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Berlin Brandenburg

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  • 1
    Language: English
    In: Angewandte Chemie International Edition, 03 January 2014, Vol.53(1), pp.169-172
    Description: DNA double strand breaks (DSBs) are deadly lesions that can lead to genetic defects and cell apoptosis. Techniques that directly detect DNA DSBs include scanning electron microscopy, atomic force microscopy (AFM), and fluorescence based approaches. While these techniques can be used to identify DSBs they provide no information on the molecular events occurring at the break. Tip‐enhanced Raman scattering (TERS) can provide molecular information from DNA at the nanoscale and in combination with AFM provides a new way to visualize and characterize the molecular structure of DSBs. DSBs result from cleavage at the 3’‐ and 5’‐bonds of deoxyribose upon exposure to UVC radiation based on the observation of POH and methyl/methylene deformation modes enhanced in the TERS spectra. It is hypothesized that strand fragments are hydrogen‐terminated at the lesion, indicating the action of free radicals during photon exposure. (DSBs) were first detected and located by atomic force microscopy, and the molecular structure of this damage was characterized with tip‐enhanced Raman scattering (see picture) using a top‐down configuration and a reflective substrate. The first experimental evidence is reported confirming that individual DSBs result from cleavage at the 3′‐ and 5′‐bonds of deoxyribose upon exposure to ultraviolet C radiation.
    Keywords: Atomic Force Microscopy ; Dna Damage ; Double Strand Breaks ; Tip‐Enhanced Raman Scattering
    ISSN: 1433-7851
    E-ISSN: 1521-3773
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  • 2
    Language: English
    In: Angewandte Chemie International Edition, 09 July 2018, Vol.57(28), pp.8519-8524
    Description: The aggregation pathways of neurodegenerative peptides determine the disease etiology, and their better understanding can lead to strategies for early disease treatment. Previous research has allowed modelling of hypothetic aggregation pathways. However, their direct experimental observation has been elusive owing to methodological limitations. Herein, we demonstrate that nanoscale chemical mapping by tip‐enhanced Raman spectroscopy of single amyloid fibrils at various stages of aggregation captures the fibril formation process. We identify changes in TERS/Raman marker bands for Aβ, including the amide III band (above 1255 cm for turns/random coil and below 1255 cm for β‐sheet conformation). The spatial distribution of β‐sheets in aggregates is determined, allowing verification of a particular fibrillogenesis pathway, starting from aggregation of monomers to ‐stable oligomers, which then rearrange to ordered β‐sheets, already at the oligomeric or protofibrillar stage. : Tip‐enhanced Raman spectroscopy of single amyloid‐β fibrils at various stages of aggregation captures the fibril formation process. The spatial distribution of β‐sheets in aggregates was determined based on amide III band position, allowing verification of a fibrillogenesis pathway, from aggregation of monomers to metastable oligomers, which then rearrange into ordered β‐sheets, already at the oligomeric or protofibrillar stage.
    Keywords: Alzheimer'S Disease ; Protein Aggregation Pathway ; Secondary Structure ; Tip-Enhanced Raman Spectroscopy ; Β-Amyloid
    ISSN: 1433-7851
    E-ISSN: 1521-3773
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  • 3
    Language: English
    In: Chemosphere, May 2014, Vol.103, pp.250-255
    Description: Sewage sludge ash (SSA) based P-fertilisers were produced by thermochemical treatment of SSA with Cl-donors at approximately 1000 °C. During this thermochemical process heavy metals are separated as heavy metal chlorides via the gas phase. Chromium cannot be separated under normal conditions. The risk of the development of toxic Cr(VI) during the thermochemical process was investigated. X-ray Absorption Spectroscopy measurements showed that SSA and thermochemically treated SSA with CaCl , MgCl and NaCl contain Cr(III) compounds only. In contrast, treating SSA with elevated quantities of Na CO , to enhance the plant-availability of the phosphate phases of the fertiliser, developed approximately 10–15% Cr(VI). Furthermore, Raman microspectroscopy showed that using Mg-carbonate reduces the risk of a Cr(VI) development during thermochemical treatment. Additionally, leaching tests showed that only a Cr–water solubility 〉10% is an indicator for Cr(VI) in SSA based P-fertilisers.
    Keywords: Chromium ; Fertiliser ; Sewage Sludge Ash ; Raman Microspectroscopy ; X-Ray Absorption Spectroscopy ; Chemistry ; Ecology
    ISSN: 0045-6535
    E-ISSN: 1879-1298
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  • 4
    Language: English
    In: Analytical chemistry, 19 June 2018, Vol.90(12), pp.7644-7650
    Description: Exposure to ionizing radiation can induce cellular defense mechanisms including cell activation and rapid proliferation prior to metastasis and in extreme cases can result in cell death. Herewith we apply infrared nano- and microspectroscopy combined with multidimensional data analysis to characterize the effect of ionizing radiation on single glioblastoma nuclei isolated from cells treated with 10 Gy of X-rays or 1 and 10 Gy of protons. We observed chromatin fragmentation related to the formation of apoptotic bodies following X-ray exposure. Following proton irradiation we detected evidence of a DNA conformational change (B-DNA to A-DNA transition) related to DNA repair and accompanied by an increase in protein content related to the synthesis of peptide enzymes involved in DNA repair. We also show that proton exposure can increase cholesterol and sterol ester synthesis, which are important lipids involved in the metastatic process changing the fluidity of the cellular membrane in preparation for rapid proliferation.
    Keywords: Nanotechnology ; Protons ; Brain Neoplasms -- Pathology ; Glioblastoma -- Pathology
    ISSN: 00032700
    E-ISSN: 1520-6882
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  • 5
    Language: English
    In: Macromolecules, 01/26/2016, Vol.49(2), pp.643-652
    Description: DNA adopts different conformations based on its environment We reveal conditions that either preserve the DNA's physiological B-conformation, even upon its placement in UHV, or lead to a partial B-form to A-form reorganization upon DNA's deposition on a surface. We use high-resolution AFM to image DNA with a well-defined number of base pairs deposited on mica. To enable the DNA's adhesion, we either add divalent cations to the DNA solution or functionalize the surface with a silane layer. The contour length of DNA on the silane is always in perfect agreement with the B-form conformation, whereas cation-deposited DNA is always, in some cases up to 20% shorter. We varied the equilibration time, the DNA length, and sequence and compared nicked to non-nicked molecules, thus identifying several factors controlling the DNA's length. We performed TERS measurements confirming spectroscopically that cation-deposited DNA undergoes a partial B-form to A-form conformational transition upon drying and pinpointed positions along the DNA where this transition was more probable, namely the ends of the molecules. Controlling the conformation of DNA is essential for its nanotechnology applications such as nanotemplating. Our findings could also shed a whole new light on DNA polymer physics, the mechanisms of DNA binding to surfaces, or the abundant contradictory data on DNA's electrical behavior.
    Keywords: Kation ; Mica ; Dns-Polymerase ; Adhäsion ; Nanotechnologie ; Elektrische Eigenschaft ; Chemistry;
    ISSN: 0024-9297
    E-ISSN: 1520-5835
    Source: American Chemical Society (via CrossRef)
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  • 6
    In: Small, September 2016, Vol.12(35), pp.4821-4829
    Description: , DNA could become a biological standard sample in the field of nanospectroscopy. Tip‐enhanced Raman spectroscopy (TERS) provides new insights into individual DNA molecules immobilized on flat mica crystals. The high sensitivity of TERS is used to assess the chemical changes that appear in DNA upon different surface immobilization protocols.
    Keywords: Dna ; Dna Conformation ; Ters ; Nanospectroscopy
    ISSN: 1613-6810
    E-ISSN: 1613-6829
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  • 7
    Language: English
    In: Journal of Bioinformatics and Computational Biology, February 2016, Vol.14(1)
    Description: Raman spectroscopy (including surface enhanced Raman spectroscopy (SERS) and tip enhanced Raman spectroscopy (TERS)) is a highly promising experimental method for investigations of biomolecule damage induced by ionizing radiation. However, proper interpretation of changes in experimental spectra for complex systems is often difficult or impossible, thus Raman spectra calculations based on density functional theory (DFT) provide an invaluable tool as an additional layer of understanding of underlying processes. There are many works that address the problem of basis set dependence for energy and bond length consideration, nevertheless there is still lack of consistent research on basis set influence on Raman spectra intensities for biomolecules. This study fills this gap by investigating of the influence of basis set choice for the interpretation of Raman spectra of the thymine molecule calculated using the DFT/B3LYP framework and comparing these results with experimental spectra. Among 19 selected Pople’s basis sets, the best agreement was achieved using 6-31 + (d,p), 6-31 + + (d,p) and 6-11 + + G(d,p) sets. Adding diffuse functions or polarized functions for small basis set or use of a medium or large basis set without diffuse or polarized functions is not sufficient to reproduce Raman intensities correctly. The introduction of the diffuse functions ( + + ) on hydrogen atoms is not necessary for gas phase calculations. This work serves as a benchmark for further research on the interaction of ionizing radiation with DNA molecules by means of ab initio calculations and Raman spectroscopy. Moreover, this work provides a set of new scaling factors for Raman spectra calculation in the framework of DFT/B3LYP method.
    Keywords: Ab Initio Computations ; Density Functional Theory ; Thymine Molecule ; Raman Spectrum ; Biology
    ISSN: 0219-7200
    E-ISSN: 1757-6334
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  • 8
    Language: English
    In: Biophysical Journal, 29 March 2016, Vol.110(6), pp.1304-1311
    Description: The biological influence of radiation on living matter has been studied for years; however, several questions about the detailed mechanism of radiation damage formation remain largely unanswered. Among all biomolecules exposed to radiation, DNA plays an important role because any damage to its molecular structure can affect the whole cell and may lead to chromosomal rearrangements resulting in genomic instability or cell death. To identify and characterize damage induced in the DNA sugar-phosphate backbone, in this work we performed x-ray absorption spectroscopy at the P K-edge on DNA irradiated with either UVA light or protons. By combining the experimental results with theoretical calculations, we were able to establish the types and relative ratio of lesions produced by both UVA and protons around the phosphorus atoms in DNA.
    Keywords: Biology
    ISSN: 0006-3495
    E-ISSN: 1542-0086
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  • 9
    Language: English
    In: Angewandte Chemie, 09 July 2018, Vol.130(28), pp.8655-8660
    Description: The aggregation pathways of neurodegenerative peptides determine the disease etiology, and their better understanding can lead to strategies for early disease treatment. Previous research has allowed modelling of hypothetic aggregation pathways. However, their direct experimental observation has been elusive owing to methodological limitations. Herein, we demonstrate that nanoscale chemical mapping by tip‐enhanced Raman spectroscopy of single amyloid fibrils at various stages of aggregation captures the fibril formation process. We identify changes in TERS/Raman marker bands for Aβ, including the amide III band (above 1255 cm for turns/random coil and below 1255 cm for β‐sheet conformation). The spatial distribution of β‐sheets in aggregates is determined, allowing verification of a particular fibrillogenesis pathway, starting from aggregation of monomers to ‐stable oligomers, which then rearrange to ordered β‐sheets, already at the oligomeric or protofibrillar stage. an einzelnen Amyloid‐β‐Fibrillen in verschiedenen Aggregationsstadien zeichnet ein Bild der Fibrillenentstehung. Die räumliche Verteilung von β‐Faltblättern in Aggregaten wurde anhand der Amid‐III‐Bandenlage bestimmt. In der Fibrillogenese, über die Aggregation von Monomeren zu metastabilen Oligomeren, zeigt sich, dass im Protofibrillenstadium geordnete β‐Faltblätter und ungeordnete Aggregate gleichzeitig vorliegen.
    Keywords: Alzheimer-Krankheit ; Proteinaggregationspfad ; Sekundärstrukturen ; Spitzenverstärkte Raman-Spektroskopie ; Β-Amyloid
    ISSN: 0044-8249
    E-ISSN: 1521-3757
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  • 10
    Language: English
    In: The Journal of membrane biology, July 2014, Vol.247(7), pp.581-9
    Description: The effectiveness of two alkylphosphocholines (APCs), hexadecylphosphocholine (miltefosine) and erucylphosphocholine to combat prostate cancer has been studied in vitro with artificial cancerous membrane, modelled with the Langmuir monolayer technique, and on cell line (Du-145). Studies performed with the Langmuir method indicate that both the investigated drugs have the affinity to the monolayer mimicking prostate cancer membrane (composed of cholesterol:POPC = 0.428) and the drug-membrane interactions are stronger for erucylphosphocholine as compared to hexadecylphosphocholine. Moreover, both studied drugs were found to fluidize the model membrane, which may lead to apoptosis. Indeed, biological studies confirmed that in Du-145 cell line both investigated alkylphosphocholines cause cell death primarily by apoptosis while necrotic cells constitute only a small percentage of APC-treated cells.
    Keywords: Cell Membrane -- Metabolism ; Phosphorylcholine -- Metabolism ; Prostatic Neoplasms -- Metabolism
    ISSN: 00222631
    E-ISSN: 1432-1424
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