Janina Kopyra

Bio: Janina Kopyra is an academic researcher from Siedlce University of Natural Sciences and Humanities. The author has contributed to research in topics: Ion & Electron. The author has an hindex of 16, co-authored 69 publications receiving 1150 citations. Previous affiliations of Janina Kopyra include Free University of Berlin & Sapienza University of Rome.

Electron-induced damage of DNA and its components: Experiments and theoretical models

Abstract: It is now over ten years since the seminal experiments of Leon Sanche’s group in Sherbrooke have compellingly shown that subexcitation electrons interacting with DNA could cause the occurrence of specific resonant processes which in turn would eventually lead to either single or double strand breaks in DNA materials, to the damaging of its molecular components and possibly to biological apoptosis. Since then a great deal of activity has been spurred by that initial work, with experiments and computations being carried out in several laboratories around the world. Hence, several components of the DNA molecular structure and make-up, i.e. from the purinic and pyrimidinic bases to the sugar and phosphate fragments, have been analysed in detail in the gas phase, on thin-film deposits on noble metals, and in some form of condensed phase, in interaction with low energy electrons. Likewise, several theoretical and computational approaches have been directed at the study of the molecular processes deemed to be crucially involved in the various steps of the energy deposition by the impinging electron onto the molecular networks. The aim of the present review is therefore to put together, after these ten years of intense activity, the major findings which have been consolidated from the broad variety of existing experiments and, at the same time, the main computational approaches which describe the extent of molecular damage following the initial electron attachment process. The present field, in fact, is becoming mature enough to profitably stand an overall evaluation of its experimental and theoretical/computational results and to further construct, from such a review, a starting point for the assessment of its future directions. After a detailed analysis of the experimental data, in the gas phase and in other phases, we shall therefore report the main computational tools and theoretical concepts employed today for the interpretation of the measurements at the molecular level. An overall analysis of the subject will be attempted in the last Section of this review.

Selective Excision of C5 from D‐Ribose in the Gas Phase by Low‐Energy Electrons (0–1 eV): Implications for the Mechanism of DNA Damage

Abstract: Sugar is the central unit within a nucleotide connecting the DNA base with the phosphate group, which itself couples to the neighboring nucleotides within single-stranded DNA. The study of the excitation, ionization, and fragmentation of biomolecular systems is essential for the understanding of many problems in the area of life sciences such as the mechanism of radiation damage in cellular systems or the action of radiosensitisers used in tumor therapy. The passage of high-energy radiation through dense media such as water or a living cell leaves a trace of free electrons. These secondary electrons are created in numbers (5 \" 10 per MeV of deposited energy) that makes them the most abundant radiolytic species. In the course of thermalization they can induce further ionization or excitation processes, but they can also efficiently attach at specific energies (resonances) and sites to DNA, forming transient negative ions that subsequently dissociate (dissociative electron attachment, DEA). Ample evidence exists that DEA with its unique features plays an important role in the nascent states of cellular DNA radiolysis. To date, these phenomena have been investigated at two extremes of DNA complexity, namely, plasmid DNA and isolated nucleobases in the gas phase. Experiments on plasmid DNA have demonstrated that low-energy electrons can efficiently induce single-strand breaks (SSBs), as well as double-strand breaks (DSBs). In the very low-energy domain (0–3 eV), below the threshold of electronic excitation, only SSBs are observed. In these experiments it became apparent that the efficiency of both DSBs and SSBs as a function of the primary electron energy exhibits a resonant behavior, indicating that the formation of negativeion resonances is the initial step. Studies on isolate nucleobases (NBs) in the gas phase have demonstrated that they undergo DEA in the range of roughly 6–9 eV and also at much lower energies (< 3 eV) where SSBs are observed. While the high-energy feature leads to loss of H and further fragment ions associated with the rupture of the NB ring structure, the low-energy resonance exclusively leads to the loss of neutral hydrogen with the excess charge remaining on the nucleobase. In a recent theoretical study modeling a section of DNA composed of cytosine, sugar, and the phosphate group, an interesting mechanism for electron-initiated strand breaks was proposed. The calculations predict a low-lying anionic potential energy surface that connects the initial p* anion state of the base to a s* state in the backbone. An electron captured by a DNA base may thereby be transferred to the backbone, leading to rupture of the C O bond between the phosphate and the sugar. On the other hand, very recent experiments on thymidine (thymine coupled to sugar) indicate that such an electron transfer is not operative; instead it appears that sugar moiety itself has a pronounced ability to capture low-energy electrons with subsequent fragmentation. For the detailed investigation of the response of sugar following electron attachment we use d-ribose (C5H10O5) and some isotopically labeled analogues (1C, 5C, C,1-D). For simplicity we will use the term ribose for dribose throughout this manuscript. A previous study by the Innsbruck Laboratory on deoxyribose (C5H10O4) revealed that electron capture at energies already close to 0 eV induces a variety of fragmentation reactions. As we shall demonstrate, isotopic labeling enables us to identify the underlying decomposition process and to specify the site of the target molecule involved. This provides essential information for the molecular process of DNA damage by low-energy electrons. The experiments were carried out in a crossed electron molecular beam arrangement consisting of an electron source, an oven, and a quadrupole mass analyzer (QMA). The components were housed in a ultrahigh-vacuum chamber at a base pressure of 10 8 mbar. A well-defined electron beam generated from a trochoidal electron monochromator (resolution 90–120 meV fwhm) intersected orthogonally with an effusive molecular beam consisting of ribose molecules. They emanated from a resistively heated oven directly connected to the reaction chamber by a capillary. At a temperature of about 370 K (measured by a platinum resistance) the density of intact ribose molecules was high enough to yield a reasonable negative-ion signal. The generated anions were extracted by a small electric field towards the entrance of the QMA where they were analyzed and detected by a single-pulse counting technique. The energy scale was calibrated using the well-known resonance in SF6 near 0 eV generating metastable SF6 . To prevent ion– molecule reactions involving SF6 ions, the flow of the calibration gas was switched off prior to each measurement. Ribose and the 5-C analogue were obtained from Sigma Aldrich (stated purity 98 and 99%, respectively), [1-C]ribose and [C,1-D]ribose were obtained from Cambridge Isotope Laboratories, Inc. (stated purity 99 and 98%, respectively). All samples were used as delivered. [*] Dipl.-Chem. I. Bald, Dr. J. Kopyra, Prof. Dr. E. Illenberger Institut f*r Chemie und Biochemie Physikalische und Theoretische Chemie Freie Universit1t Berlin Takustrasse 3, 14195 Berlin (Germany) Fax: (+49)30-838-55378 E-mail: iln@chemie.fu-berlin.de [] Permanent address: Chemistry Department, University of Podlasie 08-110 Siedlce (Poland)

Dissociative electron attachment to phosphoric acid esters: the direct mechanism for single strand breaks in DNA.

Abstract: The phosphate group is the central unit along the DNA backbone connecting the two 2-deoxyribose moieties of the two adjacent nucleosides via the P-O-C5 and P-O-C3 bonds, respectively (Fig. 1). The study of the response of the phosphate group to the interaction of low energy electrons is of particular interest since cleavage of any of the PO-C bonds would represent a single strand break in DNA. The study of DNA damage by low energy electrons is directly relevant for the general problem of radiation damage in cellular systems and, correspondingly, for the action of radiosensitizers used in tumor therapy. Here we study dissociative electron attachment (DEA) to dibutyl phosphate (DBP) and triethyl phosphate (TEP) by means of a crossed electron-molecule beam experiment and mass spectrometric detection of the anions. DBP can directly be viewed as model system for the phosphate group coupled in the molecular network of DNA. The passage of high-energy radiation through a living cell leaves a trace of free electrons [1]. There is ample evidence that DEA with its unique features plays a particular role in the nascent states of cellular DNA radiolysis [2]. So far these phenomena have been investigated at two extremes of DNA complexity, namely, plasmid DNA versus isolated DNA building blocks in the gas phase. Experiments on plasmid DNA have demonstrated that low energy electrons can efficiently induce single strand breaks (SSBs), as well as double strand breaks (DSBs) [3]. In the very low energy domain (0–3 eV), below the threshold of electronic excitation, only SSBs are observed [4]. In any of these experiments it became obvious that the efficiency of both DSBs and SSBs as a function of the primary electron energy exhibits a resonant behavior indicating that the formation of negative ion resonances is the initial step. Concerning the single gas phase DNA building blocks, experiments so far have been performed for the different DNA nucleobases [5–11], for 2-deoxyribose [12] [and related sugar compounds [13] ] and for thymidine [14], representing a thymine coupled to 2-deoxyribose via the N1-C1 glycosidic bond. These gas phase studies revealed that (i) isolated nucleobases (NBs) undergo DEA in the range � 6– 9e Vand also at much lower energies (< 3e V) where SSBs are observed [5], (ii) sugar molecules are remarkably sensitive towards low energy electrons which already at very low energies (close to zero eV) induce complex DEA reactions associated with the degradation of the ring structure. Within the study of the intrinsic properties of the isolated gas phase DNA building blocks, the phosphate group is the missing unit. In DNA the phosphate group is negatively charged which is compensated by an appropriate counterion. The adjacent sugar units are linked by the C5-O-P and P-O-C3 bonds, respectively (Fig. 1). The use of a phosphodiester (in the present case DBP) then serves as an appropriate model to explore the behavior of the phosphate group in the DNA network. Density functional theory (DFT) calculations on a sugarphosphate-sugar unit [15] suggested that near zero eV electrons can induce strand breaks via rupture of the C3-O and C5-O bond, respectively. A study on the electron

Selective bond breaking in β-D-ribose by gas-phase electron attachment around 8 eV

Abstract: Electron attachment experiments are carried out on the β-d-ribose molecule in the gas phase for the energy region around 8 eV, and clear fragmentation products are observed for different mass values. A computational analysis of the relevant dynamics is also carried out for the β-d-ribose in both the furanosic and pyranosic form as gaseous targets around that energy range. The quantum scattering attributes obtained from the calculations reveal in both systems the presence of transient negative ions (TNIs). An analysis of the spatial features of the excess resonant electron, together with the computation and characterization of the target molecular normal modes, suggests possible break-up pathways of the initial, metastable molecular species.

Fast parallel algorithms for short-range molecular dynamics

Abstract: Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Biomolecular Damage Induced by Ionizing Radiation: The Direct and Indirect Effects of Low-Energy Electrons on DNA

Abstract: Many experimental and theoretical advances have recently allowed the study of direct and indirect effects of low-energy electrons (LEEs) on DNA damage. In an effort to explain how LEEs damage the human genome, researchers have focused efforts on LEE interactions with bacterial plasmids, DNA bases, sugar analogs, phosphate groups, and longer DNA moieties. Here, we summarize the current understanding of the fundamental mechanisms involved in LEE-induced damage of DNA and complex biomolecule films. Results obtained by several laboratories on films prepared and analyzed by different methods and irradiated with different electron-beam current densities and fluencies are presented. Despite varied conditions (e.g., film thicknesses and morphologies, intrinsic water content, substrate interactions, and extrinsic atmospheric compositions), comparisons show a striking resemblance in the types of damage produced and their yield functions. The potential of controlling this damage using molecular and nanoparticle targets with high LEE yields in targeted radiation-based cancer therapies is also discussed.

Precursors of solvated electrons in radiobiological physics and chemistry.

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Electron-induced damage of DNA and its components: Experiments and theoretical models

Abstract: It is now over ten years since the seminal experiments of Leon Sanche’s group in Sherbrooke have compellingly shown that subexcitation electrons interacting with DNA could cause the occurrence of specific resonant processes which in turn would eventually lead to either single or double strand breaks in DNA materials, to the damaging of its molecular components and possibly to biological apoptosis. Since then a great deal of activity has been spurred by that initial work, with experiments and computations being carried out in several laboratories around the world. Hence, several components of the DNA molecular structure and make-up, i.e. from the purinic and pyrimidinic bases to the sugar and phosphate fragments, have been analysed in detail in the gas phase, on thin-film deposits on noble metals, and in some form of condensed phase, in interaction with low energy electrons. Likewise, several theoretical and computational approaches have been directed at the study of the molecular processes deemed to be crucially involved in the various steps of the energy deposition by the impinging electron onto the molecular networks. The aim of the present review is therefore to put together, after these ten years of intense activity, the major findings which have been consolidated from the broad variety of existing experiments and, at the same time, the main computational approaches which describe the extent of molecular damage following the initial electron attachment process. The present field, in fact, is becoming mature enough to profitably stand an overall evaluation of its experimental and theoretical/computational results and to further construct, from such a review, a starting point for the assessment of its future directions. After a detailed analysis of the experimental data, in the gas phase and in other phases, we shall therefore report the main computational tools and theoretical concepts employed today for the interpretation of the measurements at the molecular level. An overall analysis of the subject will be attempted in the last Section of this review.

A hitherto unrecognized source of low-energy electrons in water

Abstract: Most of the low-energy electrons emitted from a material when it is subjected to ionization radiation are believed to be directly ionized secondary electrons. Coincidence measurements of the electrons ejected from water clusters suggests many are produced by a quantitatively new mechanism, known as intermolecular Coulombic decay. Low-energy electrons are the most abundant product of ionizing radiation in condensed matter. The origin of these electrons is most commonly understood to be secondary electrons1 ionized from core or valence levels by incident radiation and slowed by multiple inelastic scattering events. Here, we investigate the production of low-energy electrons in amorphous medium-sized water clusters, which simulate water molecules in an aqueous environment. We identify a hitherto unrecognized extra source of low-energy electrons produced by a non-local autoionization process called intermolecular coulombic decay2 (ICD). The unequivocal signature of this process is observed in coincidence measurements of low-energy electrons and photoelectrons generated from inner-valence states with vacuum-ultraviolet light. As ICD is expected to take place universally in weakly bound aggregates containing light atoms between carbon and neon in the periodic table2,3, these results could have implications for our understanding of ionization damage in living tissues.