Tihomir Solomun

DNA Damage by Low-Energy Electron Impact: Dependence on Guanine Content.

Single-stranded DNA oligonucleotides (33-mers) containing different numbers of guanines (n=1-4) were tethered to a gold surface and exposed to 1 eV electrons. The electrons induced DNA damage, which was analyzed with fluorescence and infrared spectroscopy methods. The damage was identified as strand breaks and found to correlate linearly with the number of guanines in the sequence. This sequence dependence indicates that the electron capture by the DNA bases plays an important role in the damage reaction mechanism.

Influence of the Compatible Solute Ectoine on the Local Water Structure: Implications for the Binding of the Protein G5P to DNA

Microorganisms accumulate molar concentrations of compatible solutes like ectoine to prevent proteins from denaturation. Direct structural or spectroscopic information on the mechanism and about the hydration shell around ectoine are scarce. We combined surface plasmon resonance (SPR), confocal Raman spectroscopy, molecular dynamics simulations, and density functional theory (DFT) calculations to study the local hydration shell around ectoine and its influence on the binding of a gene-5-protein (G5P) to a single-stranded DNA (dT25). Due to the very high hygroscopicity of ectoine, it was possible to analyze the highly stable hydration shell by confocal Raman spectroscopy. Corresponding molecular dynamics simulation results revealed a significant change of the water dielectric constant in the presence of a high molar ectoine concentration as compared to pure water. The SPR data showed that the amount of protein bound to DNA decreases in the presence of ectoine, and hence, the protein-DNA dissociation constant increases in a concentration-dependent manner. Concomitantly, the Raman spectra in terms of the amide I region revealed large changes in the protein secondary structure. Our results indicate that ectoine strongly affects the molecular recognition between the protein and the oligonucleotide, which has important consequences for osmotic regulation mechanisms.

Combined influence of ectoine and salt: spectroscopic and numerical evidence for compensating effects on aqueous solutions

Ectoine is an important osmolyte, which allows microorganisms to survive in extreme environmental salinity. The hygroscopic effects of ectoine in pure water can be explained by a strong water binding behavior whereas a study on the effects of ectoine in salty solution is yet missing. We provide Raman spectroscopic evidence that the influence of ectoine and NaCl are opposing and completely independent of each other. The effect can be explained by the formation of strongly hydrogen-bonded water molecules around ectoine which compensate the influence of the salt on the water dynamics. The mechanism is corroborated by first principles calculations and broadens our understanding of zwitterionic osmolytes in aqueous solution. Our findings allow us to provide a possible explanation for the relatively high osmolyte concentrations in halotolerant bacteria.

Alkali-metal-induced bond length contraction of acetonitrile (CH3CN) on Au(100)

Abstract The interaction of acetonitrile (CH 3 CN) with the clean and the alkali metal (Na, K) promoted Au(100)-(5 X 20) surface was studied by near edge X-ray absorption fine structure (NEXAFS). On clean Au(100), CH 3 CN is essentially physisorbed in an almost flat-lying configuration with an angle of 81° ± 10° between the CCN axis and the surface normal. The molecular interaction with coadsorbed alkali metal atoms reduces the CN bond length by 0.04 A (Na) and 0.07 A (K), respectively. This is the first report of a contraction of an intramolecular bond of an adsorbed molecule in the presence of coadsorbed alkali metal.

Potassium-induced reconstructive phase transitions on Au(100)

The adsorption of potassium on the quasi-hexagonally reconstructed (“5 × 20”) Au(100) surface has been studied in the temperature range between 130 K and 300 K employing LEED, AES, XPS, and work function (Δф) measurements. At room temperature, an intermediate work function maximum is correlated with a transition of the quasi-hexagonal substrate surface into a (1 × 2) phase caused by a missing-row reconstruction of the Au(100) surface. The lifting of the quasi-hexagonal Au reconstruction is also accompanied by a sudden decrease of the potassium 2p32 core level binding energy by ∼ 0.9 eV. Further adsorption of potassium leads to the formation of complex LEED patterns (among others a c(4 × 4) phase) until the monolayer saturation is attained around Θ ≈ 0.38. Lowering the surface temperature to 130 K does not stabilize the clean surface reconstruction sufficiently to allow formation of stable potassium overlayer phases on the (“5 × 20”)-reconstructed Au(100) surface; instead Δф and LEED measurements at 130 K indicate disorder and partial inhibition of the transition into the reconstructed (1 × 2) phase pointing to a thermally activated process. All in all, we confirm results of a recent STM/LEED/AES study on the Au(100)K system and provide further evidence for the idea whereafter elevated potassium coverages may favor interlayer mixing and/or growth of a potassium—gold alloy.

Binding states and structural phase transformations upon iodine adsorption on a gold (100) surface

Abstract We have studied phase transformations induced by iodine onto a Au(100) surface at 130 and 300 K by means of LEED, Δφ measurements, and thermal desorption spectroscopy (TDS). At 130 K, the inherent Au(5 × 20) reconstruction is stable up to θI ≈ 0.2, before the Au(1 × 1) phase forms. The low-temperature phases are metastable; annealing to 270 K causes among others a c(2 2 × 2 )R45° pattern at θ I,abs = 0.5 ≙ 6.03 × 10 14 iodine atoms/cm2. Δφ and TDS data are correlated with each with the structural transformations including the Au(5 × 20) → (1 × 1) transition. Exposure at 130 K reveals a four-state TD spectrum (β1; β2; α2; α3) and is accompanied by a small Δφ increase, whereas 300 K adsorption produces a five-state TD spectrum with an additional α1-state and a (somewhat larger) initial Δφ decrease. The β-states appear in a T-range between 500 and 800 K, the α-states between 400 and 450 K. The adsorption of molecular iodine which occurs beyond the monolayer coverage is associated with a rather larger Δφ increase of ∼640 meV and narrow TD states around 230 K.

Ectoine protects DNA from damage by ionizing radiation

Ectoine plays an important role in protecting biomolecules and entire cells against environmental stressors such as salinity, freezing, drying and high temperatures. Recent studies revealed that ectoine also provides effective protection for human skin cells from damage caused by UV-A radiation. These protective properties make ectoine a valuable compound and it is applied as an active ingredient in numerous pharmaceutical devices and cosmetics. Interestingly, the underlying mechanism resulting in protecting cells from radiation is not yet fully understood. Here we present a study on ectoine and its protective influence on DNA during electron irradiation. Applying gel electrophoresis and atomic force microscopy, we demonstrate for the first time that ectoine prevents DNA strand breaks caused by ionizing electron radiation. The results presented here point to future applications of ectoine for instance in cancer radiation therapy.

Measurements and simulations of microscopic damage to DNA in water by 30 keV electrons: A general approach applicable to other radiation sources and biological targets

The determination of the microscopic dose-damage relationship for DNA in an aqueous environment is of a fundamental interest for dosimetry and applications in radiation therapy and protection. We combine geant4 particle-scattering simulations in water with calculations concerning the movement of biomolecules to obtain the energy deposit in the biologically relevant nanoscopic volume. We juxtaposition these results to the experimentally determined damage to obtain the dose-damage relationship at a molecular level. This approach is tested for an experimentally challenging system concerning the direct irradiation of plasmid DNA (pUC19) in water with electrons as primary particles. Here a microscopic target model for the plasmid DNA based on the relation of lineal energy and radiation quality is used to calculate the effective target volume. It was found that on average fewer than two ionizations within a 7.5-nm radius around the sugar-phosphate backbone are sufficient to cause a single strand break, with a corresponding median lethal energy deposit being E_{1/2}=6±4 eV. The presented method is applicable for ionizing radiation (e.g., γ rays, x rays, and electrons) and a variety of targets, such as DNA, proteins, or cells.

Ectoine can enhance structural changes in DNA in vitro

Strand breaks and conformational changes of DNA have consequences for the physiological role of DNA. The natural protecting molecule ectoine is beneficial to entire bacterial cells and biomolecules such as proteins by mitigating detrimental effects of environmental stresses. It was postulated that ectoine-like molecules bind to negatively charged spheres that mimic DNA surfaces. We investigated the effect of ectoine on DNA and whether ectoine is able to protect DNA from damages caused by ultraviolet radiation (UV-A). In order to determine different isoforms of DNA, agarose gel electrophoresis and atomic force microscopy experiments were carried out with plasmid pUC19 DNA. Our quantitative results revealed that a prolonged incubation of DNA with ectoine leads to an increase in transitions from supercoiled (undamaged) to open circular (single-strand break) conformation at pH 6.6. The effect is pH dependent and no significant changes were observed at physiological pH of 7.5. After UV-A irradiation in ectoine solution, changes in DNA conformation were even more pronounced and this effect was pH dependent. We hypothesize that ectoine is attracted to the negatively charge surface of DNA at lower pH and therefore fails to act as a stabilizing agent for DNA in our in vitro experiments.

Surface modification of polyamides by direct fluorination

Abstract Bulk samples and thin films of polyamides (PA6 and PA12) were exposed to fluorine (1 - 10 vol.-% F2 in N2) and analysed with photoelectron (XPS) and infrared spectroscopy. Fluorination affects both, the amide and the hydrocarbon parts of the polymers. However, only the carbon atom next to the carbonyl is readily fluorinated. Chemical modification of the amide group is apparent in a large binding energy shift (+5 eV) of the N1s level and the appearance of a νCO band at 1734 cm-1. It is concluded that the amide C-N bond is cleaved in the fluorination process and that COOH and NF2 end groups are formed. This conclusion is corroborated by the appearance of ester oxygen in the XPS and by the 19F NMR spectra of the volatile products that show fluorine signals chemically shifted about 200 ppm towards lower field as compared with the CHF environment.