Mechanisms for Low-Energy (0.5−30 eV) Electron-Induced Pyrimidine Ring Fragmentation within Thymine- and Halogen-Substituted Single Strands of DNA

Abstract

Low-energy (0.5-30 eV) electron irradiation of the thymine-and halogen-substituted nonamers Au/Cy* 6 T 3 and Au/Cy* 6 (FU,BrU,IU) 3 , chemisorbed onto a gold surface, leads to the desorption of neutral CN and OCN from fragmentation of the DNA base ring. No neutral halogen-containing species are detected. The cross sections at 15 eV for CN and OCN desorbing from the substituted oligomers bromouracil, fluorouracil, iodoracil, and thymine are measured to be 7.5-, 4.5-, (2.5-3.0)-, and (3.0-3.5) × 10 -17 cm 2 , respectively; the difference between T and BrU is about 2-to 3-fold over the investigated energy range. The decrease of neutral species produced, in the sequence BrU > FU > IU ≈ T, is observed over the entire 0.5-30 eV range. Unimolecular dissociation of resonant and nonresonant electron-induced uracil-like radicals is likely to be responsible for the formation/desorption of these neutral species. Above 20 eV incident electron energy, the initial process essentially involves nonresonant interactions, whereas within the 5-20 eV energy range, core-excited resonances are implicated. At lower energy, the neutral fragments, which are observed only for bromouracil-substituted oligonucleotides, are induced via a shape resonance. The behavior of the magnitude of the CN and OCN yields with incident electron energy, along with empirical threshold calculations for neutral fragment formation and considerations of transient anion dissociation dynamics, led us to propose possible mechanisms for pyrimidine ring fragmentation by slow electron impact.

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

“…The studies [157][158][159][160][161][162][163][164][165][166][167] confirmed the prediction of Zimbrick and coworkers [168] that the radiosensitizing properties of these compounds arose from DEA of solvated electrons, and further showed that DEA of higher energy (0-7eV) electrons was also involved in radiosensitization. Platinum bromide, aromatic compounds containing nitro group and other halogenated thymidine derivatives were found to play similar roles [58, 70, 71, 163-165, 169, 170].…”

“…Following early investigations with solvated electrons [168], a relatively large number of experiments have been performed both in the gas (see Section 4.4) and condensed phases [160,161,165] to study electron scattering from--and attachment to--halogenated pyrimidines. Several experiments were performed using SAMs of BrdU-containing oligonucleotides [157,158,171]. These included the detection of the electron-stimulated desorption of ion and neutral species and HPLC analysis of damaged films, as well as electronic and vibrational electronenergy loss spectra for gaseous bromouracil [159].…”

Low Energy Electron Interactions with Uracil: The Energetics Predicted by Theory

“…8,11,12 Here we show the most likely products resulting from breaking of the N-H or C-H bonds. Figure 4 exhibits the spin density on the departing H as the N-H or C-H distance is stretched.…”

“…It was also found that LEEs can induce ring fragmentation of DNA bases, such as thymine and halouracils. 11,12 The reason uracil dissociates so easily on LEE attachment has been attributed to the high electron affinities (EA) of the U-yl radicals, 8 which are formed by detaching one of the four hydrogen atoms at the N 1 , N 3 , C 5 , or C 6 positions. The energy released by the binding of an electron to the U-yl radical reduces the overall energy needed to fragment an N-H or C-H bond.…”

X-ray Photoelectron Spectroscopy Analysis of Gold Surfaces after Removal of Thiolated DNA Oligomers by Ultraviolet/Ozone Treatment

“…Hence their effective ranges is short; so that their interactions with bio-molecules can be studied using electron impact techniques on thin sample films, and for such work, self-assembled monolayers (SAMs) offer certain advantages, in particular their (relatively) easy preparation, uniformity, and high density and supposed high order. Previous researchers from our laboratory have adsorbed thiolated DNA onto gold to determine electron attenuation lengths and effective damage cross sections in DNA SAMs [26] and to measure the electron stimulated desorption (ESD) of neutral [27,28] and of anionic [22] species from DNA. In this latter work, single-and double-stranded (ss and ds, respectively) DNA oligonucleotides of 40 base pairs, were attached to gold by either a single terminal thiol (1S) or by five thiols (5S) positioned with a spacing of ~8 base pairs along the sugar-phosphate backbone.…”