TY - THES A1 - Mostafa, Amr T1 - DNA origami nanoforks: A platform for cytochrome c single molecule surface enhanced Raman spectroscopy N2 - This thesis presents a comprehensive exploration of the application of DNA origami nanofork antennas (DONAs) in the field of spectroscopy, with a particular focus on the structural analysis of Cytochrome C (CytC) at the single-molecule level. The research encapsulates the design, optimization, and application of DONAs in enhancing the sensitivity and specificity of Raman spectroscopy, thereby offering new insights into protein structures and interactions. The initial phase of the study involved the meticulous optimization of DNA origami structures. This process was pivotal in developing nanoscale tools that could significantly enhance the capabilities of Raman spectroscopy. The optimized DNA origami nanoforks, in both dimer and aggregate forms, demonstrated an enhanced ability to detect and analyze molecular vibrations, contributing to a more nuanced understanding of protein dynamics. A key aspect of this research was the comparative analysis between the dimer and aggregate forms of DONAs. This comparison revealed that while both configurations effectively identified oxidation and spin states of CytC, the aggregate form offered a broader range of detectable molecular states due to its prolonged signal emission and increased number of molecules. This extended duration of signal emission in the aggregates was attributed to the collective hotspot area, enhancing overall signal stability and sensitivity. Furthermore, the study delved into the analysis of the Amide III band using the DONA system. Observations included a transient shift in the Amide III band's frequency, suggesting dynamic alterations in the secondary structure of CytC. These shifts, indicative of transitions between different protein structures, were crucial in understanding the protein’s functional mechanisms and interactions. The research presented in this thesis not only contributes significantly to the field of spectroscopy but also illustrates the potential of interdisciplinary approaches in biosensing. The use of DNA origami-based systems in spectroscopy has opened new avenues for research, offering a detailed and comprehensive understanding of protein structures and interactions. The insights gained from this research are expected to have lasting implications in scientific fields ranging from drug development to the study of complex biochemical pathways. This thesis thus stands as a testament to the power of integrating nanotechnology, biochemistry, and spectroscopic techniques in addressing complex scientific questions. N2 - Diese Dissertation präsentiert eine umfassende Untersuchung der Anwendung von DNA-Origami-Nanogabelantennen (DONAs) im Bereich der Spektroskopie, mit einem besonderen Fokus auf der strukturellen Analyse von Cytochrom C (CytC) auf Einzelmolekülebene. Die Forschung umfasst das Design, die Optimierung und die Anwendung von DONAs zur Steigerung der Sensitivität und Spezifität der Raman-Spektroskopie und bietet somit neue Einblicke in Proteinstrukturen und -interaktionen. Die erste Phase der Studie beinhaltete die sorgfältige Optimierung von DNA-Origami-Strukturen. Dieser Prozess war entscheidend für die Entwicklung von Nanowerkzeugen, die die Fähigkeiten der Raman-Spektroskopie erheblich verbessern könnten. Die optimierten DNA-Origami-Nanogabeln, sowohl in Dimer- als auch in Aggregatform, zeigten eine verbesserte Fähigkeit, molekulare Schwingungen zu detektieren und zu analysieren, was zu einem nuancierteren Verständnis der Proteindynamik beitrug. Ein Schlüsselaspekt dieser Forschung war die vergleichende Analyse zwischen den Dimer- und Aggregatformen von DONAs. Dieser Vergleich zeigte, dass beide Konfigurationen effektiv Oxidations- und Spin-Zustände von CytC identifizieren konnten, wobei die Aggregatform aufgrund ihrer längeren Signalemission und der erhöhten Anzahl von Molekülen ein breiteres Spektrum an detektierbaren molekularen Zuständen bot. Die verlängerte Dauer der Signalemission in den Aggregaten wurde auf den kollektiven Hotspot-Bereich zurückgeführt, der die Gesamtsignalstabilität und -empfindlichkeit erhöhte. Darüber hinaus ging die Studie auf die Analyse der Amid-III-Bande unter Verwendung des DONA-Systems ein. Zu den Beobachtungen gehörte eine vorübergehende Verschiebung der Frequenz der Amid-III-Bande, was auf dynamische Veränderungen in der Sekundärstruktur von CytC hindeutete. Diese Verschiebungen, die auf Übergänge zwischen verschiedenen Proteinstrukturen hindeuteten, waren entscheidend für das Verständnis der funktionellen Mechanismen und Interaktionen des Proteins. Die in dieser Dissertation präsentierte Forschung leistet nicht nur einen bedeutenden Beitrag zum Gebiet der Spektroskopie, sondern veranschaulicht auch das Potenzial interdisziplinärer Ansätze in der Biosensorik. Der Einsatz von DNA-Origami-basierten Systemen in der Spektroskopie hat neue Wege für die Forschung eröffnet und bietet ein detailliertes und umfassendes Verständnis von Proteinstrukturen und -interaktionen. Die aus dieser Forschung gewonnenen Erkenntnisse werden voraussichtlich langfristige Auswirkungen auf wissenschaftliche Bereiche haben, die von der Arzneimittelentwicklung bis hin zur Untersuchung komplexer biochemischer Prozesse reichen. Diese Dissertation steht somit als Zeugnis für die Kraft der Integration von Nanotechnologie, Biochemie und spektroskopischen Techniken bei der Beantwortung komplexer wissenschaftlicher Fragen. KW - DNA origami KW - DNA origami nanoantennas (DONA) KW - SERS KW - Cytochrome C Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-635482 ER - TY - JOUR A1 - Schneider, Matthias A1 - Fritzsche, Nora A1 - Puciul-Malinowska, Agnieszka A1 - Baliś, Andrzej A1 - Mostafa, Amr A1 - Bald, Ilko A1 - Zapotoczny, Szczepan A1 - Taubert, Andreas T1 - Surface etching of 3D printed poly(lactic acid) with NaOH BT - a systematic approach JF - Polymers N2 - The article describes a systematic investigation of the effects of an aqueous NaOH treatment of 3D printed poly(lactic acid) (PLA) scaffolds for surface activation. The PLA surface undergoes several morphology changes and after an initial surface roughening, the surface becomes smoother again before the material dissolves. Erosion rates and surface morphologies can be controlled by the treatment. At the same time, the bulk mechanical properties of the treated materials remain unaltered. This indicates that NaOH treatment of 3D printed PLA scaffolds is a simple, yet viable strategy for surface activation without compromising the mechanical stability of PLA scaffolds. KW - surface modification KW - sodium hydroxide etching KW - poly(lactic acid) KW - 3D KW - printing KW - roughness KW - wettability KW - erosion Y1 - 2020 U6 - https://doi.org/10.3390/polym12081711 SN - 2073-4360 VL - 12 IS - 8 PB - MDPI CY - Basel ER - TY - GEN A1 - Schneider, Matthias A1 - Fritzsche, Nora A1 - Puciul-Malinowska, Agnieszka A1 - Balis, Andrzej A1 - Mostafa, Amr A1 - Bald, Ilko A1 - Zapotoczny, Szczepan A1 - Taubert, Andreas T1 - Surface etching of 3D printed poly(lactic acid) with NaOH: a systematic approach T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The article describes a systematic investigation of the effects of an aqueous NaOH treatment of 3D printed poly(lactic acid) (PLA) scaffolds for surface activation. The PLA surface undergoes several morphology changes and after an initial surface roughening, the surface becomes smoother again before the material dissolves. Erosion rates and surface morphologies can be controlled by the treatment. At the same time, the bulk mechanical properties of the treated materials remain unaltered. This indicates that NaOH treatment of 3D printed PLA scaffolds is a simple, yet viable strategy for surface activation without compromising the mechanical stability of PLA scaffolds. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1212 KW - surface modification KW - sodium hydroxide etching KW - poly(lactic acid) KW - 3D printing KW - roughness KW - wettability KW - erosion Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-525088 SN - 1866-8372 IS - 8 ER - TY - JOUR A1 - Schneider, Matthias A1 - Fritzsche, Nora A1 - Puciul-Malinowska, Agnieszka A1 - Balis, Andrzej A1 - Mostafa, Amr A1 - Bald, Ilko A1 - Zapotoczny, Szczepan A1 - Taubert, Andreas T1 - Surface etching of 3D printed poly(lactic acid) with NaOH: a systematic approach JF - Polymers N2 - The article describes a systematic investigation of the effects of an aqueous NaOH treatment of 3D printed poly(lactic acid) (PLA) scaffolds for surface activation. The PLA surface undergoes several morphology changes and after an initial surface roughening, the surface becomes smoother again before the material dissolves. Erosion rates and surface morphologies can be controlled by the treatment. At the same time, the bulk mechanical properties of the treated materials remain unaltered. This indicates that NaOH treatment of 3D printed PLA scaffolds is a simple, yet viable strategy for surface activation without compromising the mechanical stability of PLA scaffolds. KW - surface modification KW - sodium hydroxide etching KW - poly(lactic acid) KW - 3D printing KW - roughness KW - wettability KW - erosion Y1 - 2020 VL - 12 IS - 8 PB - MDPI CY - Basel ER - TY - JOUR A1 - Schürmann, Robin A1 - Titov, Evgenii A1 - Ebel, Kenny A1 - Kogikoski Junior, Sergio A1 - Mostafa, Amr A1 - Saalfrank, Peter A1 - Milosavljević, Aleksandar R. A1 - Bald, Ilko T1 - The electronic structure of the metal-organic interface of isolated ligand coated gold nanoparticles JF - Nanoscale Advances N2 - Light induced electron transfer reactions of molecules on the surface of noble metal nanoparticles (NPs) depend significantly on the electronic properties of the metal-organic interface. Hybridized metal-molecule states and dipoles at the interface alter the work function and facilitate or hinder electron transfer between the NPs and ligand. X-ray photoelectron spectroscopy (XPS) measurements of isolated AuNPs coated with thiolated ligands in a vacuum have been performed as a function of photon energy, and the depth dependent information of the metal-organic interface has been obtained. The role of surface dipoles in the XPS measurements of isolated ligand coated NPs is discussed and the binding energy of the Au 4f states is shifted by around 0.8 eV in the outer atomic layers of 4-nitrothiophenol coated AuNPs, facilitating electron transport towards the molecules. Moreover, the influence of the interface dipole depends significantly on the adsorbed ligand molecules. The present study paves the way towards the engineering of the electronic properties of the nanoparticle surface, which is of utmost importance for the application of plasmonic nanoparticles in the fields of heterogeneous catalysis and solar energy conversion. Y1 - 2022 U6 - https://doi.org/10.1039/d1na00737h SN - 2516-0230 VL - 4 IS - 6 SP - 1599 EP - 1607 PB - Royal Society of Chemistry CY - Cambridge ER -