Protein three-dimensional structure dynamically changes in solution depending on the presence of ligands and interacting proteins. Methods for detecting these changes in protein conformation include ‘protein footprinting,’ using mass spectrometry. We describe herein a new technique, PLIMB (Plasma Induced Modification of Biomolecules), that generates µs bursts of hydroxyl radicals from water, to measure changes in protein structure via altered solvent accessibility of amino acid side chains. PLIMB was first benchmarked with model compounds, and then applied to a biological problem, i.e., ligand (EGF) induced changes in the conformation of the external (ecto) domain of Epidermal Growth Factor Receptor (EGFR). Regions in which oxidation decreased upon adding EGF fall along the dimerization interface, consistent with models derived from crystal structures. These results demonstrate that plasma-generated hydroxyl radicals from water can be used to map protein conformational changes, and provide a readily accessible means of studying protein structure in solution.
During plasma processing, low-k dielectrics are exposed to high levels of vacuum ultraviolet (VUV) radiation that can cause severe damage to dielectric materials. The degree and nature of VUV-induced damage depend on the VUV photon energies and fluence. In this work, we examine the VUV-absorption spectrum of low-k organosilicate glass using specular X-ray reflectivity (XRR). Low-k SiCOH films were exposed to synchrotron VUV radiation with energies ranging from 7 to 21 eV, and the density vs. depth profile of the VUV-irradiated films was extracted from fitting the XRR experimental data. The results show that the depth of the VUV-induced damage layer is a function of the photon energy. Between 7 and 11 eV, the depth of the damaged layer decreases sharply from 110 nm to 60 nm and then gradually increases to 85 nm at 21 eV. The maximum VUV absorption in low-k films occurs between 11 and 15 eV. The depth of the damaged layer was found to increase with film porosity.
This work addresses the effect of ultraviolet radiation of wavelengths longer than 250 nm on Si-CH3 bonds in porous low-k dielectrics. Porous low-k films (k = 2.3) were exposed to 4.9 eV (254 nm) ultraviolet (UV) radiation in both air and vacuum for one hour. Using Fourier Transform Infrared (FTIR) spectroscopy, the chemical structures of the dielectric films were analyzed before and after the UV exposure. UV irradiation in air led to Si-CH3 bond depletion in the low-k material and made the films hydrophilic. However, no change in Si-CH3 bond concentration was observed when the same samples were exposed to UV under vacuum with a similar fluence. These results indicate that UV exposures in vacuum with wavelengths longer than ∼250 nm do not result in Si-CH3 depletion in low-k films. However, if the irradiation takes place in air, the UV irradiation removes Si-CH3 although direct photolysis of air species does not occur above ∼242nm. We propose that photons along with molecular oxygen and, water, synergistically demethylate the low-k films.
This work examines the effect of the frequency and peak applied voltage on hydroxyl-radical generation in a dielectric-barrier plasma discharge between a metallic needle electrode and one electrode covered with dielectric. The authors examine a system that can expose up to 96 liquid samples in an automated fashion without human intervention beyond setting the initial software configuration. Then, hydroxyl-radical concentration, measured through coumarin fluorescence, was measured for 5 s plasma exposures generated under different high-voltage conditions with frequencies from 2 to 16 kHz and amplitudes from 4 to 9 kV. Their results show that an increase in frequency and/or applied voltage, within the range prescribed above and the limits of the high-voltage power supply, can yield up to a 150% increase in fluorescence with an equivalent hydroxyl-radical increase. Applications using typical previous methods, such as the Fenton Reaction, are limited in that they continuously generate hydroxyl radicals over millisecond and longer intervals. These results establish the electrical parameters that can now be applied to polymers, like proteins, which show three dimensional structures that are flexible and fluctuate on a microsecond and nanosecond time scale, with hydroxyl-radical generation on this time scale using this device. Additionally, plasma exposures may be optimized for a great variety of proteins, devices and techniques, where hydroxyl-radical generation is of utmost importance, reducing exposure time and potential subjection of samples to harmful side effects.
Free radicals from processing plasmas are known to cause damage to dielectric films used in semiconductor devices. Many radicals are highly reactive and can readily interact with the material exposed to the plasma. This can modify the chemical structure of the material causing deterioration of electrical and mechanical properties of the films. This work detects the transmission of oxygen radicals through single- and double-layer silicon-nitride and silicon-dioxide freestanding films. The films were exposed to oxygen plasma. A fluorophore dye was used to detect the oxygen radicals traversing through the films. By measuring the fluorescence of the dye before and after multiple timed-plasma exposures, the transmission properties of oxygen radicals through the material were found. The results indicate that the absorption length of oxygen radicals increases with increasing plasma exposure times for Si3N4 films because the oxygen plasma oxidizes the top layer of the film and forms a less dense silicon oxynitride layer. For SiO2 films, the absorption length was found to decrease as a function of plasma exposure time because of oxidation of the SiO2 surface which leads to the formation of a denser oxide layer on the surface of the sample.
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