M. F. Politis

Strand breaks induced in plasmid DNA by ultrasoft X-rays: Influence of hydration and packing

Purpose: To study the effect of hydration level and plasmid packing on strand break induction in DNA by ultrasoft X-ray. Materials and methods: Bluescript (pBS, tight packing) and pSP189 (pSP, loose packing) plasmids were irradiated by 250, 380, and 760 eV ultrasoft X-rays at the Laboratoire pour lUtilisation du Rayonnement Electromagnétique synchrotron facility (Orsay, France). Single and double strand breaks (SSB and DSB) were quantified by gel electrophoresis. Results: The number of DSB per Gray and per Dalton in pBS plasmids were (5.6 ± 0.1), (6.3 ± 0.1) and (8.5 ± 0.4)×10−12 at 250, 380 and 760 eV, respectively. They were respectively 1.4 ± 0.1, 1.1 ± 0.1 and 1.9 ± 0.2 times larger for pSP plasmids. SSB/DSB ratios varied between 4.4 and 6.4. Conclusion: The observed dependency of strand break induction by ultrasoft X-rays on the hydration level of DNA in plasmids films may be associated with: (i) Damage transfer from the water shell to the DNA and/or (ii) change in packing. 760 eV photons which are more often absorbed in the hydration shell and yield longer range electrons than 250 and 380 eV photons, induce more DSB per Gray and per Dalton, especially for the looser plasmid (pSP).

Ionization and fragmentation of water clusters by fast highly charged ions

We study the dissociative ionization of water clusters by impact of 12 MeV/u Ni25+ ions. Cold target recoil ion momentum spectroscopy (COLTRIMS) is used to obtain information about stability, energetics and charge mobility of the ionized water clusters. An unusual stability of the H9O+4 ion is observed, which could be the signature of the so-called Eigen structure in gas-phase water clusters. From the analysis of coincidences between charged fragments, we conclude that charge mobility is very high and is responsible for the formation of protonated water clusters, (H2O)nH+, that dominate the mass spectrum. These results are supported by Car–Parrinello molecular dynamics and time-dependent density functional theory simulations, which also reveal the mechanisms of such mobility.

Theoretical investigation of the ultrafast dissociation of ionised biomolecules immersed in water: direct and indirect effects.

Theoretical simulations are particularly well suited to investigate, at a molecular level, direct and indirect effects of ionising radiations in DNA, as in the particular case of irradiation by swift heavy ions such as those used in hadron therapy. In the past recent years, we have developed the modeling at the microscopic level of the early stages of the Coulomb explosion of DNA molecules immersed in liquid water that follows the irradiation by swift heavy ions. To that end, Time-Dependent Density Functional Theory molecular dynamics simulations (TD-DFT MD) have been developed where localised Wannier orbitals are propagated. This latter enables to separate molecular orbitals of each water molecule from the molecular orbitals of the biomolecule. Our main objective is to demonstrate that the double ionisation of one molecule of the liquid sample, either one water molecule from the solvent or the biomolecule, may be in some cases responsible for the formation of an atomic oxygen as a direct consequence of the molecule Coulomb explosion. Our hypothesis is that the molecular double ionisation arising from irradiation by swift heavy ions (about 10% of ionisation events by ions whose velocity is about the third of speed of light), as a primary event, though maybe less probable than other events resulting from the electronic cascading (for instance, electronic excitations, electron attachments), may be systematically more damageable (and more lethal), as supported by experiments that have been carried out in our group in the 1990s (in studies of damages created by K holes in DNA). The chemical reactivity of the produced atomic oxygen with other radicals present in the medium will ultimately lead to chemical products that are harmful to DNA. In the present paper, we review our theoretical methodology in an attempt that the community be familiar with our new approach. Results on the production of atomic oxygen as a result of the double ionisation of water or as a result of the double ionisation of the Uracil RNA base will be presented.

Ionization of water clusters by fast Highly Charged Ions: Stability, fragmentation, energetics and charge mobility

We study dissociative ionization of water clusters by impact of fast Ni ions. Cold Target Recoil Ion Momentum Spectroscopy (COLTRIMS) is used to obtain information about stability, energetics and charge mobility of the ionized clusters. An unusual stability of the (H2O)4 H + ion is observed, which could be the signature of the so called Eigen structure in gas phase water clusters. High charge mobility, responsible for the formation of protonated water clusters that dominate the mass spectrum, is evidenced. These results are supported by CPMD and TDDFT simulations, which also reveal the mechanisms of such mobility.

Ultrafast dissociation of a core-ionized water molecule in liquid phase: Density functional theory based simulations

We investigate the dynamics of a core-ionized molecule in liquid water by performing first-principles density functional theory (DFT)-based simulations. We observe that molecular dissociation is reached within the lifetime of the induced vacancy. Our findings show that at least one of the intramolecular hydrogens migrates from the core- ionized molecule to one molecule of the first solvation shell.

Differential cross sections for single ionization of water molecules in liquid phase by electron impact at high impact energies

We compute Differential Cross Sections (DCS) for single ionization of fixed-in-space liquid water by electron impact at high impact energies. Several orientations of the molecule are considered. The DCS for different molecular orbitals exhibit a strong dependence with the molecular orientation.