10–100 eV Ar+ ion induced damage to d-ribose and 2-deoxy-d-ribose molecules in condensed phase

Bald, Ilko; Deng, Zongwu; Illenberger, Eugen; Huels, Michael A.

doi:10.1039/b514754a

Cited by 19 publications

(27 citation statements)

References 43 publications

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“…A fragmentation study made with soft X-rays [11] also shows certain global fragmentation patterns, the grouping pattern in their unresolved mass spectra can be traced in our higher resolution mass spectra up to m/q = 80. At low energies, ion-impact studies in condensed films of DNA sugars with both He + [16] and Ar + [17] ions also show a comparable cracking pattern. After hyperthermal He + impact we find that 16 fragments are in common with those observed in our study, namely, m/q = 15, 19, 27-29, 31, 41-45, 55, 57, 60, 69, and 73.…”

Section: Comparison To Other Studiesmentioning

confidence: 63%

“…[a] a) 10-100 eV Ar + ion impact in the condensed phase; [17] b) 10-100 eV He + ion impact in the condensed phase; [16] c) high-energy (keV) He 2 + ion impact in the gas phase; [12] d) soft-X rays on thin films; [11] e) 0-20 eV electron impact in the gas phase. [14] [b] The uncertainties in the measurements were estimated from propagation of error in the fitting procedure and the photon bandwidth (see 'Appearance Energies' Section).…”

Section: Discussion Mass Spectramentioning

confidence: 99%

“…The same study demonstrated that the sugar is extremely fragile compared to the DNA bases, and thus, the sugar is believed to be a fragile moiety in DNA; for example, abstraction of a hydrogen atom from deoxyribose produces a carbon-based sugar radical that can rearrange, thereby culminating in scission of the nucleic-acid strand. [15] Deng et al and Bald et al studied DNA components-2-deoxy-d-ribose among them-in the condensed phase and upon low-energy He + [16] and Ar + [17] ion impact. They observed the complete destruction of the molecules via fragmentation of the parent.…”

Section: Introductionmentioning

confidence: 98%

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Photofragmentation of 2‐Deoxy‐D‐Ribose Molecules in the Gas Phase

Vall-llosera

Huels

Coreno³

et al. 2008

ChemPhysChem

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We have measured the synchrotron-induced photofragmentation of isolated 2-deoxy-D-ribose molecules (C(5)H(10)O(4)) at four photon energies, namely, 23.0, 15.7, 14.6, and 13.8 eV. At all photon energies above the molecule's ionization threshold we observe the formation of a large variety of molecular cation fragments, including CH(3) (+), OH(+), H(3)O(+), C(2)H(3) (+), C(2)H(4) (+), CH(x)O(+) (x=1,2,3), C(2)H(x)O(+) (x=1-5), C(3)H(x)O(+) (x=3-5), C(2)H(4)O(2) (+), C(3)H(x)O(2) (+) (x=1,2,4-6), C(4)H(5)O(2) (+), C(4)H(x)O(3) (+) (x=6,7), C(5)H(7)O(3) (+), and C(5)H(8)O(3) (+). The formation of these fragments shows a strong propensity of the DNA sugar to dissociate upon absorption of vacuum ultraviolet photons. The yields of particular fragments at various excitation photon energies in the range between 10 and 28 eV are also measured and their appearance thresholds determined. At all photon energies, the most intense relative yield is recorded for the m/q=57 fragment (C(3)H(5)O(+)), whereas a general intensity decrease is observed for all other fragments- relative to the m/q=57 fragment-with decreasing excitation energy. Thus, bond cleavage depends on the photon energy deposited in the molecule. All fragments up to m/q=75 are observed at all photon energies above their respective threshold values. Most notably, several fragmentation products, for example, CH(3) (+), H(3)O(+), C(2)H(4) (+), CH(3)O(+), and C(2)H(5)O(+), involve significant bond rearrangements and nuclear motion during the dissociation time. Multibond fragmentation of the sugar moiety in the sugar-phosphate backbone of DNA results in complex strand lesions and, most likely, in subsequent reactions of the neutral or charged fragments with the surrounding DNA molecules.

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Section: Comparison To Other Studiesmentioning

confidence: 63%

Section: Discussion Mass Spectramentioning

confidence: 99%

Section: Introductionmentioning

confidence: 98%

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Photofragmentation of 2‐Deoxy‐D‐Ribose Molecules in the Gas Phase

Vall-llosera

Huels

Coreno³

et al. 2008

ChemPhysChem

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“…For the low mass range, there is remarkable qualitative agreement of the mass spectrum in Figure 2 with the ones reported by Bald et al for 100 eV Ar + impact on solid 2-deoxy-d-ribose. [21] In both cases, CH þ 3 and H 3 O + are dominating. However, the general trends of the spectra are very similar in all ion impact studies on 2-deoxy-d-ribose-small fragments are on average more intense, larger fragments only contribute weakly and no intact parent molecular ions are observed.…”

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confidence: 97%

“…It crosses a deoxyribose effusive jet evaporated from an oven operated at 335 K. The gas-phase 2-deoxyribose is likely to be in the 6-membered ring pyranose form rather than the 5-membered furanose form found in DNA. [21] An electric field of 50 V cm À1 is used to extract ionic deoxyribose fragments into a time-of-flight (TOF) mass spectrometer biased at 2 kV. A semiconductor detector mounted opposite the TOF spectrometer and biased at 18 kV is used to monitor the number of electrons emitted per collision event.…”

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confidence: 99%

Precise Determination of 2‐Deoxy‐D‐Ribose Internal Energies after keV Proton Collisions

Alvarado

Bernard

et al. 2008

ChemPhysChem

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The interaction of keV protons with building blocks of DNA is of particular biological relevance in view of the increasing number of facilities employing MeV proton irradiation for tumor treatment.[1] When ions traverse tissue and are decelerated to MeV and sub-MeV energies, the Bragg peak is reached. At ion energies in the Bragg peak region, the induced damage is highest due to maximum linear energy transfer and relative biological effectiveness. The volume selectivity given by the existence of a well-localized Bragg peak region renders proton therapy such a promising tool for cancer treatment. [2] Furthermore, biological consequences of irradiation with energetic protons from galactic cosmic rays and solar particle events are a limiting factor for human space exploration. This issue is of particular importance for future manned missions outside low earth orbit, for example, lunar or Mars missions. [3] It is well-known that biological radiation damage is the ultimate result of ionization and fragmentation of cellular DNA. To explore the molecular mechanisms underlying radiation-induced DNA damage, numerous recent studies focused on ionization and fragmentation of DNA building blocks upon irradiation with slow electrons, photons and ions. In their pioneering studies, Sanche and co-workers showed that low-energy (secondary) electrons can cause single-and doublestrand breaks of plasmid DNA. [4,5] Huels and coworkers investigated interactions of hyperthermal ions with DNA building blocks and concluded that heavy ions have the potential to induce particularly complex damage to DNA in the Bragg peak region. [6] Ionization and fragmentation of 2-deoxy-d-ribose (dR, C 5 H 10 O 4 ) molecules upon impact of keV and sub-keV ions has recently been investigated for isolated molecules [7] as well as for the condensed phase. [6] In both studies, almost complete disintegration of the molecule was observed and it was concluded that direct ion-induced DNA damage-for example in heavy ion or proton therapy of malignant tumors-may be dominated by deoxyribose fragmentation. Furthermore, Deng and coworkers have recently reported evidence for reactive scattering damage of 2-deoxy-d-ribose thin films by hyperthermal ions. [8,9] In the gas-phase studies, the mass spectrum of the fragment ions largely follows a power-law distribution with a characteristic exponent t of the order of 2, depending on the ion velocity, charge state and the atomic number of the impinging ion. From this, it was concluded that the fragmentation is to a large extent statistical. t was found to be an ideal parameter for the quantification of damage inflicted upon a molecule whose fragmentation yield is very close to 100 %, [7] but this quantification was purely phenomenological, since the fragmentation channels and the characteristic exponent could not be directly related to the amount of energy initially deposited into the deoxyribose molecules. In a study on MeV Si q + collisions with C 60 , Itoh et al. have already concluded that t carries information about the...

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Bond‐ and Energy‐Selective Carbon Abstraction from D‐Ribose by Hyperthermal Nitrogen Ions

et al. 2008

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The interaction of energetic, highly charged heavy particles with biological media bears significance in both heavy-ion cancer therapy [1] and space radiation risks for mission crews. [2,3] Heavy-ion traversal of living cells produces extremely high concentrations of secondary electrons, ions, and excited neutral species along the tracks, which can cause severe damage to the medium, including the nuclear DNA. The initial energetic secondary species are rapidly thermalized and solvated through multiple scattering energy-loss events, during and after which they interact with the DNA molecules, leading to cell death or mutations. Such genotoxic interactions have been extensively studied on the long time scales of thermally diffusion-limited chemical processes. [4] However, knowledge of the nascent (picosecond timescale) events immediately following primary ion irradiation, which link the initial physical processes and the later thermal diffusion-limited radiation chemistry, is still rudimentary, and it leads to major uncertainties in space radiation risk estimates to astronauts [3] and prohibits the development of global models for radiation damage. [5] Early secondary electron damage to DNA occurs even at subionization electron energies by dissociative electron attachment (DEA), resulting in sugar-phosphate cleavage, [6,7] base loss, [8] single-and double-strand breaks, [9,10] and so forth, while hydrogen loss by DEA was found to be both bond-and site-selective. [11][12][13][14] Regarding the formation of hyperthermal secondary species, heavy-particle radiation is distinct from conventional, sparsely ionizing photon or electron radiation in the sense that it imparts much higher kinetic energies to the secondary ion and neutral fragments. Recent measurements show that a primary heavy ion (MeV range) can produce secondary C n+ , O n+ , and N n+ ions (n = 1-3) from DNA bases with hyperthermal energies up to several 100 eV, [15,16] which is not observed for photon impact even at high energies. These hyperthermal ion fragments can cause further complex damage to DNA components in subsequent scattering events by collisional (physical) pathways at energies down to approximately 10 eV, [17] and reactive scattering (physicochemical) pathways at energies down to approximately 1 eV.[18] For example, the N + ion efficiently abstracts hydrogen atoms from DNA components at energies down to about 1 eV. Hydrogen abstraction is found to be bond-and chargestate-selective.[18] However, herein we show for the first time that the more severely damaging carbon abstraction from within the ring structure of d-ribose molecules by hyperthermal nitrogen ions exhibits a strong atom-site and energy selectivity, and we demonstrate that this selectivity is determined by the local chemical bond strengths.Our experiments were conducted with a hyperthermal ion beam system. [17][18][19] It delivers a well focused, mass-and energy-selected, positive ion beam in the 1-100 eV energy range onto molecular films condensed on a polycrystalline platinum sub...

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10–100 eV Ar+ ion induced damage to d-ribose and 2-deoxy-d-ribose molecules in condensed phase

Cited by 19 publications

References 43 publications

Photofragmentation of 2‐Deoxy‐D‐Ribose Molecules in the Gas Phase

Photofragmentation of 2‐Deoxy‐D‐Ribose Molecules in the Gas Phase

Precise Determination of 2‐Deoxy‐D‐Ribose Internal Energies after keV Proton Collisions

Bond‐ and Energy‐Selective Carbon Abstraction from D‐Ribose by Hyperthermal Nitrogen Ions

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