--- _id: '46023' abstract: - lang: eng text: This article presents the potential-dependent adsorption of two proteins, bovine serum albumin (BSA) and lysozyme (LYZ), on Ti6Al4V alloy at pH 7.4 and 37 °C. The adsorption process was studied on an electropolished alloy under cathodic and anodic overpotentials, compared to the open circuit potential (OCP). To analyze the adsorption process, various complementary interface analytical techniques were employed, including PM-IRRAS (polarization-modulation infrared reflection-absorption spectroscopy), AFM (atomic force microscopy), XPS (X-ray photoelectron spectroscopy), and E-QCM (electrochemical quartz crystal microbalance) measurements. The polarization experiments were conducted within a potential range where charging of the electric double layer dominates, and Faradaic currents can be disregarded. The findings highlight the significant influence of the interfacial charge distribution on the adsorption of BSA and LYZ onto the alloy surface. Furthermore, electrochemical analysis of the protein layers formed under applied overpotentials demonstrated improved corrosion protection properties. These studies provide valuable insights into protein adsorption on titanium alloys under physiological conditions, characterized by varying potentials of the passive alloy. article_number: '5109' author: - first_name: Belma full_name: Duderija, Belma last_name: Duderija - first_name: Alejandro full_name: González-Orive, Alejandro last_name: González-Orive - first_name: Christoph full_name: Ebbert, Christoph last_name: Ebbert - first_name: Vanessa full_name: Neßlinger, Vanessa last_name: Neßlinger - first_name: Adrian full_name: Keller, Adrian last_name: Keller - first_name: Guido full_name: Grundmeier, Guido last_name: Grundmeier citation: ama: Duderija B, González-Orive A, Ebbert C, Neßlinger V, Keller A, Grundmeier G. Electrode Potential-Dependent Studies of Protein Adsorption on Ti6Al4V Alloy. Molecules. 2023;28(13). doi:10.3390/molecules28135109 apa: Duderija, B., González-Orive, A., Ebbert, C., Neßlinger, V., Keller, A., & Grundmeier, G. (2023). Electrode Potential-Dependent Studies of Protein Adsorption on Ti6Al4V Alloy. Molecules, 28(13), Article 5109. https://doi.org/10.3390/molecules28135109 bibtex: '@article{Duderija_González-Orive_Ebbert_Neßlinger_Keller_Grundmeier_2023, title={Electrode Potential-Dependent Studies of Protein Adsorption on Ti6Al4V Alloy}, volume={28}, DOI={10.3390/molecules28135109}, number={135109}, journal={Molecules}, publisher={MDPI AG}, author={Duderija, Belma and González-Orive, Alejandro and Ebbert, Christoph and Neßlinger, Vanessa and Keller, Adrian and Grundmeier, Guido}, year={2023} }' chicago: Duderija, Belma, Alejandro González-Orive, Christoph Ebbert, Vanessa Neßlinger, Adrian Keller, and Guido Grundmeier. “Electrode Potential-Dependent Studies of Protein Adsorption on Ti6Al4V Alloy.” Molecules 28, no. 13 (2023). https://doi.org/10.3390/molecules28135109. ieee: 'B. Duderija, A. González-Orive, C. Ebbert, V. Neßlinger, A. Keller, and G. Grundmeier, “Electrode Potential-Dependent Studies of Protein Adsorption on Ti6Al4V Alloy,” Molecules, vol. 28, no. 13, Art. no. 5109, 2023, doi: 10.3390/molecules28135109.' mla: Duderija, Belma, et al. “Electrode Potential-Dependent Studies of Protein Adsorption on Ti6Al4V Alloy.” Molecules, vol. 28, no. 13, 5109, MDPI AG, 2023, doi:10.3390/molecules28135109. short: B. Duderija, A. González-Orive, C. Ebbert, V. Neßlinger, A. Keller, G. Grundmeier, Molecules 28 (2023). date_created: 2023-07-12T07:55:40Z date_updated: 2024-02-06T12:33:55Z department: - _id: '321' - _id: '302' doi: 10.3390/molecules28135109 intvolume: ' 28' issue: '13' keyword: - Chemistry (miscellaneous) - Analytical Chemistry - Organic Chemistry - Physical and Theoretical Chemistry - Molecular Medicine - Drug Discovery - Pharmaceutical Science language: - iso: eng publication: Molecules publication_identifier: issn: - 1420-3049 publication_status: published publisher: MDPI AG status: public title: Electrode Potential-Dependent Studies of Protein Adsorption on Ti6Al4V Alloy type: journal_article user_id: '54863' volume: 28 year: '2023' ... --- _id: '45828' abstract: - lang: eng text: This article presents the potential-dependent adsorption of two proteins, bovine serum albumin (BSA) and lysozyme (LYZ), on Ti6Al4V alloy at pH 7.4 and 37 °C. The adsorption process was studied on an electropolished alloy under cathodic and anodic overpotentials, compared to the open circuit potential (OCP). To analyze the adsorption process, various complementary interface analytical techniques were employed, including PM-IRRAS (polarization-modulation infrared reflection-absorption spectroscopy), AFM (atomic force microscopy), XPS (X-ray photoelectron spectroscopy), and E-QCM (electrochemical quartz crystal microbalance) measurements. The polarization experiments were conducted within a potential range where charging of the electric double layer dominates, and Faradaic currents can be disregarded. The findings highlight the significant influence of the interfacial charge distribution on the adsorption of BSA and LYZ onto the alloy surface. Furthermore, electrochemical analysis of the protein layers formed under applied overpotentials demonstrated improved corrosion protection properties. These studies provide valuable insights into protein adsorption on titanium alloys under physiological conditions, characterized by varying potentials of the passive alloy. author: - first_name: Belma full_name: Duderija, Belma id: '54863' last_name: Duderija - first_name: Alejandro full_name: González-Orive, Alejandro last_name: González-Orive - first_name: Christoph full_name: Ebbert, Christoph id: '7266' last_name: Ebbert - first_name: Vanessa full_name: Neßlinger, Vanessa last_name: Neßlinger - first_name: Adrian full_name: Keller, Adrian id: '48864' last_name: Keller orcid: 0000-0001-7139-3110 - first_name: Guido full_name: Grundmeier, Guido id: '194' last_name: Grundmeier citation: ama: Duderija B, González-Orive A, Ebbert C, Neßlinger V, Keller A, Grundmeier G. Electrode Potential-Dependent Studies of Protein Adsorption on Ti6Al4V Alloy. Molecules. 2023;28(13):5109. doi:10.3390/molecules28135109 apa: Duderija, B., González-Orive, A., Ebbert, C., Neßlinger, V., Keller, A., & Grundmeier, G. (2023). Electrode Potential-Dependent Studies of Protein Adsorption on Ti6Al4V Alloy. Molecules, 28(13), 5109. https://doi.org/10.3390/molecules28135109 bibtex: '@article{Duderija_González-Orive_Ebbert_Neßlinger_Keller_Grundmeier_2023, title={Electrode Potential-Dependent Studies of Protein Adsorption on Ti6Al4V Alloy}, volume={28}, DOI={10.3390/molecules28135109}, number={13}, journal={Molecules}, publisher={MDPI AG}, author={Duderija, Belma and González-Orive, Alejandro and Ebbert, Christoph and Neßlinger, Vanessa and Keller, Adrian and Grundmeier, Guido}, year={2023}, pages={5109} }' chicago: 'Duderija, Belma, Alejandro González-Orive, Christoph Ebbert, Vanessa Neßlinger, Adrian Keller, and Guido Grundmeier. “Electrode Potential-Dependent Studies of Protein Adsorption on Ti6Al4V Alloy.” Molecules 28, no. 13 (2023): 5109. https://doi.org/10.3390/molecules28135109.' ieee: 'B. Duderija, A. González-Orive, C. Ebbert, V. Neßlinger, A. Keller, and G. Grundmeier, “Electrode Potential-Dependent Studies of Protein Adsorption on Ti6Al4V Alloy,” Molecules, vol. 28, no. 13, p. 5109, 2023, doi: 10.3390/molecules28135109.' mla: Duderija, Belma, et al. “Electrode Potential-Dependent Studies of Protein Adsorption on Ti6Al4V Alloy.” Molecules, vol. 28, no. 13, MDPI AG, 2023, p. 5109, doi:10.3390/molecules28135109. short: B. Duderija, A. González-Orive, C. Ebbert, V. Neßlinger, A. Keller, G. Grundmeier, Molecules 28 (2023) 5109. date_created: 2023-07-03T08:06:28Z date_updated: 2023-07-03T08:07:55Z department: - _id: '302' doi: 10.3390/molecules28135109 intvolume: ' 28' issue: '13' keyword: - Chemistry (miscellaneous) - Analytical Chemistry - Organic Chemistry - Physical and Theoretical Chemistry - Molecular Medicine - Drug Discovery - Pharmaceutical Science language: - iso: eng page: '5109' publication: Molecules publication_identifier: issn: - 1420-3049 publication_status: published publisher: MDPI AG status: public title: Electrode Potential-Dependent Studies of Protein Adsorption on Ti6Al4V Alloy type: journal_article user_id: '48864' volume: 28 year: '2023' ... --- _id: '46542' abstract: - lang: eng text: Multiprotein adsorption from complex body fluids represents a highly important and complicated phenomenon in medicine. In this work, multiprotein adsorption from diluted human serum at gold and oxidized iron surfaces is investigated at different serum concentrations and pH values. Adsorption-induced changes in surface topography and the total amount of adsorbed proteins are quantified by atomic force microscopy (AFM) and polarization-modulation infrared reflection absorption spectroscopy (PM-IRRAS), respectively. For both surfaces, stronger protein adsorption is observed at pH 6 compared to pH 7 and pH 8. PM-IRRAS furthermore provides some qualitative insights into the pH-dependent alterations in the composition of the adsorbed multiprotein films. Changes in the amide II/amide I band area ratio and in particular side-chain IR absorption suggest that the increased adsorption at pH 6 is accompanied by a change in protein film composition. Presumably, this is mostly driven by the adsorption of human serum albumin, which at pH 6 adsorbs more readily and thereby replaces other proteins with lower surface affinities in the resulting multiprotein film. article_number: '6060' author: - first_name: Jingyuan full_name: Huang, Jingyuan last_name: Huang - first_name: Yunshu full_name: Qiu, Yunshu last_name: Qiu - first_name: Felix full_name: Lücke, Felix last_name: Lücke - first_name: Jiangling full_name: Su, Jiangling last_name: Su - first_name: Guido full_name: Grundmeier, Guido id: '194' last_name: Grundmeier - first_name: Adrian full_name: Keller, Adrian id: '48864' last_name: Keller orcid: 0000-0001-7139-3110 citation: ama: Huang J, Qiu Y, Lücke F, Su J, Grundmeier G, Keller A. Multiprotein Adsorption from Human Serum at Gold and Oxidized Iron Surfaces Studied by Atomic Force Microscopy and Polarization-Modulation Infrared Reflection Absorption Spectroscopy. Molecules. 2023;28(16). doi:10.3390/molecules28166060 apa: Huang, J., Qiu, Y., Lücke, F., Su, J., Grundmeier, G., & Keller, A. (2023). Multiprotein Adsorption from Human Serum at Gold and Oxidized Iron Surfaces Studied by Atomic Force Microscopy and Polarization-Modulation Infrared Reflection Absorption Spectroscopy. Molecules, 28(16), Article 6060. https://doi.org/10.3390/molecules28166060 bibtex: '@article{Huang_Qiu_Lücke_Su_Grundmeier_Keller_2023, title={Multiprotein Adsorption from Human Serum at Gold and Oxidized Iron Surfaces Studied by Atomic Force Microscopy and Polarization-Modulation Infrared Reflection Absorption Spectroscopy}, volume={28}, DOI={10.3390/molecules28166060}, number={166060}, journal={Molecules}, publisher={MDPI AG}, author={Huang, Jingyuan and Qiu, Yunshu and Lücke, Felix and Su, Jiangling and Grundmeier, Guido and Keller, Adrian}, year={2023} }' chicago: Huang, Jingyuan, Yunshu Qiu, Felix Lücke, Jiangling Su, Guido Grundmeier, and Adrian Keller. “Multiprotein Adsorption from Human Serum at Gold and Oxidized Iron Surfaces Studied by Atomic Force Microscopy and Polarization-Modulation Infrared Reflection Absorption Spectroscopy.” Molecules 28, no. 16 (2023). https://doi.org/10.3390/molecules28166060. ieee: 'J. Huang, Y. Qiu, F. Lücke, J. Su, G. Grundmeier, and A. Keller, “Multiprotein Adsorption from Human Serum at Gold and Oxidized Iron Surfaces Studied by Atomic Force Microscopy and Polarization-Modulation Infrared Reflection Absorption Spectroscopy,” Molecules, vol. 28, no. 16, Art. no. 6060, 2023, doi: 10.3390/molecules28166060.' mla: Huang, Jingyuan, et al. “Multiprotein Adsorption from Human Serum at Gold and Oxidized Iron Surfaces Studied by Atomic Force Microscopy and Polarization-Modulation Infrared Reflection Absorption Spectroscopy.” Molecules, vol. 28, no. 16, 6060, MDPI AG, 2023, doi:10.3390/molecules28166060. short: J. Huang, Y. Qiu, F. Lücke, J. Su, G. Grundmeier, A. Keller, Molecules 28 (2023). date_created: 2023-08-16T10:51:48Z date_updated: 2023-08-16T10:53:08Z department: - _id: '302' doi: 10.3390/molecules28166060 intvolume: ' 28' issue: '16' keyword: - Chemistry (miscellaneous) - Analytical Chemistry - Organic Chemistry - Physical and Theoretical Chemistry - Molecular Medicine - Drug Discovery - Pharmaceutical Science language: - iso: eng publication: Molecules publication_identifier: issn: - 1420-3049 publication_status: published publisher: MDPI AG status: public title: Multiprotein Adsorption from Human Serum at Gold and Oxidized Iron Surfaces Studied by Atomic Force Microscopy and Polarization-Modulation Infrared Reflection Absorption Spectroscopy type: journal_article user_id: '48864' volume: 28 year: '2023' ... --- _id: '63922' author: - first_name: Nargiz B. full_name: Asanbaeva, Nargiz B. last_name: Asanbaeva - first_name: Sergey A. full_name: Dobrynin, Sergey A. last_name: Dobrynin - first_name: Denis A. full_name: Morozov, Denis A. last_name: Morozov - first_name: Nadia full_name: Haro-Mares, Nadia last_name: Haro-Mares - first_name: Torsten full_name: Gutmann, Torsten id: '118165' last_name: Gutmann - first_name: Gerd full_name: Buntkowsky, Gerd last_name: Buntkowsky - first_name: Elena G. full_name: Bagryanskaya, Elena G. last_name: Bagryanskaya citation: ama: Asanbaeva NB, Dobrynin SA, Morozov DA, et al. An EPR Study on Highly Stable Nitroxyl-Nitroxyl Biradicals for Dynamic Nuclear Polarization Applications at High Magnetic Fields. Molecules. 2023;28(4):1926. doi:10.3390/molecules28041926 apa: Asanbaeva, N. B., Dobrynin, S. A., Morozov, D. A., Haro-Mares, N., Gutmann, T., Buntkowsky, G., & Bagryanskaya, E. G. (2023). An EPR Study on Highly Stable Nitroxyl-Nitroxyl Biradicals for Dynamic Nuclear Polarization Applications at High Magnetic Fields. Molecules, 28(4), 1926. https://doi.org/10.3390/molecules28041926 bibtex: '@article{Asanbaeva_Dobrynin_Morozov_Haro-Mares_Gutmann_Buntkowsky_Bagryanskaya_2023, title={An EPR Study on Highly Stable Nitroxyl-Nitroxyl Biradicals for Dynamic Nuclear Polarization Applications at High Magnetic Fields}, volume={28}, DOI={10.3390/molecules28041926}, number={4}, journal={Molecules}, author={Asanbaeva, Nargiz B. and Dobrynin, Sergey A. and Morozov, Denis A. and Haro-Mares, Nadia and Gutmann, Torsten and Buntkowsky, Gerd and Bagryanskaya, Elena G.}, year={2023}, pages={1926} }' chicago: 'Asanbaeva, Nargiz B., Sergey A. Dobrynin, Denis A. Morozov, Nadia Haro-Mares, Torsten Gutmann, Gerd Buntkowsky, and Elena G. Bagryanskaya. “An EPR Study on Highly Stable Nitroxyl-Nitroxyl Biradicals for Dynamic Nuclear Polarization Applications at High Magnetic Fields.” Molecules 28, no. 4 (2023): 1926. https://doi.org/10.3390/molecules28041926.' ieee: 'N. B. Asanbaeva et al., “An EPR Study on Highly Stable Nitroxyl-Nitroxyl Biradicals for Dynamic Nuclear Polarization Applications at High Magnetic Fields,” Molecules, vol. 28, no. 4, p. 1926, 2023, doi: 10.3390/molecules28041926.' mla: Asanbaeva, Nargiz B., et al. “An EPR Study on Highly Stable Nitroxyl-Nitroxyl Biradicals for Dynamic Nuclear Polarization Applications at High Magnetic Fields.” Molecules, vol. 28, no. 4, 2023, p. 1926, doi:10.3390/molecules28041926. short: N.B. Asanbaeva, S.A. Dobrynin, D.A. Morozov, N. Haro-Mares, T. Gutmann, G. Buntkowsky, E.G. Bagryanskaya, Molecules 28 (2023) 1926. date_created: 2026-02-07T08:57:19Z date_updated: 2026-02-20T08:12:12Z doi: 10.3390/molecules28041926 extern: '1' intvolume: ' 28' issue: '4' language: - iso: eng page: '1926' publication: Molecules publication_identifier: issn: - 1420-3049 status: public title: An EPR Study on Highly Stable Nitroxyl-Nitroxyl Biradicals for Dynamic Nuclear Polarization Applications at High Magnetic Fields type: journal_article user_id: '100715' volume: 28 year: '2023' ... --- _id: '63923' author: - first_name: Nargiz B. full_name: Asanbaeva, Nargiz B. last_name: Asanbaeva - first_name: Larisa Yu full_name: Gurskaya, Larisa Yu last_name: Gurskaya - first_name: Yuliya F. full_name: Polienko, Yuliya F. last_name: Polienko - first_name: Tatyana V. full_name: Rybalova, Tatyana V. last_name: Rybalova - first_name: Maxim S. full_name: Kazantsev, Maxim S. last_name: Kazantsev - first_name: Alexey A. full_name: Dmitriev, Alexey A. last_name: Dmitriev - first_name: Nina P. full_name: Gritsan, Nina P. last_name: Gritsan - first_name: Nadia full_name: Haro-Mares, Nadia last_name: Haro-Mares - first_name: Torsten full_name: Gutmann, Torsten id: '118165' last_name: Gutmann - first_name: Gerd full_name: Buntkowsky, Gerd last_name: Buntkowsky - first_name: Evgeny V. full_name: Tretyakov, Evgeny V. last_name: Tretyakov - first_name: Elena G. full_name: Bagryanskaya, Elena G. last_name: Bagryanskaya citation: ama: Asanbaeva NB, Gurskaya LY, Polienko YF, et al. Effects of Spiro-Cyclohexane Substitution of Nitroxyl Biradicals on Dynamic Nuclear Polarization. Molecules. 2022;27(10):3252. doi:10.3390/molecules27103252 apa: Asanbaeva, N. B., Gurskaya, L. Y., Polienko, Y. F., Rybalova, T. V., Kazantsev, M. S., Dmitriev, A. A., Gritsan, N. P., Haro-Mares, N., Gutmann, T., Buntkowsky, G., Tretyakov, E. V., & Bagryanskaya, E. G. (2022). Effects of Spiro-Cyclohexane Substitution of Nitroxyl Biradicals on Dynamic Nuclear Polarization. Molecules, 27(10), 3252. https://doi.org/10.3390/molecules27103252 bibtex: '@article{Asanbaeva_Gurskaya_Polienko_Rybalova_Kazantsev_Dmitriev_Gritsan_Haro-Mares_Gutmann_Buntkowsky_et al._2022, title={Effects of Spiro-Cyclohexane Substitution of Nitroxyl Biradicals on Dynamic Nuclear Polarization}, volume={27}, DOI={10.3390/molecules27103252}, number={10}, journal={Molecules}, author={Asanbaeva, Nargiz B. and Gurskaya, Larisa Yu and Polienko, Yuliya F. and Rybalova, Tatyana V. and Kazantsev, Maxim S. and Dmitriev, Alexey A. and Gritsan, Nina P. and Haro-Mares, Nadia and Gutmann, Torsten and Buntkowsky, Gerd and et al.}, year={2022}, pages={3252} }' chicago: 'Asanbaeva, Nargiz B., Larisa Yu Gurskaya, Yuliya F. Polienko, Tatyana V. Rybalova, Maxim S. Kazantsev, Alexey A. Dmitriev, Nina P. Gritsan, et al. “Effects of Spiro-Cyclohexane Substitution of Nitroxyl Biradicals on Dynamic Nuclear Polarization.” Molecules 27, no. 10 (2022): 3252. https://doi.org/10.3390/molecules27103252.' ieee: 'N. B. Asanbaeva et al., “Effects of Spiro-Cyclohexane Substitution of Nitroxyl Biradicals on Dynamic Nuclear Polarization,” Molecules, vol. 27, no. 10, p. 3252, 2022, doi: 10.3390/molecules27103252.' mla: Asanbaeva, Nargiz B., et al. “Effects of Spiro-Cyclohexane Substitution of Nitroxyl Biradicals on Dynamic Nuclear Polarization.” Molecules, vol. 27, no. 10, 2022, p. 3252, doi:10.3390/molecules27103252. short: N.B. Asanbaeva, L.Y. Gurskaya, Y.F. Polienko, T.V. Rybalova, M.S. Kazantsev, A.A. Dmitriev, N.P. Gritsan, N. Haro-Mares, T. Gutmann, G. Buntkowsky, E.V. Tretyakov, E.G. Bagryanskaya, Molecules 27 (2022) 3252. date_created: 2026-02-07T08:57:49Z date_updated: 2026-02-20T08:13:29Z doi: 10.3390/molecules27103252 extern: '1' intvolume: ' 27' issue: '10' language: - iso: eng page: '3252' publication: Molecules publication_identifier: issn: - 1420-3049 status: public title: Effects of Spiro-Cyclohexane Substitution of Nitroxyl Biradicals on Dynamic Nuclear Polarization type: journal_article user_id: '100715' volume: 27 year: '2022' ... --- _id: '23023' abstract: - lang: eng text: DNA origami nanostructures (DONs) are promising substrates for the single-molecule investigation of biomolecular reactions and dynamics by in situ atomic force microscopy (AFM). For this, they are typically immobilized on mica substrates by adding millimolar concentrations of Mg2+ ions to the sample solution, which enable the adsorption of the negatively charged DONs at the like-charged mica surface. These non-physiological Mg2+ concentrations, however, present a serious limitation in such experiments as they may interfere with the reactions and processes under investigation. Therefore, we here evaluate three approaches to efficiently immobilize DONs at mica surfaces under essentially Mg2+-free conditions. These approaches rely on the pre-adsorption of different multivalent cations, i.e., Ni2+, poly-l-lysine (PLL), and spermidine (Spdn). DON adsorption is studied in phosphate-buffered saline (PBS) and pure water. In general, Ni2+ shows the worst performance with heavily deformed DONs. For 2D DON triangles, adsorption at PLL- and in particular Spdn-modified mica may outperform even Mg2+-mediated adsorption in terms of surface coverage, depending on the employed solution. For 3D six-helix bundles, less pronounced differences between the individual strategies are observed. Our results provide some general guidance for the immobilization of DONs at mica surfaces under Mg2+-free conditions and may aid future in situ AFM studies. author: - first_name: Yang full_name: Xin, Yang last_name: Xin - first_name: Amir Ardalan full_name: Zargariantabrizi, Amir Ardalan last_name: Zargariantabrizi - first_name: Guido full_name: Grundmeier, Guido id: '194' last_name: Grundmeier - first_name: Adrian full_name: Keller, Adrian id: '48864' last_name: Keller orcid: 0000-0001-7139-3110 citation: ama: Xin Y, Zargariantabrizi AA, Grundmeier G, Keller A. Magnesium-Free Immobilization of DNA Origami Nanostructures at Mica Surfaces for Atomic Force Microscopy. Molecules. 2021;26:4798. doi:10.3390/molecules26164798 apa: Xin, Y., Zargariantabrizi, A. A., Grundmeier, G., & Keller, A. (2021). Magnesium-Free Immobilization of DNA Origami Nanostructures at Mica Surfaces for Atomic Force Microscopy. Molecules, 26, 4798. https://doi.org/10.3390/molecules26164798 bibtex: '@article{Xin_Zargariantabrizi_Grundmeier_Keller_2021, title={Magnesium-Free Immobilization of DNA Origami Nanostructures at Mica Surfaces for Atomic Force Microscopy}, volume={26}, DOI={10.3390/molecules26164798}, journal={Molecules}, author={Xin, Yang and Zargariantabrizi, Amir Ardalan and Grundmeier, Guido and Keller, Adrian}, year={2021}, pages={4798} }' chicago: 'Xin, Yang, Amir Ardalan Zargariantabrizi, Guido Grundmeier, and Adrian Keller. “Magnesium-Free Immobilization of DNA Origami Nanostructures at Mica Surfaces for Atomic Force Microscopy.” Molecules 26 (2021): 4798. https://doi.org/10.3390/molecules26164798.' ieee: Y. Xin, A. A. Zargariantabrizi, G. Grundmeier, and A. Keller, “Magnesium-Free Immobilization of DNA Origami Nanostructures at Mica Surfaces for Atomic Force Microscopy,” Molecules, vol. 26, p. 4798, 2021. mla: Xin, Yang, et al. “Magnesium-Free Immobilization of DNA Origami Nanostructures at Mica Surfaces for Atomic Force Microscopy.” Molecules, vol. 26, 2021, p. 4798, doi:10.3390/molecules26164798. short: Y. Xin, A.A. Zargariantabrizi, G. Grundmeier, A. Keller, Molecules 26 (2021) 4798. date_created: 2021-08-09T06:17:59Z date_updated: 2022-01-06T06:55:45Z department: - _id: '302' doi: 10.3390/molecules26164798 intvolume: ' 26' language: - iso: eng page: '4798' publication: Molecules publication_identifier: issn: - 1420-3049 publication_status: published status: public title: Magnesium-Free Immobilization of DNA Origami Nanostructures at Mica Surfaces for Atomic Force Microscopy type: journal_article user_id: '48864' volume: 26 year: '2021' ... --- _id: '19679' abstract: - lang: eng text: In the present work, we provide an electronic structure based method for the “on-the-fly” determination of vibrational sum frequency generation (v-SFG) spectra. The predictive power of this scheme is demonstrated at the air-water interface. While the instantaneous fluctuations in dipole moment are obtained using the maximally localized Wannier functions, the fluctuations in polarizability are approximated to be proportional to the second moment of Wannier functions. The spectrum henceforth obtained captures the signatures of hydrogen bond stretching, bending, as well as low-frequency librational modes. article_number: '3939' author: - first_name: Deepak full_name: Ojha, Deepak last_name: Ojha - first_name: Thomas D. full_name: Kühne, Thomas D. last_name: Kühne citation: ama: Ojha D, Kühne TD. “On-The-Fly” Calculation of the Vibrational Sum-Frequency Generation Spectrum at the Air-Water Interface. Molecules. 2020;25. doi:10.3390/molecules25173939 apa: Ojha, D., & Kühne, T. D. (2020). “On-The-Fly” Calculation of the Vibrational Sum-Frequency Generation Spectrum at the Air-Water Interface. Molecules, 25. https://doi.org/10.3390/molecules25173939 bibtex: '@article{Ojha_Kühne_2020, title={“On-The-Fly” Calculation of the Vibrational Sum-Frequency Generation Spectrum at the Air-Water Interface}, volume={25}, DOI={10.3390/molecules25173939}, number={3939}, journal={Molecules}, author={Ojha, Deepak and Kühne, Thomas D.}, year={2020} }' chicago: Ojha, Deepak, and Thomas D. Kühne. “‘On-The-Fly’ Calculation of the Vibrational Sum-Frequency Generation Spectrum at the Air-Water Interface.” Molecules 25 (2020). https://doi.org/10.3390/molecules25173939. ieee: D. Ojha and T. D. Kühne, “‘On-The-Fly’ Calculation of the Vibrational Sum-Frequency Generation Spectrum at the Air-Water Interface,” Molecules, vol. 25, 2020. mla: Ojha, Deepak, and Thomas D. Kühne. “‘On-The-Fly’ Calculation of the Vibrational Sum-Frequency Generation Spectrum at the Air-Water Interface.” Molecules, vol. 25, 3939, 2020, doi:10.3390/molecules25173939. short: D. Ojha, T.D. Kühne, Molecules 25 (2020). date_created: 2020-09-25T08:34:34Z date_updated: 2022-01-06T06:54:09Z department: - _id: '304' doi: 10.3390/molecules25173939 intvolume: ' 25' language: - iso: eng project: - _id: '52' name: Computing Resources Provided by the Paderborn Center for Parallel Computing publication: Molecules publication_identifier: issn: - 1420-3049 publication_status: published status: public title: “On-The-Fly” Calculation of the Vibrational Sum-Frequency Generation Spectrum at the Air-Water Interface type: journal_article user_id: '71692' volume: 25 year: '2020' ... --- _id: '22645' abstract: - lang: eng text: Immobile Holliday junctions represent not only the most fundamental building block of structural DNA nanotechnology but are also of tremendous importance for the in vitro investigation of genetic recombination and epigenetics. Here, we present a detailed study on the room-temperature assembly of immobile Holliday junctions with the help of the single-strand annealing protein Redβ. Individual DNA single strands are initially coated with protein monomers and subsequently hybridized to form a rigid blunt-ended four-arm junction. We investigate the efficiency of this approach for different DNA/protein ratios, as well as for different DNA sequence lengths. Furthermore, we also evaluate the potential of Redβ to anneal sticky-end modified Holliday junctions into hierarchical assemblies. We demonstrate the Redβ-mediated annealing of Holliday junction dimers, multimers, and extended networks several microns in size. While these hybrid DNA–protein nanostructures may find applications in the crystallization of DNA–protein complexes, our work shows the great potential of Redβ to aid in the synthesis of functional DNA nanostructures under mild reaction conditions. author: - first_name: Saminathan full_name: Ramakrishnan, Saminathan last_name: Ramakrishnan - first_name: Sivaraman full_name: Subramaniam, Sivaraman last_name: Subramaniam - first_name: Charlotte full_name: Kielar, Charlotte last_name: Kielar - first_name: Guido full_name: Grundmeier, Guido id: '194' last_name: Grundmeier - first_name: A. Francis full_name: Stewart, A. Francis last_name: Stewart - first_name: Adrian full_name: Keller, Adrian id: '48864' last_name: Keller orcid: 0000-0001-7139-3110 citation: ama: Ramakrishnan S, Subramaniam S, Kielar C, Grundmeier G, Stewart AF, Keller A. Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures. Molecules. 2020;25:5099. doi:10.3390/molecules25215099 apa: Ramakrishnan, S., Subramaniam, S., Kielar, C., Grundmeier, G., Stewart, A. F., & Keller, A. (2020). Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures. Molecules, 25, 5099. https://doi.org/10.3390/molecules25215099 bibtex: '@article{Ramakrishnan_Subramaniam_Kielar_Grundmeier_Stewart_Keller_2020, title={Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures}, volume={25}, DOI={10.3390/molecules25215099}, journal={Molecules}, author={Ramakrishnan, Saminathan and Subramaniam, Sivaraman and Kielar, Charlotte and Grundmeier, Guido and Stewart, A. Francis and Keller, Adrian}, year={2020}, pages={5099} }' chicago: 'Ramakrishnan, Saminathan, Sivaraman Subramaniam, Charlotte Kielar, Guido Grundmeier, A. Francis Stewart, and Adrian Keller. “Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures.” Molecules 25 (2020): 5099. https://doi.org/10.3390/molecules25215099.' ieee: S. Ramakrishnan, S. Subramaniam, C. Kielar, G. Grundmeier, A. F. Stewart, and A. Keller, “Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures,” Molecules, vol. 25, p. 5099, 2020. mla: Ramakrishnan, Saminathan, et al. “Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures.” Molecules, vol. 25, 2020, p. 5099, doi:10.3390/molecules25215099. short: S. Ramakrishnan, S. Subramaniam, C. Kielar, G. Grundmeier, A.F. Stewart, A. Keller, Molecules 25 (2020) 5099. date_created: 2021-07-08T11:59:55Z date_updated: 2022-01-06T06:55:37Z department: - _id: '302' doi: 10.3390/molecules25215099 intvolume: ' 25' language: - iso: eng page: '5099' publication: Molecules publication_identifier: issn: - 1420-3049 publication_status: published status: public title: Protein-Assisted Room-Temperature Assembly of Rigid, Immobile Holliday Junctions and Hierarchical DNA Nanostructures type: journal_article user_id: '48864' volume: 25 year: '2020' ... --- _id: '22654' abstract: - lang: eng text: 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 °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. author: - first_name: Charlotte full_name: Kielar, Charlotte last_name: Kielar - first_name: Yang full_name: Xin, Yang last_name: Xin - first_name: Xiaodan full_name: Xu, Xiaodan last_name: Xu - first_name: Siqi full_name: Zhu, Siqi last_name: Zhu - first_name: Nelli full_name: Gorin, Nelli last_name: Gorin - first_name: Guido full_name: Grundmeier, Guido id: '194' last_name: Grundmeier - first_name: Christin full_name: Möser, Christin last_name: Möser - first_name: David M. full_name: Smith, David M. last_name: Smith - first_name: Adrian full_name: Keller, Adrian id: '48864' last_name: Keller orcid: 0000-0001-7139-3110 citation: ama: Kielar C, Xin Y, Xu X, et al. Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability. Molecules. 2019;24:2577. doi:10.3390/molecules24142577 apa: Kielar, C., Xin, Y., Xu, X., Zhu, S., Gorin, N., Grundmeier, G., … Keller, A. (2019). Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability. Molecules, 24, 2577. https://doi.org/10.3390/molecules24142577 bibtex: '@article{Kielar_Xin_Xu_Zhu_Gorin_Grundmeier_Möser_Smith_Keller_2019, title={Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability}, volume={24}, DOI={10.3390/molecules24142577}, journal={Molecules}, author={Kielar, Charlotte and Xin, Yang and Xu, Xiaodan and Zhu, Siqi and Gorin, Nelli and Grundmeier, Guido and Möser, Christin and Smith, David M. and Keller, Adrian}, year={2019}, pages={2577} }' chicago: 'Kielar, Charlotte, Yang Xin, Xiaodan Xu, Siqi Zhu, Nelli Gorin, Guido Grundmeier, Christin Möser, David M. Smith, and Adrian Keller. “Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability.” Molecules 24 (2019): 2577. https://doi.org/10.3390/molecules24142577.' ieee: C. Kielar et al., “Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability,” Molecules, vol. 24, p. 2577, 2019. mla: Kielar, Charlotte, et al. “Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability.” Molecules, vol. 24, 2019, p. 2577, doi:10.3390/molecules24142577. short: C. Kielar, Y. Xin, X. Xu, S. Zhu, N. Gorin, G. Grundmeier, C. Möser, D.M. Smith, A. Keller, Molecules 24 (2019) 2577. date_created: 2021-07-08T12:12:53Z date_updated: 2022-01-06T06:55:38Z department: - _id: '302' doi: 10.3390/molecules24142577 intvolume: ' 24' language: - iso: eng page: '2577' publication: Molecules publication_identifier: issn: - 1420-3049 publication_status: published status: public title: Effect of Staple Age on DNA Origami Nanostructure Assembly and Stability type: journal_article user_id: '48864' volume: 24 year: '2019' ... --- _id: '17077' abstract: - lang: eng text: Cyanobacteriochromes are compact and spectrally diverse photoreceptor proteins that are promising candidates for biotechnological applications. Computational studies can contribute to an understanding at a molecular level of their wide spectral tuning and diversity. In this contribution, we benchmark methods to model a 110 nm shift in the UV/Vis absorption spectrum from a red- to a green-absorbing form of the cyanobacteriochrome Slr1393g3. Based on an assessment of semiempirical methods to describe the chromophore geometries of both forms in vacuo, we find that DFTB2+D leads to structures that are the closest to the reference method. The benchmark of the excited state calculations is based on snapshots from quantum mechanics/molecular mechanics molecular dynamics simulations. In our case, the methods RI-ADC(2) and sTD-DFT based on CAM-B3LYP ground state calculations perform the best, whereas no functional can be recommended to simulate the absorption spectra of both forms with time-dependent density functional theory. Furthermore, the difference in absorption for the lowest energy absorption maxima of both forms can already be modelled with optimized structures, but sampling is required to improve the shape of the absorption bands of both forms, in particular for the second band. This benchmark study can guide further computational studies, as it assesses essential components of a protocol to model the spectral tuning of both cyanobacteriochromes and the related phytochromes. article_number: '1720' author: - first_name: Christian full_name: Wiebeler, Christian last_name: Wiebeler - first_name: Igor full_name: Schapiro, Igor last_name: Schapiro citation: ama: Wiebeler C, Schapiro I. QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra. Molecules. 2019. doi:10.3390/molecules24091720 apa: Wiebeler, C., & Schapiro, I. (2019). QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra. Molecules. https://doi.org/10.3390/molecules24091720 bibtex: '@article{Wiebeler_Schapiro_2019, title={QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra}, DOI={10.3390/molecules24091720}, number={1720}, journal={Molecules}, author={Wiebeler, Christian and Schapiro, Igor}, year={2019} }' chicago: Wiebeler, Christian, and Igor Schapiro. “QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra.” Molecules, 2019. https://doi.org/10.3390/molecules24091720. ieee: C. Wiebeler and I. Schapiro, “QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra,” Molecules, 2019. mla: Wiebeler, Christian, and Igor Schapiro. “QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra.” Molecules, 1720, 2019, doi:10.3390/molecules24091720. short: C. Wiebeler, I. Schapiro, Molecules (2019). date_created: 2020-06-04T07:27:03Z date_updated: 2022-01-06T06:53:04Z doi: 10.3390/molecules24091720 keyword: - pc2-ressources language: - iso: eng project: - _id: '52' name: Computing Resources Provided by the Paderborn Center for Parallel Computing publication: Molecules publication_identifier: issn: - 1420-3049 publication_status: published status: public title: QM/MM Benchmarking of Cyanobacteriochrome Slr1393g3 Absorption Spectra type: journal_article user_id: '61189' year: '2019' ... --- _id: '22683' author: - first_name: Ilko full_name: Bald, Ilko last_name: Bald - first_name: Adrian full_name: Keller, Adrian id: '48864' last_name: Keller orcid: 0000-0001-7139-3110 citation: ama: Bald I, Keller A. Molecular Processes Studied at a Single-Molecule Level Using DNA Origami Nanostructures and Atomic Force Microscopy. Molecules. 2014;19:13803-13823. doi:10.3390/molecules190913803 apa: Bald, I., & Keller, A. (2014). Molecular Processes Studied at a Single-Molecule Level Using DNA Origami Nanostructures and Atomic Force Microscopy. Molecules, 19, 13803–13823. https://doi.org/10.3390/molecules190913803 bibtex: '@article{Bald_Keller_2014, title={Molecular Processes Studied at a Single-Molecule Level Using DNA Origami Nanostructures and Atomic Force Microscopy}, volume={19}, DOI={10.3390/molecules190913803}, journal={Molecules}, author={Bald, Ilko and Keller, Adrian}, year={2014}, pages={13803–13823} }' chicago: 'Bald, Ilko, and Adrian Keller. “Molecular Processes Studied at a Single-Molecule Level Using DNA Origami Nanostructures and Atomic Force Microscopy.” Molecules 19 (2014): 13803–23. https://doi.org/10.3390/molecules190913803.' ieee: I. Bald and A. Keller, “Molecular Processes Studied at a Single-Molecule Level Using DNA Origami Nanostructures and Atomic Force Microscopy,” Molecules, vol. 19, pp. 13803–13823, 2014. mla: Bald, Ilko, and Adrian Keller. “Molecular Processes Studied at a Single-Molecule Level Using DNA Origami Nanostructures and Atomic Force Microscopy.” Molecules, vol. 19, 2014, pp. 13803–23, doi:10.3390/molecules190913803. short: I. Bald, A. Keller, Molecules 19 (2014) 13803–13823. date_created: 2021-07-08T13:01:44Z date_updated: 2022-01-06T06:55:38Z department: - _id: '302' doi: 10.3390/molecules190913803 intvolume: ' 19' language: - iso: eng page: 13803-13823 publication: Molecules publication_identifier: issn: - 1420-3049 publication_status: published status: public title: Molecular Processes Studied at a Single-Molecule Level Using DNA Origami Nanostructures and Atomic Force Microscopy type: journal_article user_id: '48864' volume: 19 year: '2014' ...