@article{RibarHuberSmialeketal.2018, author = {Ribar, Anita and Huber, Stefan E. and Smialek, Malgorzata A. and Tanzer, Katrin and Neustetter, Michael and Sch{\"u}rmann, Robin and Bald, Ilko and Denifl, Stephan}, title = {Hydroperoxyl radical and formic acid formation from common DNA stabilizers upon low energy electron attachment}, series = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, volume = {20}, journal = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, number = {8}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9076}, doi = {10.1039/c7cp07697e}, pages = {5578 -- 5585}, year = {2018}, abstract = {2-Amino-2-(hydroxymethyl)-1,3-propanediol (TRIS) and ethylenediaminetetraacetic acid ( EDTA) are key components of biological buffers and are frequently used as DNA stabilizers in irradiation studies. Such surface or liquid phase studies are done with the aim to understand the fundamental mechanisms of DNA radiation damage and to improve cancer radiotherapy. When ionizing radiation is used, abundant secondary electrons are formed during the irradiation process, which are able to attach to the molecular compounds present on the surface. In the present study we experimentally investigate low energy electron attachment to TRIS and methyliminodiacetic acid ( MIDA), an analogue of EDTA, supported by quantum chemical calculations. The most prominent dissociation channel for TRIS is through hydroperoxyl radical formation, whereas the dissociation of MIDA results in the formation of formic and acetic acid. These compounds are well-known to cause DNA modifications, like strand breaks. The present results indicate that buffer compounds may not have an exclusive protecting effect on DNA as suggested previously.}, language = {en} } @article{RackwitzBald2018, author = {Rackwitz, Jenny and Bald, Ilko}, title = {Low-energy electron-induced strand breaks in telomere-derived DNA sequences}, series = {Chemistry - a European journal}, volume = {24}, journal = {Chemistry - a European journal}, number = {18}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {0947-6539}, doi = {10.1002/chem.201705889}, pages = {4680 -- 4688}, year = {2018}, abstract = {During cancer radiation therapy high-energy radiation is used to reduce tumour tissue. The irradiation produces a shower of secondary low-energy (<20 eV) electrons, which are able to damage DNA very efficiently by dissociative electron attachment. Recently, it was suggested that low-energy electron-induced DNA strand breaks strongly depend on the specific DNA sequence with a high sensitivity of G-rich sequences. Here, we use DNA origami platforms to expose G-rich telomere sequences to low-energy (8.8 eV) electrons to determine absolute cross sections for strand breakage and to study the influence of sequence modifications and topology of telomeric DNA on the strand breakage. We find that the telomeric DNA 5′-(TTA GGG)2 is more sensitive to low-energy electrons than an intermixed sequence 5′-(TGT GTG A)2 confirming the unique electronic properties resulting from G-stacking. With increasing length of the oligonucleotide (i.e., going from 5′-(GGG ATT)2 to 5′-(GGG ATT)4), both the variety of topology and the electron-induced strand break cross sections increase. Addition of K+ ions decreases the strand break cross section for all sequences that are able to fold G-quadruplexes or G-intermediates, whereas the strand break cross section for the intermixed sequence remains unchanged. These results indicate that telomeric DNA is rather sensitive towards low-energy electron-induced strand breakage suggesting significant telomere shortening that can also occur during cancer radiation therapy.}, language = {en} } @article{MeilingSchuermannVogeletal.2018, author = {Meiling, Till Thomas and Sch{\"u}rmann, Robin Mathis and Vogel, Stefanie and Ebel, Kenny and Nicolas, Christophe and Milosavljevic, Aleksandar R. and Bald, Ilko}, title = {Photophysics and Chemistry of Nitrogen-Doped Carbon Nanodots with High Photoluminescence Quantum Yield}, series = {The journal of physical chemistry : C, Nanomaterials and interfaces}, volume = {122}, journal = {The journal of physical chemistry : C, Nanomaterials and interfaces}, number = {18}, publisher = {American Chemical Society}, address = {Washington}, issn = {1932-7447}, doi = {10.1021/acs.jpcc.8b00748}, pages = {10217 -- 10230}, year = {2018}, abstract = {Fluorescent carbon nanodots (CNDs) are very promising nanomaterials for a broad range of applications because of their high photostability, presumed selective luminescence, and low cost at which they can be produced. In this respect, CNDs are superior to well-established semiconductor quantum dots and organic dyes. However, reported synthesis protocols for CNDs typically lead to low photoluminescence quantum yield (PLQY) and low reproducibility, resulting in a poor understanding of the CND chemistry and photophysics. Here, we report a one-step synthesis of nitrogen-doped carbon nanodots (N-CNDs) from various carboxylic acids, Tris, and ethylenediaminetetraacetic acid resulting in high PLQY of up to 90\%. The reaction conditions in terms of starting materials, temperature, and reaction time are carefully optimized and their influence on the photophysical properties is characterized. We find that citric acid-derived N-CNDs can result in a very high PLQY of 90\%, but they do not show selective luminescence. By contrast, acetic acid-derived N-CNDs show selective luminescence but a PLQY of 50\%. The chemical composition of the surface and core of these two selected N-CND types is characterized among others by high-resolution synchrotron X-ray photoelectron spectroscopy using single isolated N-CND clusters. The results indicate that photoexcitation occurs in the N-CND core, whereas the emission properties are determined by the N-CND surface groups.}, language = {en} } @article{HeckKanehiraKneippetal.2018, author = {Heck, Christian and Kanehira, Yuya and Kneipp, Janina and Bald, Ilko}, title = {Placement of Single Proteins within the SERS Hot Spots of Self-Assembled Silver Nanolenses}, series = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition}, volume = {57}, journal = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition}, number = {25}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {1433-7851}, doi = {10.1002/anie.201801748}, pages = {7444 -- 7447}, year = {2018}, abstract = {This study demonstrates the bottom-up synthesis of silver nanolenses. A robust coating protocol enabled the functionalization of differently sized silver nanoparticles with DNA single strands of orthogonal sequence. Coated particles 10nm, 20nm, and 60nm in diameter were self-assembled by DNA origami scaffolds to form silver nanolenses. Single molecules of the protein streptavidin were selectively placed in the gap of highest electric field enhancement. Streptavidin labelled with alkyne groups served as model analyte in surface-enhanced Raman scattering (SERS) experiments. By correlated Raman mapping and atomic force microscopy, SERS signals of the alkyne labels of a single streptavidin molecule, from a single silver nanolens, were detected. The discrete, self-similar aggregates of solid silver nanoparticles are promising for plasmonic applications.}, language = {en} } @article{ChoiKotthoffOlejkoetal.2018, author = {Choi, Youngeun and Kotthoff, Lisa and Olejko, Lydia and Resch-Genger, Ute and Bald, Ilko}, title = {DNA origami-based forster resonance energy-transfer Nanoarrays and their application as ratiometric sensors}, series = {ACS applied materials \& interfaces}, volume = {10}, journal = {ACS applied materials \& interfaces}, number = {27}, publisher = {American Chemical Society}, address = {Washington}, issn = {1944-8244}, doi = {10.1021/acsami.8b03585}, pages = {23295 -- 23302}, year = {2018}, abstract = {DNA origami nanostructures provide a platform where dye molecules can be arranged with nanoscale accuracy allowing to assemble multiple fluorophores without dye-dye aggregation. Aiming to develop a bright and sensitive ratiometric sensor system, we systematically studied the optical properties of nanoarrays of dyes built on DNA origami platforms using a DNA template that provides a high versatility of label choice at minimum cost. The dyes are arranged at distances, at which they efficiently interact by Forster resonance energy transfer (FRET). To optimize array brightness, the FRET efficiencies between the donor fluorescein (FAM) and the acceptor cyanine 3 were determined for different sizes of the array and for different arrangements of the dye molecules within the array. By utilizing nanoarrays providing optimum FRET efficiency and brightness, we subsequently designed a ratiometric pH nanosensor using coumarin 343 as a pH-inert FRET donor and FAM as a pH responsive acceptor. Our results indicate that the sensitivity of a ratiometric sensor can be improved simply by arranging the dyes into a well-defined array. The dyes used here can be easily replaced by other analyte-responsive dyes, demonstrating the huge potential of DNA nanotechnology for light harvesting, signal enhancement, and sensing schemes in life sciences.}, language = {en} } @article{SchuermannVogelEbeletal.2018, author = {Sch{\"u}rmann, Robin Mathis and Vogel, Stefanie and Ebel, Kenny and Bald, Ilko}, title = {The physico-chemical basis of DNA radiosensitization}, series = {Chemistry - a European journal}, volume = {24}, journal = {Chemistry - a European journal}, number = {41}, publisher = {Wiley-VCH}, address = {Weinheim}, issn = {0947-6539}, doi = {10.1002/chem.201800804}, pages = {10271 -- 10279}, year = {2018}, abstract = {High-energy radiation is used in combination with radiosensitizing therapeutics to treat cancer. The most common radiosensitizers are halogenated nucleosides and cisplatin derivatives, and recently also metal nanoparticles have been suggested as potential radiosensitizing agents. The radiosensitizing action of these compounds can at least partly be ascribed to an enhanced reactivity towards secondary low-energy electrons generated along the radiation track of the high-energy primary radiation, or to an additional emission of secondary reactive electrons close to the tumor tissue. This is referred to as physico-chemical radiosensitization. In this Concept article we present current experimental methods used to study fundamental processes of physico-chemical radiosensitization and discuss the most relevant classes of radiosensitizers. Open questions in the current discussions are identified and future directions outlined, which can lead to optimized treatment protocols or even novel therapeutic concepts.}, language = {en} } @article{RuehlmannBuecheleOstermannetal.2018, author = {R{\"u}hlmann, Madlen and B{\"u}chele, Dominique and Ostermann, Markus and Bald, Ilko and Schmid, Thomas}, title = {Challenges in the quantification of nutrients in soils using laser-induced breakdown spectroscopy}, series = {Spectrochimica Acta Part B: Atomic Spectroscopy}, volume = {146}, journal = {Spectrochimica Acta Part B: Atomic Spectroscopy}, publisher = {Elsevier}, address = {Oxford}, issn = {0584-8547}, doi = {10.1016/j.sab.2018.05.003}, pages = {115 -- 121}, year = {2018}, abstract = {The quantification of the elemental content in soils with laser-induced breakdown spectroscopy (LIBS) is challenging because of matrix effects strongly influencing the plasma formation and LIBS signal. Furthermore, soil heterogeneity at the micrometre scale can affect the accuracy of analytical results. In this paper, the impact of univariate and multivariate data evaluation approaches on the quantification of nutrients in soil is discussed. Exemplarily, results for calcium are shown, which reflect trends also observed for other elements like magnesium, silicon and iron. For the calibration models, 16 certified reference soils were used. With univariate and multivariate approaches, the calcium mass fractions in 60 soils from different testing grounds in Germany were calculated. The latter approach consisted of a principal component analysis (PCA) of adequately pre-treated data for classification and identification of outliers, followed by partial least squares regression (PLSR) for quantification. For validation, the soils were also characterised with inductively coupled plasma optical emission spectroscopy (ICP OES) and X-ray fluorescence (XRF) analysis. Deviations between the LIBS quantification results and the reference analytical results are discussed.}, language = {en} } @misc{HeckMichaeliBaldetal.2018, author = {Heck, Christian and Michaeli, Yael and Bald, Ilko and Ebenstein, Yuval}, title = {Analytical epigenetics}, series = {Current Opinion in Biotechnology}, volume = {55}, journal = {Current Opinion in Biotechnology}, publisher = {Elsevier}, address = {London}, issn = {0958-1669}, doi = {10.1016/j.copbio.2018.09.006}, pages = {151 -- 158}, year = {2018}, abstract = {The field of epigenetics describes the relationship between genotype and phenotype, by regulating gene expression without changing the canonical base sequence of DNA. It deals with molecular genomic information that is encoded by a rich repertoire of chemical modifications and molecular interactions. This regulation involves DNA, RNA and proteins that are enzymatically tagged with small molecular groups that alter their physical and chemical properties. It is now clear that epigenetic alterations are involved in development and disease, and thus, are the focus of intensive research. The ability to record epigenetic changes and quantify them in rare medical samples is critical for next generation diagnostics. Optical detection offers the ultimate single-molecule sensitivity and the potential for spectral multiplexing. Here we review recent progress in ultrasensitive optical detection of DNA and histone modifications.}, language = {en} } @book{BechmannBald2018, author = {Bechmann, Wolfgang and Bald, Ilko}, title = {Einstieg in die Physikalische Chemie f{\"u}r Naturwissenschaftler}, series = {Studienb{\"u}cher Chemie Lehrbuch}, journal = {Studienb{\"u}cher Chemie Lehrbuch}, edition = {6}, publisher = {Springer}, address = {Berlin}, isbn = {978-3-662-55857-7}, publisher = {Universit{\"a}t Potsdam}, pages = {492}, year = {2018}, abstract = {Mit einer ausgewogenen Stoffauswahl aus den Teilgebieten Chemische Thermodynamik, Reaktionskinetik und Elektrochemie wird der Leser an das Studium der Physikalischen Chemie herangef{\"u}hrt. Das Verst{\"a}ndnis der Theorie wird durch zahlreiche Aufgabenstellungen und die Angabe ihrer L{\"o}sungswege erleichtert. Das Buch gibt dem Studenten dar{\"u}ber hinaus Anregungen f{\"u}r ausgew{\"a}hlte Experimente zu den behandelten Teilgebieten, mit denen sich ein Grundverst{\"a}ndnis physikalisch-chemischer Zusammenh{\"a}nge entwickeln l{\"a}sst.}, language = {de} }