@article{KellerRackwitzCauetetal.2014, author = {Keller, Adrian and Rackwitz, Jenny and Cauet, Emilie and Lievin, Jacques and K{\"o}rzd{\"o}rfer, Thomas and Rotaru, Alexandru and Gothelf, Kurt V. and Besenbacher, Flemming and Bald, Ilko}, title = {Sequence dependence of electron-induced DNA strand breakage revealed by DNA nanoarrays}, series = {Scientific reports}, volume = {4}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep07391}, pages = {6}, year = {2014}, language = {en} } @misc{BaldKopyraKeller2014, author = {Bald, Ilko and Kopyra, Janina and Keller, Adrian}, title = {On the role of fluoro-substituted nucleosides in DNA radiosensitization for tumor radiation therapy}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-73412}, pages = {6825 -- 6829}, year = {2014}, abstract = {Gemcitabine (2′,2′-difluorocytidine) is a well-known radiosensitizer routinely applied in concomitant chemoradiotherapy. During irradiation of biological media with high-energy radiation secondary low-energy (<10 eV) electrons are produced that can directly induce chemical bond breakage in DNA by dissociative electron attachment (DEA). Here, we investigate and compare DEA to the three molecules 2′-deoxycytidine, 2′-deoxy-5-fluorocytidine, and gemcitabine. Fluorination at specific molecular sites, i.e., nucleobase or sugar moiety, is found to control electron attachment and subsequent dissociation pathways. The presence of two fluorine atoms at the sugar ring results in more efficient electron attachment to the sugar moiety and subsequent bond cleavage. For the formation of the dehydrogenated nucleobase anion, we obtain an enhancement factor of 2.8 upon fluorination of the sugar, whereas the enhancement factor is 5.5 when the nucleobase is fluorinated. The observed fragmentation reactions suggest enhanced DNA strand breakage induced by secondary electrons when gemcitabine is incorporated into DNA.}, language = {en} } @article{BaldKellerKopyra2014, author = {Bald, Ilko and Keller, Adrian and Kopyra, Janina}, title = {On the role of fluoro-substituted nucleosides in DNA radiosensitization for tumor radiation therapy}, series = {RSC Advances : an international journal to further the chemical sciences}, volume = {4}, journal = {RSC Advances : an international journal to further the chemical sciences}, number = {13}, publisher = {Royal Society of Chemistry}, issn = {2046-2069}, doi = {10.1039/C3RA46735J}, pages = {6825 -- 6829}, year = {2014}, abstract = {Gemcitabine (2′,2′-difluorocytidine) is a well-known radiosensitizer routinely applied in concomitant chemoradiotherapy. During irradiation of biological media with high-energy radiation secondary low-energy (<10 eV) electrons are produced that can directly induce chemical bond breakage in DNA by dissociative electron attachment (DEA). Here, we investigate and compare DEA to the three molecules 2′-deoxycytidine, 2′-deoxy-5-fluorocytidine, and gemcitabine. Fluorination at specific molecular sites, i.e., nucleobase or sugar moiety, is found to control electron attachment and subsequent dissociation pathways. The presence of two fluorine atoms at the sugar ring results in more efficient electron attachment to the sugar moiety and subsequent bond cleavage. For the formation of the dehydrogenated nucleobase anion, we obtain an enhancement factor of 2.8 upon fluorination of the sugar, whereas the enhancement factor is 5.5 when the nucleobase is fluorinated. The observed fragmentation reactions suggest enhanced DNA strand breakage induced by secondary electrons when gemcitabine is incorporated into DNA.}, language = {en} } @misc{BaldKeller2014, author = {Bald, Ilko and Keller, Adrian}, title = {Molecular processes studied at a single-molecule level using DNA origami nanostructures and atomic force microscopy}, series = {Molecules}, volume = {19}, journal = {Molecules}, number = {9}, publisher = {MDPI}, address = {Basel}, issn = {1420-3049}, doi = {10.3390/molecules190913803}, pages = {13803 -- 13823}, year = {2014}, abstract = {DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM) which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates.}, language = {en} } @misc{BaldKeller2014, author = {Bald, Ilko and Keller, Adrian}, title = {Molecular processes studied at a single-molecule level using DNA origami nanostructures and atomic force microscopy}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {9}, issn = {1866-8372}, doi = {10.25932/publishup-47584}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-475843}, pages = {13803 -- 13823}, year = {2014}, abstract = {DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM) which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates.}, language = {en} } @article{KellerKopyraGothelfetal.2013, author = {Keller, Adrian and Kopyra, Janina and Gothelf, Kurt V. and Bald, Ilko}, title = {Electron-induced damage of biotin studied in the gas phase and in the condensed phase at a single-molecule level}, series = {New journal of physics : the open-access journal for physics}, volume = {15}, journal = {New journal of physics : the open-access journal for physics}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1367-2630}, doi = {10.1088/1367-2630/15/8/083045}, pages = {14}, year = {2013}, abstract = {Biotin is an essential vitamin that is, on the one hand, relevant for the metabolism, gene expression and in the cellular response to DNA damage and, on the other hand, finds numerous applications in biotechnology. The functionality of biotin is due to two particular sub-structures, the ring structure and the side chain with carboxyl group. The heterocyclic ring structure results in the capability of biotin to form strong intermolecular hydrogen and van der Waals bonds with proteins such as streptavidin, whereas the carboxyl group can be employed to covalently bind biotin to other complex molecules. Dissociative electron attachment (DEA) to biotin results in a decomposition of the ring structure and the carboxyl group, respectively, within resonant features in the energy range 0-12 eV, thereby preventing the capability of biotin for intermolecular binding and covalent coupling to other molecules. Specifically, the fragment anions (M-H)(-), (M-O)(-), C3N2O-, CH2O2-, OCN-, CN-, OH- and O- are observed, and exemplarily the DEA cross section of OCN- formation is determined to be 3 x 10(-19) cm(2). To study the response of biotin to electrons within a complex condensed environment, we use the DNA origami technique and determine a dissociation yield of (1.1 +/- 0.2) x 10(-14) cm(2) at 18 eV electron energy, which represents the most relevant energy for biomolecular damage induced by secondary electrons. The present results thus have important implications for the use of biotin as a label in radiation experiments.}, language = {en} } @article{KielarXinXuetal.2019, author = {Kielar, Charlotte and Xin, Yang and Xu, Xiaodan and Zhu, Siqi and Gorin, Nelli and Grundmeier, Guido and M{\"o}ser, Christin and Smith, David M. and Keller, Adrian}, title = {Effect of staple age on DNA origami nanostructure assembly and stability}, series = {Molecules}, volume = {24}, journal = {Molecules}, number = {14}, publisher = {MDPI}, address = {Basel}, issn = {1420-3049}, doi = {10.3390/molecules24142577}, pages = {12}, year = {2019}, abstract = {DNA origami nanostructures are widely employed in various areas of fundamental and applied research. Due to the tremendous success of the DNA origami technique in the academic field, considerable efforts currently aim at the translation of this technology from a laboratory setting to real-world applications, such as nanoelectronics, drug delivery, and biosensing. While many of these real-world applications rely on an intact DNA origami shape, they often also subject the DNA origami nanostructures to rather harsh and potentially damaging environmental and processing conditions. Furthermore, in the context of DNA origami mass production, the long-term storage of DNA origami nanostructures or their pre-assembled components also becomes an issue of high relevance, especially regarding the possible negative effects on DNA origami structural integrity. Thus, we investigated the effect of staple age on the self-assembly and stability of DNA origami nanostructures using atomic force microscopy. Different harsh processing conditions were simulated by applying different sample preparation protocols. Our results show that staple solutions may be stored at -20 degrees C for several years without impeding DNA origami self-assembly. Depending on DNA origami shape and superstructure, however, staple age may have negative effects on DNA origami stability under harsh treatment conditions. Mass spectrometry analysis of the aged staple mixtures revealed no signs of staple fragmentation. We, therefore, attribute the increased DNA origami sensitivity toward environmental conditions to an accumulation of damaged nucleobases, which undergo weaker base-pairing interactions and thus lead to reduced duplex stability.}, language = {en} } @article{PrinzSchreiberOlejkoetal.2013, author = {Prinz, Julia and Schreiber, Benjamin and Olejko, Lydia and Oertel, Jana and Rackwitz, Jenny and Keller, Adrian and Bald, Ilko}, title = {DNA origami substrates for highly sensitive surface-enhanced raman scattering}, series = {The journal of physical chemistry letters}, volume = {4}, journal = {The journal of physical chemistry letters}, number = {23}, publisher = {American Chemical Society}, address = {Washington}, issn = {1948-7185}, doi = {10.1021/jz402076b}, pages = {4140 -- 4145}, year = {2013}, abstract = {DNA nanotechnology holds great promise for the fabrication of novel plasmonic nanostructures and the potential to carry out single-molecule measurements using optical spectroscopy. Here, we demonstrate for the first time that DNA origami nanostructures can be exploited as substrates for surface-enhanced Raman scattering (SERS). Gold nanoparticles (AuNPs) have been arranged into dimers to create intense Raman scattering hot spots in the interparticle gaps. AuNPs (15 nm) covered with TAMRA-modified DNA have been placed at a nominal distance of 25 nm to demonstrate the formation of Raman hot spots. To control the plasmonic coupling between the nanoparticles and thus the field enhancement in the hot spot, the size of AuNPs has been varied from 5 to 28 nm by electroless Au deposition. By the precise positioning of a specific number of TAMRA molecules in these hot spots, SERS with the highest sensitivity down to the few-molecule level is obtained.}, language = {en} } @article{OertelKellerPrinzetal.2016, author = {Oertel, Jana and Keller, Adrian and Prinz, Julia and Schreiber, Benjamin and Huebner, Rene and Kerbusch, Jochen and Bald, Ilko and Fahmy, Karim}, title = {Anisotropic metal growth on phospholipid nanodiscs via lipid bilayer expansion}, series = {Scientific reports}, volume = {6}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep26718}, pages = {9}, year = {2016}, abstract = {Self-assembling biomolecules provide attractive templates for the preparation of metallic nanostructures. However, the intuitive transfer of the "outer shape" of the assembled macromolecules to the final metallic particle depends on the intermolecular forces among the biomolecules which compete with interactions between template molecules and the metal during metallization. The shape of the bio-template may thus be more dynamic than generally assumed. Here, we have studied the metallization of phospholipid nanodiscs which are discoidal particles of similar to 10 nm diameter containing a lipid bilayer similar to 5 nm thick. Using negatively charged lipids, electrostatic adsorption of amine-coated Au nanoparticles was achieved and followed by electroless gold deposition. Whereas Au nanoparticle adsorption preserves the shape of the bio-template, metallization proceeds via invasion of Au into the hydrophobic core of the nanodisc. Thereby, the lipidic phase induces a lateral growth that increases the diameter but not the original thickness of the template. Infrared spectroscopy reveals lipid expansion and suggests the existence of internal gaps in the metallized nanodiscs, which is confirmed by surface-enhanced Raman scattering from the encapsulated lipids. Interference of metallic growth with non-covalent interactions can thus become itself a shape-determining factor in the metallization of particularly soft and structurally anisotropic biomaterials.}, language = {en} }