Interactions of Electrons with Bare and Hydrated Biomolecules: From Nucleic Acid Bases to DNA Segments

Gu, Jiande; Leszczyński, Jerzy; Schaefer, Henry F.

doi:10.1021/cr3000219

Cited by 189 publications

(245 citation statements)

References 242 publications

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“…The results presented in Ref. [1] motivated a large amount of both experimental [11,30,31,32,33] and theoretical [34,35,36] work that aimed at elucidating the role played by LEE in DNA damage. In recent years, this research has moved on from idealized systems, e.g.…”

Section: Radiation Damage Of Dnamentioning

confidence: 94%

“…The BLYP affinity is fortuitously close to the PS experimental value. [36] Experimental Reference PS 0.15 ± 0.12 [117] More accurate functionals are constructed by combining GGAs with HF (exact) exchange in an appropriate proportion. This is the case for the hybrid B3LYP functional [124,125], which has proved itself to be particularly reliable for predicting AEAs of DNA components [122].…”

Section: Electron Affinitiesmentioning

confidence: 99%

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Interactions between low energy electrons and DNA: a perspective from first-principles simulations

Kohanoff¹,

McAllister²,

Tribello³

et al. 2017

J. Phys.: Condens. Matter

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Abstract. DNA damage caused by irradiation has been studied for many decades. Such studies allow us to better assess the dangers posed by radiation, and to increase the efficiency of the radiotherapies that are used to combat cancer. A full description of the irradiation process involves multiple size and time scales. It starts from the interaction of radiation -either photons or swift ions -with the biological medium. Such interactions cause electronic excitation and ionisation. The two main products of ionising radiation are thus electrons and radicals. Both of these species can cause damage to biological molecules, in particular DNA. In the long run, this molecular level damage can prevent cells from replicating and can hence lead to cell death. For a long time it was assumed that the main actors in the damage process were the radicals. However, experiments in a seminal paper by the group of Leon Sanche in 2000 showed that low-energy electrons (LEE), such as those generated when ionising biological targets, can also cause bond breaks in biomolecules, in particular strand breaks in plasmid DNA [1]. These results prompted a significant amount of experimental and theoretical work aimed at elucidating the role played by LEE in DNA damage.In this Topical Review we provide a general overview of the problem. We discuss experimental findings and theoretical results hand in hand with the aim of describing the physics and chemistry that occurs during the process of radiation damage, from the initial stages of electronic excitation, through the inelastic propagation of electrons in the medium, the interaction of electrons with DNA, and the chemical end-point effects on DNA. A very important aspect of this discussion is the consideration of a realistic, physiological environment. The role played by the aqueous solution and the amino acids from the histones in chromatin must be considered. Moreover, thermal fluctuations must be incorporated when studying these phenomena. Hence, a special place in this Topical Review is occupied by our recent first-principles molecular dynamics simulations that address the issue of how the environment favours or prevents LEEs from causing damage to DNA. We finish by summarising the conclusions achieved so far, and by suggesting a number of possible directions for further study.

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Section: Radiation Damage Of Dnamentioning

confidence: 94%

Section: Electron Affinitiesmentioning

confidence: 99%

Interactions between low energy electrons and DNA: a perspective from first-principles simulations

Kohanoff¹,

McAllister²,

Tribello³

et al. 2017

J. Phys.: Condens. Matter

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“…Theoretical simulations of electron scattering and electron capture via "shape" resonances support the role of LEEs in DNA strand breaks [94]. Theoretical calculations on scattering and attachment of LEEs to DNA components up to supercoiled plasmid DNA have been intensively reviewed in recent years [95,96].…”

Section: Electron Attachment To Short Single-stranded and Plasmid Dnamentioning

confidence: 99%

Transient Anions in Radiobiology and Radiotherapy: From Gaseous Biomolecules to Condensed Organic and Biomolecular Solids

Alizadeh¹,

Ptasińska²,

Sanche³

2016

Radiation Effects in Materials

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This chapter focuses on the fundamental processes that govern interactions of lowenergy (1-30 eV) electrons with biological systems. These interactions have been investigated in the gas phase and within complex arrangements in the condensed phase. They often lead to the formation of transient molecular anions (TMAs), and their decay by autoionization or dissociation accompanied by bond dissociation. The damage caused to biomolecules via TMAs is emphasized in all sections. Such damage, which depends on a large number of factors, including electron energy, molecular environment, and type of biomolecule, and its physical and chemical interactions with radiosensitizing agents are extensively discussed. A majority of recent findings resulting from experimental and theoretical endeavors are presented. They encompass broad research areas to elucidate important roles of TMAs in irradiated biological systems, from the molecular level to nanoscale cellular dimensions. Fundamental aspects of TMA formation are stressed in this chapter, but many practical applications in a variety of radiation-related fields such as radiobiology and radiotherapy are addressed.

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“…2 Transient anion states of nucleobases have been posited to play a major role in DNA mutagenesis, perhaps via a charge-transfer process from an initially charged nucleobase moiety to a sugar-phosphate bond. 3,4 In this work, we explore the dynamics of transient anion states of uracil via time-resolved photoelectron (TRPE) imaging 5 of an iodide-uracil binary complex.The interaction of excess electrons with uracil and other nucleobases has been studied in the gas phase using low-energy electron scattering, 6,7 negative ion photoelectron spectroscopy (PES), 8−10 and Rydberg electron transfer (RET). 11 Total electron scattering cross section measurements showed structure below 2 eV associated with unoccupied π* orbitals of uracil, 6 while dissociative electron attachment (DEA) studies showed that hydrogen atom loss from the N1 position in the transient negative ion U* − occurs at collision energies as low as 0.7 eV.…”

mentioning

confidence: 99%

Time-Resolved Radiation Chemistry: Photoelectron Imaging of Transient Negative Ions of Nucleobases

2013

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Time-resolved photoelectron imaging has been utilized to probe the energetics and dynamics of the transient negative ion of the nucleobase uracil. This species was created through charge transfer from an iodide anion within a binary iodide-uracil complex using a UV pump pulse; the ensuing dynamics were followed by photodetachment with a near-IR probe pulse. The photoelectron spectra show two time-dependent features, one from probe-induced photodetachment of the transient anion state and another from very low energy electron signal attributed to autodetachment. The transient anion was observed to decay biexponentially with time constants of hundreds of femtoseconds and tens of picoseconds, depending on the excitation energy. These dynamics are interpreted in terms of autodetachment from the initially excited state and a second, longer-lived species relaxed by iodine loss. Hydrogen loss from the N1 position may also occur in parallel.T he observation that low-energy electrons can lead to DNA and RNA strand cleavage via temporary negative ion states 1 has motivated numerous studies of nucleic acid constituents. Gas-phase studies of DNA and RNA building blocks, including individual nucleobases, nucleosides, and nucleotides, have sought to provide insight into the mechanisms of this radiation damage. 2 Transient anion states of nucleobases have been posited to play a major role in DNA mutagenesis, perhaps via a charge-transfer process from an initially charged nucleobase moiety to a sugar-phosphate bond. 3,4 In this work, we explore the dynamics of transient anion states of uracil via time-resolved photoelectron (TRPE) imaging 5 of an iodide-uracil binary complex.The interaction of excess electrons with uracil and other nucleobases has been studied in the gas phase using low-energy electron scattering, 6,7 negative ion photoelectron spectroscopy (PES), 8−10 and Rydberg electron transfer (RET). 11 Total electron scattering cross section measurements showed structure below 2 eV associated with unoccupied π* orbitals of uracil, 6 while dissociative electron attachment (DEA) studies showed that hydrogen atom loss from the N1 position in the transient negative ion U* − occurs at collision energies as low as 0.7 eV. 6,7,12−14 The nature of the uracil anion has been directly probed in PES and RET studies. PES experiments have measured the binding energy of the dipole-bound species as ∼90 meV 8,9 and estimate that valence anions of uracil bind excess electrons by tens to hundreds of meV. 9−11 These species are clearly distinguishable in photoelectron (PE) spectra, as dipolebound states consist of narrow features with low electron binding energies, reflecting the similarity between the anion and neutral geometries, while valence-bound anions have characteristically broader features. 15 Only dipole-bound anions of uracil have been observed using conventional ion generation methods, 8−10 but the uracil anion can transform from a dipolebound state to a valence-bound state upon complexation with one Xe atom or water...

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Interactions of Electrons with Bare and Hydrated Biomolecules: From Nucleic Acid Bases to DNA Segments

Cited by 189 publications

References 242 publications

Interactions between low energy electrons and DNA: a perspective from first-principles simulations

Interactions between low energy electrons and DNA: a perspective from first-principles simulations

Transient Anions in Radiobiology and Radiotherapy: From Gaseous Biomolecules to Condensed Organic and Biomolecular Solids

Time-Resolved Radiation Chemistry: Photoelectron Imaging of Transient Negative Ions of Nucleobases

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