TY - JOUR A1 - Solomun, Tihomir A1 - Cordsmeier, Leo A1 - Hallier, Dorothea C. A1 - Seitz, Harald A1 - Hahn, Marc Benjamin T1 - Interaction of a Dimeric Single-Stranded DNA-Binding Protein (G5P) with DNA Hairpins. A Molecular Beacon Study N2 - Gene-V protein (G5P/GVP) is a single-stranded (ss)DNA-binding protein (SBP) of bacteriophage f1 that is required for DNA synthesis and repair. In solution, it exists as a dimer that binds two antiparallel ssDNA strands with high affinity in a cooperative manner, forming a left-handed helical protein–DNA filament. Here, we report on fluorescence studies of the interaction of G5P with different DNA oligonucleotides having a hairpin structure (molecular beacon, MB) with a seven base-pair stem (dT24-stem7, dT18-stem7), as well as with DNA oligonucleotides (dT38, dT24) without a defined secondary structure. All oligonucleotides were end-labeled with a Cy3-fluorophore and a BHQ2-quencher. In the case of DNA oligonucleotides without a secondary structure, an almost complete quenching of their strong fluorescence (with about 5% residual intensity) was observed upon the binding of G5P. This implies an exact alignment of the ends of the DNA strand(s) in the saturated complex. The interaction of the DNA hairpins with G5P led to the unzipping of the base-paired stem, as revealed by fluorescence measurements, fluorescence microfluidic mixing experiments, and electrophoretic mobility shift assay data. Importantly, the disruption of ssDNA’s secondary structure agrees with the behavior of other single-stranded DNA-binding proteins (SBPs). In addition, substantial protein-induced fluorescence enhancement (PIFE) of the Cy3-fluorescence was observed. KW - DNA KW - Protein KW - ssDNA KW - Fluorescence KW - Raman KW - G5P KW - Hairpin KW - Molecular beacon KW - Quencher KW - Amino Acids KW - SBP KW - SSB KW - Cy3 KW - PIFE KW - Protein-induced fluorescence enhancement KW - Protein–DNA filament KW - Single-stranded DNA-binding protein KW - Bacteriophage f1 KW - Oligonucleotides PY - 2023 DO - https://doi.org/10.1021/acs.jpcb.3c03669 SN - 1520-6106 VL - 127 IS - 38 SP - 8131 EP - 8138 PB - ACS Publications AN - OPUS4-58295 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 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-505772 DO - https://doi.org/10.1039/d0cp00092b 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 - Solomun, Tihomir A1 - Hahn, Marc Benjamin A1 - Smiatek, J. T1 - Raman spectroscopic signature of ectoine conformations in bulk solution and crystalline state N2 - Recent crystallographic results revealed conformational changes of zwitterionic ectoine upon hydration. By means of confocal Raman spectroscopy and density functional theory calculations, we present a detailed study of this transformation process as part of a Fermi resonance analysis. The corresponding findings highlight that all resonant couplings are lifted upon exposure to water vapor as a consequence of molecular binding processes. The importance of the involved molecular groups for water binding and conformational changes upon hydration is discussed. Our approach further Shows that the underlying rapid process can be reversed by carbon dioxide saturated atmospheres. For the first time, we also confirm that the conformational state of ectoine in aqueous bulk solution coincides with crystalline ectoine in its dihydrate state, thereby highlighting the important role of a few bound water molecules. KW - Fermi resonance KW - Ectoine hydration KW - DFT calculations of Raman spectra KW - Position of carboxylate group PY - 2020 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-509855 DO - https://doi.org/10.1002/cphc.202000457 SN - 1439-4235 SN - 1439-7641 VL - 21 IS - 17 SP - 1945 EP - 1950 PB - Wiley-VCH CY - Weinheim AN - OPUS4-50985 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - RPRT A1 - Hahn, Marc Benjamin A1 - Sturm, Heinz A1 - Bier, F A1 - Solomun, Tihomir T1 - Biologische Konsequenzen einer nanoskaligen Energiedeposition: Fokussierung auf die Rolle niederenergetischer Elektronen T1 - Biological Consequence of Nanoscale Energy Deposition: Focusing on the Role of Low-Energy Electrons N2 - Bei der Behandlung von Krebs mittels Strahlentherapie sollen Tumorzellen abgetötet werden ohne das umliegende gesunde Gewebe zu zerstören. Um Strahlentherapien für Patienten verträglicher zu machen, ist ein besseres Verständnis der zugrundeliegenden Prozesse auf der molekularen Ebene nötig. Dabei sind der Energieeintrag und die Streuprozesse der Strahlung in der Umgebung der DNA von besonderem Interesse. Durch Streuung von hochenergetischer Strahlung in Wasser werden besonders viele Sekundärelektronen mit niedriger Energie erzeugt. Zur Untersuchung der Schädigungseffizienz dieser Elektronen wurde ein Verfahren zur direkten Bestrahlung von Lösungen mittels Elektronen variabler Energien enwtickelt. Dies wurde durch einen neu entwickelten Probenhalter mit einer für Elektronen durchlässigen Nanomembran ermöglicht. Mit diesem können Bestrahlungen an DNA, Proteinen, und Zellen bei verschiedenen pH-Werten oder Salzkonzentrationen durchgeführt werden. Parallel dazu wurde der ortsabhängige Energieeintrag innerhalb des Wassers durch Elektronenstreusimulationen bestimmt. Diese neuartige Kombination von Experiment und Simulation ermöglicht die Bestimmung der Schaden-Dosis-Relation für Elektronenbestrahlung von biologischen Systemen unter realistischen physiologischen Bedingungen. So konnten für die genutzten Primärelektronen wie die mittlere letale Dosis, bei der 50 Prozent der DNA geschädigt sind, mit 1,7 Gy bestimmt. Ebenfalls wurde das für mikrodosimetrische Modellierungen und Betrachtungen der sogenannten Linear energy transfer (LET) Effekte, wichtige Verhältnis von DNA Einzelstrangbrüchen (SSB) zu Doppelstrangbrüchen (DSB) als SSB/DSB = 12/1 bestimmt. Mit Hilfe eines Modells für das Targetvolumen der DNA wurde der mittlere mikroskopische letale Energieeintrag berechnet als E1/2 = 6 ± 4 eV . Es wurde gefolgert, dass weniger als zwei Ionisationsprozesse im sensitiven Targetvolumen der DNA im Mittel zu einem Einzelstrangbruch führen. Diese Methode ist unabhängig von den Primärpartikel und geometrischen Bedingungen. Deshalb ermöglicht sie die Vergleichbarkeit experimenteller Systeme mit inhomogenen Energieverteilungen, welches sonst nicht gegeben ist. Des weiteren wurden die Strahlenschutzfunktionen des Zellschutzmoleküls Ectoines und sein Einfluss auf Wasser und Biomoleküle untersucht. Seine Schutzfunktion gegen ionisierende Strahlung wurde auf die Erhöhung des Streuquerschnitts niederenergetischer Elektronen und seine Eigenschaft als OH-Radikalfänger zurückgeführt. Aufbauend auf unseren Erkenntnissen finden in klinischen Arbeitsgruppen Untersuchungen zu Einsatzmöglichkeiten im Umfeld der Strahlentherapie statt. Projektkennung Deutsche Forschungsgemeinschaft (DFG) - Projektnummer 245767821 N2 - To cure cancer radiation therapy is used to kill tumor cells. It is based on radiation induced damage to biomolecules. Here DNA damage is of key interest due to its central role in apoptosis and mutation. Because of the high amount of water in biological tissue, most of the damage is caused by the secondary particles produced by the inelastic scattering of ionizing radiation and water. A detailed understanding of the underlying molecular processes under physiological conditions is the prerequisite to develop more efficient the-rapies. Therefore irradiations have to be performed in liquid, under consideration of the chemical environment. To make it possible to irradiate liquids with electrons within scanning electron microscopes a new sample holder was constructed incorporating an electron transparent nanomembrane. It makes it possible to irradiate DNA, proteins or cells at different pH and salinity. The median lethal dose for a model system of plasmid DNA and water was determined by the combination of experimental data, particle scattering simulations (Geant4-DNA) and diffusion calculations as D1/2 = 1.7 ± 0.3 Gy. From the convolution of plasmid positions and the spatially resolved energy deposit, as determined by electron scattering simulations, the histogram of the energy deposit within the target volume of the plasmids and the microscopic median lethal energy deposit was calculated as E1/2 = 6 ± 4 eV . It could be deduced, that on average less than two ionization Events are sufficient to cause a single-strand-break. The relation of single-strand-breaks (SSB) to double-strand-breaks (DSB), which is of importance for microdosimetric modeling, was determined as SSB : DSB = 12 : 1. The presented method for the Determination of microscopic dose-damage relations was further extended to be applicable for General irradiation experiments. It is independent of the type of primary radiation used, the experimental geometry, and the diffusional properties of the molecules under investigation. This way different experimental systems with varying, inhomogeneous energy deposit characteristics become comparable with each other, which is not possible when only macroscopic averaged values are taken into account. In addition, the radiation protection properties of the compatible solute Ectoine was investigated. The protective properties of ectoine result from the increase of the inelastic scattering probabilities of low Energy electrons at the acoustic vibrational modes of water and its properties as OH-radical scavenger. Based on our results, further investigations are conducted to evaluate the application of Ectoine in the context of radiation therapy. Projektkennung Deutsche Forschungsgemeinschaft (DFG) - Projektnummer 245767821 KW - Ectoin KW - Ectoine KW - DNS KW - DNA KW - Cancer therapy KW - DNA damage KW - DNA radiation damage KW - Dosimetry KW - DFG KW - Electron irradiation KW - Ectoine DNA interaction KW - Ectoine radiation protection KW - Hydroxyl radicals KW - OH radicals KW - LEE KW - Low energy electrons KW - Microdosimetry KW - Radiation KW - Geant4 KW - Geant4-DNA KW - Radiation therapy KW - LET PY - 2021 UR - https://gepris.dfg.de/gepris/projekt/245767821/ergebnisse?context=projekt&task=showDetail&id=245767821&selectedSubTab=2& SP - 1 EP - 14 AN - OPUS4-52389 LA - deu AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -