TY - JOUR A1 - Höpner, A. A1 - Seitz, H. A1 - Rechenberg, I. A1 - Bugge, C. A1 - Procop, Mathias A1 - Scheerschmidt, E. A1 - Queisser, A. T1 - TEM Characterization of the Interface Quality of MOVPE Grown Strained InGaAs/GaAs Heterostructures KW - TEM KW - Laser PY - 1995 SN - 1862-6300 SN - 0031-8965 VL - 150 IS - 427 SP - 427 EP - 437 PB - Wiley-VCH CY - Berlin AN - OPUS4-598 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Köster, D. A1 - Mayer-Enthart, Elke A1 - Sialelli, J. A1 - Rurack, Knut A1 - Resch-Genger, Ute A1 - Seitz, H. T1 - Hula Hoop für DNA - Eine hoch sensitive Detektionsmethode für DNA Microarrays N2 - DNA Microarrays, auch als „DNA-Chips“ bekannt, werden verwendet, um das Vorkommen von Genen bzw. Gentranskripten zu analysieren. Sie finden breite Anwendung in der Diagnostik, der Genomanalyse und bei der Erstellung von Genexpressionsprofilen. Vor der Analyse muß auf Grund der oftmals geringen Menge an Probenmaterial eine Vervielfältigung der Probe durchgeführt werden, die jedoch leicht zu Fehlern führt. Im Rahmen dieses Projektes werden zwei experimentelle Ansätze verfolgt, durch die ohne einen Verlust an Sensitivität eine Vervielfältigung der Probe vermieden werden kann, 1) das Etablieren eines RCA-basierten Microarray Assays und 2) die Optimierung des Assays für die Detektion der Fluoreszenzsignale. KW - Newsletter von GABI KW - NGFN KW - GenoMik und FUGATO mit Informationen aus der deutschen Genomforschung PY - 2008 SN - 1617-562X VL - 1 SP - 23 EP - 25 PB - DHGP CY - Berlin AN - OPUS4-17393 LA - deu AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Mayer-Enthart, Elke A1 - Sialelli, Julien A1 - Rurack, Knut A1 - Resch-Genger, Ute A1 - Köster, D. A1 - Seitz, H. T1 - Toward Improved Biochips Based on Rolling Circle Amplification - Influences of the Microenvironment on the Fluorescence Properties of Labeled DNA Oligonucleotides KW - Rolling circle amplification KW - Fluorescence KW - Biochips KW - Microarrays KW - Signal amplification KW - Cy3-labeled oligonucleotides KW - DNA technology PY - 2008 U6 - https://doi.org/10.1196/annals.1430.022 SN - 0077-8923 SN - 1749-6632 SN - 0094-8500 VL - 1130 SP - 287 EP - 292 PB - New York Academy of Sciences CY - New York, NY AN - OPUS4-17633 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Schwibbert, Karin A1 - Marin-Sanguino, A. A1 - Bagyan, I. A1 - Heidrich, Gabriele A1 - Lentzen, G. A1 - Seitz, H. A1 - Rampp, M. A1 - Schuster, S.C. A1 - Klenk, H.-P. A1 - Pfeiffer, F. A1 - Oesterheit, D. A1 - Kunte, Hans-Jörg T1 - A blueprint of ectoine metabolism from the genome of the industrial producer Halomonas elongata DSM 2581T N2 - The halophilic γ-proteobacterium Halomonas elongata DSM 2581T thrives at high salinity by synthesizing and accumulating the compatible solute ectoine. Ectoine levels are highly regulated according to external salt levels but the overall picture of its metabolism and control is not well understood. Apart from its critical role in cell adaptation to halophilic environments, ectoine can be used as a stabilizer for enzymes and as a cell protectant in skin and health care applications and is thus produced annually on a scale of tons in an industrial process using H. elongata as producer strain. This paper presents the complete genome sequence of H. elongata (4 061 296 bp) and includes experiments and analysis identifying and characterizing the entire ectoine metabolism, including a newly discovered pathway for ectoine degradation and its cyclic connection to ectoine synthesis. The degradation of ectoine (doe) proceeds via hydrolysis of ectoine (DoeA) to Nα-acetyl-L-2,4-diaminobutyric acid, followed by deacetylation to diaminobutyric acid (DoeB). In H. elongata, diaminobutyric acid can either flow off to aspartate or re-enter the ectoine synthesis pathway, forming a cycle of ectoine synthesis and degradation. Genome comparison revealed that the ectoine degradation pathway exists predominantly in non-halophilic bacteria unable to synthesize ectoine. Based on the resulting genetic and biochemical data, a metabolic flux model of ectoine metabolism was derived that can be used to understand the way H. elongata survives under varying salt stresses and that provides a basis for a model-driven improvement of industrial ectoine production. KW - Genom KW - Ectoin KW - Biotechnologie KW - Halophile Bakterien PY - 2011 U6 - https://doi.org/10.1111/j.1462-2920.2010.02336.x SN - 1462-2912 SN - 1462-2920 VL - 13 IS - 8 SP - 1973 EP - 1994 PB - Blackwell Science CY - Oxford AN - OPUS4-22344 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Solomun, Tihomir A1 - Seitz, H. A1 - Sturm, Heinz T1 - DNA damage by low-energy electron impact: dependence on guanine content KW - DNA oligonucleotide KW - Low energy electrons KW - Secondary electrons KW - Damage KW - Guanine content PY - 2009 U6 - https://doi.org/10.1021/jp905263x SN - 1520-6106 SN - 1089-5647 VL - 113 IS - 34 SP - 11557 EP - 11559 PB - Soc. CY - Washington, DC AN - OPUS4-20704 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Solomun, Tihomir A1 - Sturm, Heinz A1 - Wellhausen, Robert A1 - Seitz, H. T1 - Interaction of a single-stranded DNA-binding protein g5p with DNA oligonucleotides immobilised on a gold surface N2 - We report surface plasmon resonance (spr) and confocal fluorescence results concerning the interaction of a gene-5-protein (g5p) with single-stranded DNA oligonucleotides (dT25) tethered to a gold surface. The spr data show that a highly stable g5p–ssDNA complex is readily formed on a gold surface with koff = 1.7 × 10-3 s-1. The extent of the complexion indicated involvement of the cooperative protein–protein interactions within the binding to DNA. In the experiments where dT25 coexist with g5p in the solution, the fluorescence data show that g5p also mediates the binding between the non-complementary oligonucleotides in the solution and those immobilised on the surface. KW - Single stranded DNA KW - g5p protein PY - 2012 U6 - https://doi.org/10.1016/j.cplett.2012.03.017 SN - 0009-2614 SN - 1873-4448 VL - 533 SP - 92 EP - 94 PB - North-Holland Publ. Co. CY - Amsterdam AN - OPUS4-26525 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Smales, Glen Jacob A1 - Hahn, Marc Benjamin A1 - Hallier, Dorothea C. A1 - Seitz, H. T1 - X-ray scattering datasets and simulations associated with the publication "Bio-SAXS of single-stranded DNA-binding proteins: Radiation protection by the compatible solute ectoine" N2 - This dataset contains the processed and analysed small-angle X-ray scattering data associated with all samples from the publications "Bio-SAXS of Single-Stranded DNA-Binding Proteins: Radiation Protection by the Compatible Solute Ectoine" (https://doi.org/10.1039/D2CP05053F). Files associated with McSAS3 analyses are included, alongside the relevant SAXS data, with datasets labelled in accordance to the protein (G5P), its concentration (1, 2 or 4 mg/mL), and if Ectoine is present (Ect) or absent (Pure). PEPSIsaxs simulations of the GVP monomer (PDB structure: 1GV5 ) and dimer are also included. TOPAS-bioSAXS-dosimetry extension for TOPAS-nBio based particle scattering simulations can be obtained from https://github.com/MarcBHahn/TOPAS-bioSAXS-dosimetry which is further described in https://doi.org/10.26272/opus4-55751. This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under grant number 442240902 (HA 8528/2-1 and SE 2999/2-1). We acknowledge Diamond Light Source for time on Beamline B21 under Proposal SM29806. This work has been supported by iNEXT-Discovery, grant number 871037, funded by the Horizon 2020 program of the European Commission. KW - SAXS KW - Radiation protection KW - Microdosimetry KW - G5P KW - Ectoine KW - DNA-Binding protein PY - 2023 U6 - https://doi.org/10.5281/zenodo.7515394 PB - Zenodo CY - Geneva AN - OPUS4-56811 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Solomun, Tihomir A1 - Seitz, H. A1 - Sturm, Heinz T1 - Electron irradiation of immobilized DNA in solution through a silicon nano-membrane N2 - In fields involving irradiated aqueous solutions, such as radiotherapy and nuclear waste remediation, it is often unclear whether the principal reactive species are OH° radicals or secondary (low-energy) electrons. This is mostly because both are rapidly attenuated in water. Presently a large part of the evidence for the involvement of low-energy electrons in biological radiation damage is based on 'dry' DNA samples. We demonstrate irradiation of DNA in solution by direct injection of electrons through a 40-nm thin SiO2 membrane, followed by in-situ detection of the DNA damage by a fluorescence-based method. Corresponding Monte Carlo simulations show that the spatial distribution of ionizing events in water with respect to the membrane is controlled by the electron impact energy. By immobilizing DNA to the solution side of the membrane, and because dynamics and reaction ranges of OH° radicals and low-energy electrons are dramatically different, it is possible to tune into the OH° radical or into the electron 'reaction modes' by simply changing the electron impact energy. Such experiments have the potential to provide important information on the radio-sensitivity at a level of a single biomolecule and to contribute to the development of new dosage concepts. KW - Radiation chemistry KW - Low-energy electrons KW - DNA damage KW - Monte Carlo PY - 2013 U6 - https://doi.org/10.1016/j.radphyschem.2013.02.035 SN - 0969-806X SN - 0020-7055 SN - 0146-5724 VL - 88 SP - 70 EP - 73 PB - Pergamon Press CY - Oxford [u.a.] ; Frankfurt, M. AN - OPUS4-30321 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Hahn, Marc Benjamin A1 - Meyer, Susann A1 - Schröter, Maria-Astrid A1 - Seitz, H. A1 - Kunte, Hans-Jörg A1 - Solomun, Tihomir A1 - Sturm, Heinz T1 - Direct electron irradiation of DNA in fully aqueous environment. Damage determination in combination with Monte Carlo simulations N2 - We report on a study in which plasmid DNA in water was irradiated with 30 keV electrons generated by a scanning electron microscope and passed through a 100 nm thick Si3N4 membrane. The corresponding Monte Carlo simulations suggest that the kinetic energy spectrum of the electrons throughout the water is dominated by low energy electrons (<100 eV). The DNA radiation damage, single-strand breaks (SSB) and double-strand breaks (DSB), was determined by electrophoresis. The median lethal dose of D1/2 = 1.7 ± 0.3 Gy was found to be much smaller compared to partially or fully hydrated DNA irradiated under vacuum conditions. The ratio of DSB to SSB was found to be (1:12) as compared to 1:88) found for hydrated DNA. Our method enables quantitative measurements of radiation damage to biomolecules (DNA, proteins) in solutions under varying conditions (pH, salinity, cosolutes) for an electron energy range which is difficult to probe by standard methods. KW - Plasmid DNA in water KW - Monte Carlo simulation KW - Low energy electrons KW - DNA radiation damage KW - Single-strand break (SSB) KW - Double-strand break (DSB) KW - Lethal dose KW - Radiation damage to biomolecules KW - Solutions (pH, salinity, cosolutes) PY - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:b43-386981 SN - 1463-9076 SN - 1463-9084 VL - 19 IS - 3 SP - 1798 EP - 1805 PB - Royal Society of Chemistry AN - OPUS4-38698 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Hahn, Marc Benjamin A1 - Solomun, Tihomir A1 - Wellhausen, Robert A1 - Herrmann, S A1 - Seitz, H A1 - Meyer, Susann A1 - Kunte, Hans-Jörg A1 - Zeman, J. A1 - Uhlig, F A1 - Smiatek, J A1 - Sturm, Heinz T1 - Influence of the Compatible Solute Ectoine on the Local Water Structure: Implications for the Binding of the Protein G5P to DNA N2 - 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-S-protein (G5P) to a single-stranded DNA (dT(25)). 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 oligonudeotide, which has important consequences for osmotic regulation mechanisms. KW - Aqueous solution KW - Biological structure KW - Raman spectroscopy KW - Organic osmolytes KW - High throughput KW - Gene-5 protein KW - Amino acid KW - Water structure PY - 2015 U6 - https://doi.org/10.1021/acs.jpcb.5b09506 SN - 1520-6106 SN - 1089-5647 SN - 1520-5207 VL - 119 IS - 49 SP - 15212 EP - 15220 AN - OPUS4-35800 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Hahn, Marc Benjamin A1 - Smales, Glen Jacob A1 - Seitz, H. A1 - Solomun, Tihomir A1 - Sturm, Heinz T1 - Ectoine interaction with DNA: Influence on ultraviolet radiation damage N2 - Ectoine is a small zwitterionic osmolyte and compatible solute, which does not interfere with cell metabolism even at molar concentrations. Plasmid DNA (pUC19) was irradiated with ultraviolet radiation (UV-C at 266 nm) under quasi physiological conditions (PBS) and in pure water in the presence and absence of ectoine (THP(B)) and hydroxyectoine (THP(A)). Different types of UV induced DNA damage were analysed: DNA single-strand breaks (SSBs), abasic sites and cyclobutane pyrimidine dimers (CPDs). A complex interplay between these factors was observed with respect to the nature and occurrence of DNA damage with 266 nm photons. In PBS, the cosolutes showed efficient protection against base damage, whilst in pure water, a dramatic shift from SSB damage to base damage was observed when cosolutes were added. To test whether these effects are caused by ectoine binding to DNA, further experiments were conducted: small-angle X-ray scattering (SAXS), surface-plasmon resonance (SPR) measurements and Raman spectroscopy. The results show, for the first time, a close interaction between ectoine and DNA. This is in stark contrast to the assumption made by preferential exclusion models, which are often used to interpret the behaviour of compatible solutes within cells and with biomolecules. It is tentatively proposed that the alterations of UV damage to DNA are attributed to ectoine influence on nucleobases through the direct interaction between ectoine and DNA. KW - Ectoine KW - DNA KW - Radiation damage KW - Radiation protection KW - SSB KW - DNA damage KW - DNA protection KW - Compatible solute KW - Zwitterion KW - Hydroxyectoine KW - Salt KW - PBS KW - UV absorption KW - DNA strand-break KW - DNA base damage KW - Ectoine UV absorption KW - Ectoine DNA protection KW - Excited states KW - UV irradiation KW - UV-A KW - UV-B KW - UV-C KW - 266nm KW - UV photons KW - Ectoine-DNA binding KW - Raman spectroscopy KW - UV-Vis KW - Radical scavenger KW - OH scavenger KW - Hydroxyl radicals KW - CPD KW - Abasic site KW - Agarose gel electrophorese KW - SYBR gold KW - DNA melting temperature KW - Counterions KW - Preferential exclusion KW - Cancer KW - Therapy KW - UV protection KW - Sunscreen PY - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:b43-505772 SN - 1463-9076 SN - 1463-9084 VL - 22 IS - 13 SP - 6984 EP - 6992 PB - Royal Society of Chemistry CY - Cambridge AN - OPUS4-50577 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Hallier, Dorothea C. A1 - Smales, Glen Jacob A1 - Seitz, H. A1 - Hahn, Marc Benjamin T1 - Inside back cover for the article "Bio-SAXS of single-stranded DNA-binding proteins: Radiation protection by the compatible solute ectoine" N2 - Showcasing research from the Federal Institute for Material Research and Testing Berlin and Fraunhofer Institute for Celltherapy and Immunology Branch Bioanalytics and Bioprocesses Potsdam. Bio-SAXS of single-stranded DNA-binding proteins: Radiation protection by the compatible solute ectoine. We aimed to increase the possible undisturbed exposure time during bio-SAXS measurements of single-stranded DNA-binding proteins. Therefore small angle X-ray scattering was performed on Gene-V Protein (G5P/GVP), which is involved in DNA repair processes. To achieve this, irradiations were performed in presence and absence of the hydroxyl-radical scavenger and osmolyte Ectoine, which showed efficient radiation protection and prevented protein aggregation, thus allows for a non-disturbing way to improve structure-determination of biomolecules. KW - Bio-SAXS KW - BioSAXS KW - Cosolute KW - DNA KW - Dosimetry KW - Ectoin KW - Ectoine KW - G5P KW - GVP KW - Geant4 KW - Geant4-DNA KW - Ionizing radiation damage KW - LEE KW - McSAS3 KW - Microdosimetry KW - Monte-Carlo simulations KW - OH Radical KW - OH radical scavenger KW - Protein KW - Protein unfolding KW - Radiation damage KW - Radical Scavenger KW - SAXS KW - Single-stranded DNA-binding proteins KW - Small-angle xray scattering KW - Topas-MC KW - Topas-nBio KW - TopasMC KW - X-ray scattering KW - Particle scatterin simulations KW - ssDNA PY - 2023 U6 - https://doi.org/10.1039/D3CP90056H SN - 1463-9076 SN - 1463-9084 VL - 25 IS - 7 SP - 5889 PB - Royal Society of Chemistry CY - Cambridge AN - OPUS4-57006 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Hallier, Dorothea C. A1 - Smales, Glen Jacob A1 - Seitz, H. A1 - Hahn, Marc Benjamin T1 - Bio-SAXS of single-stranded DNA-binding proteins: Radiation protection by the compatible solute ectoine N2 - Small-angle X-ray scattering (SAXS) can be used for structural determination of biological macromolecules and polymers in their native states (e.g. liquid phase). This means that the structural changes of (bio-)polymers, such as proteins and DNA, can be monitored in situ to understand their sensitivity to changes in chemical environments. In an attempt to improve the reliability of such experiments, the reduction of radiation damage occurring from exposure to X-rays is required. One such method, is to use scavenger molecules to protect macromolecules against radicals produced during radiation exposure, such as reactive oxygen species (ROS). In this study we investigate the feasibility of applying the compatible solute, osmolyte and radiation protector Ectoine (THP(B)), as a scavenger molecule during SAXS measurements of the single-stranded DNA-binding protein Gene-V Protein (G5P/GVP). In this case, we monitor the radiation induced changes of G5P during bio-SAXS measurments and the resulting microscopic energy-damage relation was determined from microdosimetric calculations by Monte-Carlo based particle scattering simulations with TOPAS/Geant4 and a custom target-model. This resulted in a median-lethal energy deposit of pure G5P at 4 mg mL−1 of E1/2 = 7 ± 5 eV, whereas a threefold increase of energy-deposit was needed under the presence of Ectoine to reach the same level of damage. This indicates that Ectoine increases the possible exposure time before radiation-damage to G5P is observed. Furthermore, the dominant type of damage shifted from aggregation in pure solutions towards a fragmentation for solutions containing Ectoine as a cosolute. These results are interpreted in terms of indirect radiation damage by reactive secondary species, as well as post-irradiation effects, related to preferential-exclusion of the cosolute from the protein surface. Hence, Ectoine is shown to provide a non-disturbing way to improve structure-determination of proteins via bio-SAXS in future studies. KW - BioSAXS KW - Bio-SAXS KW - Cosolute KW - Ectoine KW - G5P KW - GVP KW - Radiation damage KW - Radical Scavenger KW - Single-stranded DNA-binding proteins KW - X-ray scattering KW - DNA KW - ssDNA KW - Protein KW - SAXS KW - Small-angle xray scattering KW - McSAS3 KW - Dosimetry KW - Microdosimetry KW - Geant4 KW - Geant4-DNA KW - Topas KW - Topas-MC KW - Monte-Carlo simulations KW - Particle scattering simulations KW - Topas-nBio KW - OH Radical KW - OH radical scavenger KW - LEE KW - Ionizing radiation damage KW - Protein unfolding KW - Ectoin PY - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:b43-568909 SN - 1463-9076 SN - 1463-9084 VL - 25 IS - 7 SP - 5372 EP - 5382 PB - Royal Society of Chemistry CY - Cambridge AN - OPUS4-56890 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -