations in the molecule being dephased by bond stretching which eventually localizes the final position of the charge. This demonstration offers a clear template for observing and controlling this phenomenon in the future.
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Affiliation(s)
- Louise Belshaw
- †Centre for Plasma Physics, School of Maths and Physics, Queen's University Belfast, BT7 1NN, United Kingdom
| | - Francesca Calegari
- ‡Politecnico di Milano, Department of Physics, Institute of Photonics and Nanotechnologies, CNR-IFN, I-20133 Milan, Italy
| | - Martin J Duffy
- †Centre for Plasma Physics, School of Maths and Physics, Queen's University Belfast, BT7 1NN, United Kingdom
| | - Andrea Trabattoni
- ‡Politecnico di Milano, Department of Physics, Institute of Photonics and Nanotechnologies, CNR-IFN, I-20133 Milan, Italy
| | - Luca Poletto
- §Institute of Photonics and Nanotechnologies, CNR-IFN, I-35131 Padua, Italy
| | - Mauro Nisoli
- ‡Politecnico di Milano, Department of Physics, Institute of Photonics and Nanotechnologies, CNR-IFN, I-20133 Milan, Italy
| | - Jason B Greenwood
- †Centre for Plasma Physics, School of Maths and Physics, Queen's University Belfast, BT7 1NN, United Kingdom
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Kumar A, Pottiboyina V, Sevilla MD. One-electron oxidation of neutral sugar radicals of 2'-deoxyguanosine and 2'-deoxythymidine: a density functional theory (DFT) study. J Phys Chem B 2012; 116:9409-16. [PMID: 22793263 DOI: 10.1021/jp3059068] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One electron oxidation of neutral sugar radicals has recently been suggested to lead to important intermediates in the DNA damage process culminating in DNA strand breaks. In this work, we investigate sugar radicals in a DNA model system to understand the energetics of sugar radical formation and oxidation. The geometries of neutral sugar radicals C(1')(•), C(2')(•), C(3')(•), C(4')(•), and C(5')(•) of 2'-deoxyguanosine (dG) and 2'-deoxythymidine (dT) were optimized in the gas phase and in solution using the B3LYP and ωB97x functionals and 6-31++G(d) basis set. Their corresponding cations (C(1')(+), C(2')(+), C(3')(+), C(4')(+), and C(5')(+)) were generated by removing an electron (one-electron oxidation) from the neutral sugar radicals, and their geometries were also optimized using the same methods and basis set. The calculation predicts the relative stabilities of the neutral sugar radicals in the order C(1')(•) > C(4')(•) > C(5')(•) > C(3')(•) > C(2')(•), respectively. Of the neutral sugar radicals, C(1')(•) has the lowest vertical ionization potential (IP(vert)), ca. 6.33 eV in the gas phase and 4.71 eV in solution. C(2')(•) has the highest IP(vert), ca. 8.02 eV, in the gas phase, and the resultant C(2') cation is predicted to undergo a barrierless hydride transfer from the C(1') site to produce the C(1') cation. One electron oxidation of C(2')(•) in dG is predicted to result in a low lying triplet state consisting of G(+•) and C(2')(•). The 5',8-cyclo-2'-deoxyguanosin-7-yl radical formed by intramolecular bonding between C(5')(•) and C(8) of guanine transfers spin density from C(5') site to guanine, and this structure has IP(vert) 6.25 and 5.48 eV in the gas phase and in solution.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
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11
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Adhikary A, Becker D, Palmer BJ, Heizer AN, Sevilla MD. Direct formation of the C5'-radical in the sugar-phosphate backbone of DNA by high-energy radiation. J Phys Chem B 2012; 116:5900-6. [PMID: 22553971 DOI: 10.1021/jp3023919] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Neutral sugar radicals formed in DNA sugar-phosphate backbone are well-established as precursors of biologically important damage such as DNA strand scission and cross-linking. In this work, we present electron spin resonance (ESR) evidence showing that the sugar radical at C5' (C5'(•)) is one of the most abundant (ca. 30%) sugar radicals formed by γ- and Ar ion-beam irradiated hydrated DNA samples. Taking dimethyl phosphate as a model of sugar-phosphate backbone, ESR and theoretical (DFT) studies of γ-irradiated dimethyl phosphate were carried out. CH(3)OP(O(2)(-))OCH(2)(•) is formed via deprotonation from the methyl group of directly ionized dimethyl phosphate at 77 K. The formation of CH(3)OP(O(2)(-))OCH(2)(•) is independent of dimethyl phosphate concentration (neat or in aqueous solution) or pH. ESR spectra of C5'(•) found in DNA and of CH(3)OP(O(2)(-))OCH(2)(•) do not show an observable β-phosphorus hyperfine coupling (HFC). Furthermore, C5'(•) found in DNA does not show a significant C4'-H β-proton HFC. Applying the DFT/B3LYP/6-31G(d) method, a study of conformational dependence of the phosphorus HFC in CH(3)OP(O(2)(-))OCH(2)(•) shows that in its minimum energy conformation, CH(3)OP(O(2)(-))OCH(2)(•), has a negligible β-phosphorus HFC. On the basis of these results, the formation of radiation-induced C5'(•) is proposed to occur via a very rapid deprotonation from the directly ionized sugar-phosphate backbone, and the rate of this deprotonation must be faster than that of energetically downhill transfer of the unpaired spin (hole) from ionized sugar-phosphate backbone to the DNA bases. Moreover, C5'(•) in irradiated DNA is found to be in a conformation that does not exhibit β-proton or β-phosphorus HFCs.
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Affiliation(s)
- Amitava Adhikary
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
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12
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Kumar A, Sevilla MD. Density functional theory studies of the extent of hole delocalization in one-electron oxidized adenine and guanine base stacks. J Phys Chem B 2011; 115:4990-5000. [PMID: 21417208 PMCID: PMC3084348 DOI: 10.1021/jp200537t] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study investigates the extent of hole delocalization in one-electron oxidized adenine (A) and guanine (G) stacks and shows that new IR vibrational bands are predicted that are characteristic of hole delocalization within A-stacks. The geometries of A-stacks (A(i); i = 2-8) and G-stacks (GG and GGG) in their neutral and one-electron oxidized states were optimized with the bases in a B-DNA conformation using the M06-2X/6-31G* method. The highest occupied molecular orbital (HOMO) is localized on a single adenine in A-stacks and on a single guanine in GG and GGG stacks located at the 5'-site of the stack. On one-electron oxidation (removal of an electron from the HOMO of the neutral A- and G-stacks) a "hole" is created. Mulliken charge analysis shows that these "holes" are delocalized over two to three adenine bases in the A-stack. The calculated spin density distribution of A(i)(•+) (i = 2-8) also showed delocalization of the hole predominantly on two adenine bases, with some delocalization on a neighboring base. For GG and GGG radical cations, the hole was found to be localized on a single G in the stack. The calculated HFCCs of GG and GGG are in good agreement with the experiment. Further, from the vibrational frequency analysis, it was found that IR spectra of neutral and the corresponding one-electron oxidized adenine stacks are quite different. The IR spectra of A(2)(•+) has intense IR peaks between 900 and 1500 cm(-1) that are not present in the neutral A(2) stack. The presence of A(2)(•+) in the adenine stack has a characteristic intense peak at ~1100 cm(-1). Thus, IR and Raman spectroscopy has potential for monitoring the extent of hole delocalization in A stacks.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
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Shkrob IA, Marin TM, Adhikary A, Sevilla MD. Photooxidation of nucleic acids on metal oxides: physico-chemical and astrobiological perspectives. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2011; 115:3393-3403. [PMID: 21399705 PMCID: PMC3049938 DOI: 10.1021/jp110682c] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Photocatalytic oxidation of nucleic acid components on aqueous metal oxides (TiO(2), α-FeOOH, and α-Fe(2)O(3)) has been studied. The oxidation of purine nucleotides results in the formation of the purine radical cations and sugar-phosphate radicals, whereas the oxidation of pyrimidine nucleotides other than thymine results in the oxidation of only the sugar-phosphate. The oxidation of the thymine (and to a far less extent for the 5-methylcytosine) derivatives results in deprotonation from the methyl group of the base. Some single stranded (ss) oligoribonucleotides and wild-type ss RNA were oxidized at purine sites. In contrast, double stranded (ds) oligoribonucleotides and DNA were not oxidized. These results account for observations suggesting that cellular ds DNA is not damaged by exposure to photoirradiated TiO(2) nanoparticles inserted into the cell, whereas ss RNA is extensively damaged. The astrobiological import of our observations is that the rapid degradation of monomer nucleotides make them poor targets as biosignatures, whereas duplex DNA is a better target as it is resilient to oxidative diagenesis. Another import of our studies is that ds DNA (as opposed to ss RNA) appears to be optimized to withstand oxidative stress both due to the advantageous polymer morphology and the subtle details of its radical chemistry. This peculiarity may account for the preference for DNA over RNA as a "molecule of life" provided that metal oxides served as the template for synthesis of polynucleotides, as suggested by Orgel and others.
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Affiliation(s)
- Ilya A. Shkrob
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439
| | - Timothy M. Marin
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 S. Cass Ave, Argonne, IL 60439
- Chemistry Department, Benedictine University, 5700 College Road, Lisle, IL 60532
| | - Amitava Adhikary
- Department of Chemistry, Oakland University, Rochester, Michigan 48309
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Kumar A, Sevilla MD. Proton-coupled electron transfer in DNA on formation of radiation-produced ion radicals. Chem Rev 2010; 110:7002-23. [PMID: 20443634 PMCID: PMC2947616 DOI: 10.1021/cr100023g] [Citation(s) in RCA: 172] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, MI 48309
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Costentin C, Hajj V, Robert M, Savéant JM, Tard C. Effect of Base Pairing on the Electrochemical Oxidation of Guanine. J Am Chem Soc 2010; 132:10142-7. [DOI: 10.1021/ja103421f] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cyrille Costentin
- Laboratoire d’Electrochimie Moléculaire, Unité Mixte de Recherche Université—CNRS No. 7591, Université Paris Diderot, Bâtiment Lavoisier, 15 rue Jean de Baïf, 75205 Paris Cedex 13, France
| | - Viviane Hajj
- Laboratoire d’Electrochimie Moléculaire, Unité Mixte de Recherche Université—CNRS No. 7591, Université Paris Diderot, Bâtiment Lavoisier, 15 rue Jean de Baïf, 75205 Paris Cedex 13, France
| | - Marc Robert
- Laboratoire d’Electrochimie Moléculaire, Unité Mixte de Recherche Université—CNRS No. 7591, Université Paris Diderot, Bâtiment Lavoisier, 15 rue Jean de Baïf, 75205 Paris Cedex 13, France
| | - Jean-Michel Savéant
- Laboratoire d’Electrochimie Moléculaire, Unité Mixte de Recherche Université—CNRS No. 7591, Université Paris Diderot, Bâtiment Lavoisier, 15 rue Jean de Baïf, 75205 Paris Cedex 13, France
| | - Cédric Tard
- Laboratoire d’Electrochimie Moléculaire, Unité Mixte de Recherche Université—CNRS No. 7591, Université Paris Diderot, Bâtiment Lavoisier, 15 rue Jean de Baïf, 75205 Paris Cedex 13, France
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Yamagami R, Kobayashi K, Tagawa S. Dynamics of the delocalized charges of a radical anion in A.T DNA duplexes. Chemistry 2010; 15:12201-3. [PMID: 19834944 DOI: 10.1002/chem.200902080] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ryuhei Yamagami
- The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki, Osaka, Japan
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Kumar A, Sevilla MD. Sugar radical formation by a proton coupled hole transfer in 2'-deoxyguanosine radical cation (2'-dG*+): a theoretical treatment. J Phys Chem B 2009; 113:13374-80. [PMID: 19754084 PMCID: PMC2765868 DOI: 10.1021/jp9058593] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Previous experimental and theoretical work has established that electronic excitation of a guanine cation radical in nucleosides or in DNA itself leads to sugar radical formation by deprotonation from the dexoxyribose sugar. In this work, we investigate a ground electronic state pathway for such sugar radical formation in a hydrated one electron oxidized 2'-deoxyguanosine (dG(*+) + 7H(2)O), using density functional theory (DFT) with the B3LYP functional and the 6-31G* basis set. We follow the stretching of the C(5')-H bond in dG(*+) to gain an understanding of the energy requirements to transfer the hole from the base to sugar ring and then to deprotonate to proton acceptor sites in solution and on the guanine ring. The geometries of reactant (dG(*+) + 7H(2)O), transition state (TS) for deprotonation of the C(5') site, and product (dG((*)C(5'), N(7)-H(+)) + 7H(2)O) were fully optimized. The zero point energy (ZPE) corrected activation energy (TS) for the proton transfer (PT) from C(5') is calculated to be 9.0 kcal/mol and is achieved by stretching the C(5')-H bond by 0.13 A from its equilibrium bond distance (1.099 A). Remarkably, this small bond stretch is sufficient to transfer the "hole" (positive charge and spin) from guanine to the C(5') site on the deoxyribose group. Beyond the TS, the proton (H(+)) spontaneously adds to water to form a hydronium ion (H(3)O(+)) as an intermediate. The proton subsequently transfers to the N(7) site of the guanine (product). The 9 kcal/mol barrier suggests slow thermal conversion of the cation radical to the sugar radical but also suggests that localized vibrational excitations would be sufficient to induce rapid sugar radical formation in DNA base cation radicals.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, MI 48309
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Pauwels E, De Cooman H, Vanhaelewyn G, Sagstuen E, Callens F, Waroquier M. Radiation-induced radicals in glucose-1-phosphate. II. DFT analysis of structures and possible formation mechanisms. J Phys Chem B 2009; 112:15054-63. [PMID: 18973365 DOI: 10.1021/jp804287c] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Four radiation-induced carbon-centered radicals in dipotassium glucose-1-phosphate dihydrate single crystals are examined with DFT methods, consistently relying on a periodic computational scheme. Starting from a set of plausible radical models, EPR hyperfine coupling tensors are calculated for optimized structures and compared with data obtained from EPR/ENDOR measurements, which are described in part I of this work. In this way, an independent structural identification is made of all the radicals that were observed in the experiments (R1-R4) and tentative reaction schemes are proposed. Also, the first strong evidence for conformational freedom in sugar radicals is established: two species are found to have the same chemical composition but different conformations and consequently different hyperfine coupling tensors. Analysis of the calculated energies for all model compounds suggests that the radiation chemistry of sugars, in general, is kinetically and not necessarily thermodynamically controlled.
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Affiliation(s)
- Ewald Pauwels
- Center for Molecular Modeling, Ghent University, Gent, Belgium.
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De Cooman H, Vanhaelewyn G, Pauwels E, Sagstuen E, Waroquier M, Callens F. Radiation-induced radicals in glucose-1-phosphate. I. Electron paramagnetic resonance and electron nuclear double resonance analysis of in situ X-irradiated single crystals at 77 K. J Phys Chem B 2009; 112:15045-53. [PMID: 18973366 DOI: 10.1021/jp804290e] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Electron magnetic resonance analysis of radiation-induced defects in dipotassium glucose-1-phosphate dihydrate single crystals in situ X-irradiated and measured at 77 K shows that at least seven different carbon-centered radical species are trapped. Four of these (R1-R4) can be fully or partly characterized in terms of proton hyperfine coupling tensors. The dominant radical (R2) is identified as a C1-centered species, assumedly formed by a scission of the sugar-phosphate junction and the concerted formation of a carbonyl group at the neighboring C2 carbon. This structure is chemically identical to a radical recently identified in irradiated sucrose single crystals. Radical species R1 and R4 most likely are C3- and C6-centered species, respectively, both formed by a net hydrogen abstraction. R3 is suggested to be chemically similar to but geometrically different from R4. Knowledge of the identity of the sugar radicals present at 77 K provides a first step in elucidating the formation mechanism of the phosphoryl radicals previously detected after X-irradiation at 280 K. In paper II, the chemical identity, precise conformation, and possible formation mechanisms of these radical species are investigated by means of DFT calculations and elementary insight into the radiation chemistry of sugar and sugar derivatives is obtained.
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Khanduri D, Collins S, Kumar A, Adhikary A, Sevilla MD. Formation of sugar radicals in RNA model systems and oligomers via excitation of guanine cation radical. J Phys Chem B 2008; 112:2168-78. [PMID: 18225886 DOI: 10.1021/jp077429y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In previous work, we have shown that photoexcitation of guanine cation radical (G*+) in frozen aqueous solutions of DNA and its model compounds at 143 K results in the formation of neutral sugar radicals with substantial yield. In this report, we present electron spin resonance (ESR) and theoretical (DFT) evidence regarding the formation of sugar radicals after photoexcitation of guanine cation radical (G*+) in frozen aqueous solutions of one-electron-oxidized RNA model compounds (nucleosides, nucleotides and oligomers) at 143 K. Specific sugar radicals C5'*, C3'* and C1'* were identified employing derivatives of Guo deuterated at specific sites in the sugar moiety, namely, C1'-, C2'-, C3'- and C5'-. These results suggest C2'* is not formed upon photoexcitation of G*+ in one-electron-oxidized Guo and deuterated Guo derivatives. Phosphate substitution at C5'- (i.e., in 5-GMP) hinders formation of C5'* via photoexcitation at 143 K but not at 77 K. For the RNA-oligomers studied, we observe on photoexcitation of oligomer-G*+ the formation of mainly C1'* and an unidentified radical with a ca. 28 G doublet. The hyperfine coupling constants of each of the possible sugar radicals were calculated employing the DFT B3LYP/6-31G* approach for comparison to experiment. This work shows that formation of specific neutral sugar radicals occurs via photoexcitation of guanine cation radical (G*+) in RNA systems but not by photoexcitation of its N1 deprotonated species (G(-H)*). Thus, our mechanism regarding neutral sugar formation via photoexcitation of base cation radicals in DNA appears to be valid for RNA systems as well.
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Affiliation(s)
- Deepti Khanduri
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
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Radiation Effects On DNA: Theoretical Investigations Of Electron, Hole And Excitation Pathways To DNA Damage. ACTA ACUST UNITED AC 2008. [DOI: 10.1007/978-1-4020-8184-2_20] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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