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At least 721 records · Page 40

Determination of human DNA polymerase utilization for the repair of a model ionizing radiation-induced DNA strand break lesion in a defined vector substrate

Human DNA polymerase and DNA ligase utilization for the repair of a major class of ionizing radiation-induced DNA lesion [DNA single-strand breaks containing 3'-phosphoglycolate (3'-PG)] was examined using a novel, chemically defined vector substrate containing a single, site-specific 3'-PG single-strand break lesion. In addition, the major human AP endonuclease, HAP1 (also known as APE1, APEX, Ref-1), was tested to determine if it was involved in initiating repair of 3'-PG-containing single-strand break lesions. DNA polymerase beta was found to be the primary polymerase responsible for nucleotide incorporation at the lesion site following excision of the 3'-PG blocking group. However, DNA polymerase delta/straightepsilon was also capable of nucleotide incorporation at the lesion site following 3'-PG excision. In addition, repair reactions catalyzed by DNA polymerase beta were found to be most effective in the presence of DNA ligase III, while those catalyzed by DNA polymerase delta/straightepsilon appeared to be more effective in the presence of DNA ligase I. Also, it was demonstrated that the repair initiating 3'-PG excision reaction was not dependent upon HAP1 activity, as judged by inhibition of HAP1 with neutralizing HAP1-specific polyclonal antibody.

Non-NASA Center↗

Isolation of novel ribozymes that ligate AMP-activated RNA substrates

BACKGROUND: The protein enzymes RNA ligase and DNA ligase catalyze the ligation of nucleic acids via an adenosine-5'-5'-pyrophosphate 'capped' RNA or DNA intermediate. The activation of nucleic acid substrates by adenosine 5'-monophosphate (AMP) may be a vestige of 'RNA world' catalysis. AMP-activated ligation seems ideally suited for catalysis by ribozymes (RNA enzymes), because an RNA motif capable of tightly and specifically binding AMP has previously been isolated. RESULTS: We used in vitro selection and directed evolution to explore the ability of ribozymes to catalyze the template-directed ligation of AMP-activated RNAs. We subjected a pool of 10(15) RNA molecules, each consisting of long random sequences flanking a mutagenized adenosine triphosphate (ATP) aptamer, to ten rounds of in vitro selection, including three rounds involving mutagenic polymerase chain reaction. Selection was for the ligation of an oligonucleotide to the 5'-capped active pool RNA species. Many different ligase ribozymes were isolated; these ribozymes had rates of reaction up to 0.4 ligations per hour, corresponding to rate accelerations of approximately 5 x10(5) over the templated, but otherwise uncatalyzed, background reaction rate. Three characterized ribozymes catalyzed the formation of 3'-5'-phosphodiester bonds and were highly specific for activation by AMP at the ligation site. CONCLUSIONS: The existence of a new class of ligase ribozymes is consistent with the hypothesis that the unusual mechanism of the biological ligases resulted from a conservation of mechanism during an evolutionary replacement of a primordial ribozyme ligase by a more modern protein enzyme. The newly isolated ligase ribozymes may also provide a starting point for the isolation of ribozymes that catalyze the polymerization of AMP-activated oligonucleotides or mononucleotides, which might have been the prebiotic analogs of nucleoside triphosphates.

NASA Discipline Exobiology↗

Trace Chemical Detection Using Intercalated MXenes as a Signal Enhancing Substrate in Optical Probes

MXenes are 2D materials composed of layered transition metal nitrides or carbides. These materials are synthesized by HF exfoliation from MAX phases (Ti{sub 3}AlC{sub 2}). The 2D nanomaterial was synthesized by the removal of the 'A' element, resulting in a Mxene product (Ti{sub 3}C{sub 2}). MXenes have the general formula M{sub n+1}X{sub n}T{sub x}, where M is an early transition metal, X is Carbon and/or Nitrogen, and T accounts for surface terminated functional groups such as Fluoride, hydroxyl, and oxygen. These materials have very unique properties, similar to graphene, that allows them to be applied in a variety of trace detection techniques including surface-enhanced Raman spectroscopy (SERS). MXenes have also been demonstrated to selectively uptake uranyl ion, UO{sub 2}{sup 2+}. If this property can be combined with SERS or fluorescence detection, it may be possible to use MXenes as the basis for an alternative method to kinetic phosphorescence analysis (KPA) for trace uranyl measurements. Objectives: To confirm that MXene Nano materials are suitable substrates for SERS and sensor development by enhancing Raman signaling. To determine if certain MXene preparation methods yield materials that are more suitable for trace sensing methods. To determine uranyl uptake properties of these MXene materials and test them for analytical signals. Sample Preparation: Preparation of Ti{sub 3}C{sub 2}MXene (at FSU). MXenes were prepared by etching Al from Ti{sub 3}AlC{sub 2} (MAX phase)material. Two etching techniques yield different MXene products: LiF/HCl: Milder reaction, larger MXene flakes. HF: Harsher reaction, smaller flakes, larger layer separation. Products washed to remove etchant, vacuum filtered, and dried. Dried MXene flakes are air-stable. Film preparation for sensor testing (at SRNL): Suspend powder in diH{sub 2}O, purge with Ar, sonicate for 30 min. Centrifuge and collect supernate with suspended particles. Observed LiF-etched Mxene yielded a higher density of particles and darker collected solution. Drop-cast (4 ml) supernate onto slides and dried with Ar. For Rhodamine B (RhB) testing, drop-cast 4 ml drops onto Mxene spots and dried with Ar. Scanning Electron Microscopy conditions: 10 kV Beam energy, high vacuum; Working distance of 8 mm; beam penetration depth appx. 4 microns, beam spot size appx. 2 nanometers. Results: Detection of aluminum correlates with bright spots on image. Presence of aluminum shows that LiF/HCl etching was less thorough than HF etching. Trace Cl detection in LiF images suggests incomplete rinsing. HF has smaller feature size, more layer structure, and increased homogeneity, consistent with expectations. Macroscopic Raman spectroscopy measurements: 532 nm excitation, ∼50 mW with a ∼100 micron spot size (InPhotonics RPB probe). Kaiser Optical Holospec f/1.8 spectrometer with cooled (-60 deg.C) Andor iDus OE420 CCD. LiF 1x supernate showed good signal for trace measurements of Rhodamine B. HF and 1/4x LiF supernates showed little Mxene or Rhodamine B signal. Low deposition densities led to excess background signal from glass slides. For LiF film, response is linear with Rhodamine B concentration over range tested. Will retest with Raman microscope (∼1 micron spot size) to characterize SERS of more dilute LiF and HF etched Mxenes. Conclusions: The LiF etched material was more suitable for macroscopic SERS measurements because it was more concentrated, resulting in a thicker film than the HF etched Mxene and diluted LiF sample. However, the other materials may give greater SERS enhancements, which we hope to determine from measurements with the Raman microscope. From characterization with SEM we concluded that the HF etched Mxene is more uniform/homogenous and has smaller particle size than the LiF etched Mxene. There is still aluminum present in both samples indicating that etching wasn't complete, but the removal of the aluminum was more efficient in the HF method. Path Forward: Observe SERS with Raman microscopy, to obtain better signals for the more diluted samples and be able to compare enhancement effects for the different MXenes. Characterize uranyl sorption into MXene films and test Raman and fluorescence signals. Revisit the etching conditions to improve removal of aluminum. FSU and SRNL will continue to collaborate to create and characterize different Mxene materials and test their usefulness for sensor applications.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Formation and Shape Changing of Conductive Helical Ribbons via Deposition of Highly Stressed Films on Mechanically Responsive Substrates

Abstract This work demonstrates that the electrodeposition of highly stressed films on compliant ribbons is a robust process to obtain helical structures with excellent mechanical stability and potentially high thermal and electrical conductance. Electrodeposition on end‐tethered ribbons alters their axial and bending stiffness while imparting mechanical stress to drive the formation of a helix with a microscale diameter and pitch in a controlled and scalable manner. The process generates helices with diameters and pitches between 80 and 200 µm and lengths as large as several millimeters. The approach is amenable to parallel processing a large number of 3D structures on any substrate, including large‐area semiconductor wafers. This phenomenon is explained in terms of the change of stress gradients as material is added. Applications of the fabricated helices include antennas, metamaterials, and slow‐wave structures in frequency ranges not previously attainable.

Chemistry↗

Strain Recovery and Defect Characterization in Mg‐Implanted Homoepitaxial GaN on High‐Quality GaN Substrates

The evolution of defects due to high‐pressure annealing of magnesium ion‐implanted epitaxial GaN grown on high‐quality GaN substrates is investigated. Changes in the implant‐induced strain are quantified as a function of annealing temperature and time. After annealing at 1300 °C for 10 min, the implant‐induced strain is fully relieved and accompanied by the presence of extended defects such as basal plane stacking faults and prismatic loops. Approximately one‐third of the original implant‐induced strain remains after annealing at 700 °C, and 5% of the original strain remains at 1000 °C for 100 min. In all cases, nearly all of the recovered strain occurs within first few minutes of annealing. A prominent increase in the asymmetric (104) triple axis X‐ray rocking curve full width at 0.01 maximum (FW0.01M) is observed after annealing at 1300 °C for 10 min. After annealing at 1300 °C for 100 min, a subsequent decrease in FW0.01M is correlated with a reduction of the extended defect density from 4 × 10 8 to 3 × 10 7 cm −2 , determined through transmission electron microscope (TEM) measurements. Further reduction in the density of the extended defects by optimizing annealing temperature and time is expected to improve the performance of GaN‐based vertical power devices.

Wang, Yekan↗

Structural Properties of Nanometer‐Sized Gold Nanoparticles on a Silicon Substrate

Properties of gold nanoparticles (Au NPs) supported on Si substrates, which have been the focus of recent attention, depend sensitively on the size, structure, and coordination of Au NPs as well as on the processes of interdiffusion and chemical bonding at the Au–Si interface. There is a great need, therefore, for developing structural techniques capable of imaging such nanosystems in atomic detail. Here, it is discussed how the atomic structure of nanometer‐sized Au NPs deposited on a silicon surface can be determined by using high‐energy X‐ray diffraction measurements in combination with an analysis based on atomic‐pair‐distribution functions and advanced reverse Monte Carlo methods. This approach delivers simple and incisive pictures of the structure of Au clusters on Si and reveals direct structural evidence for the emergence of a Au‐silicide interface following room temperature deposition of Au NPs on Si. This study will contribute to designing Au/Si nanostructures with desirable properties.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Large-Area Periodic Arrays of Atomically Flat Single-Crystal Gold Nanotriangles Formed Directly on Substrate Surfaces

The advancement of nanoenabled wafer-based devices requires the establishment of core competencies related to the deterministic positioning of nanometric building blocks over large areas. Within this realm, plasmonic single-crystal gold nanotriangles represent one of the most attractive nanoscale components but where the formation of addressable arrays at scale has heretofore proven impracticable. In this work, a benchtop process is presented for the formation of large-area periodic arrays of gold nanotriangles. The devised growth pathway sees the formation of an array of defect-laden seeds using lithographic and vapor-phase assembly processes followed by their placement in a growth solution promoting planar growth and threefold symmetric side-faceting. The nanotriangles formed in this high-yield synthesis distinguish themselves in that they are epitaxially aligned with the underlying substrate, grown to thicknesses that are not readily obtainable in colloidal syntheses, and present atomically flat pristine surfaces exhibiting gold atoms with a close-packed structure. As such, they express crisp and unambiguous plasmonic modes and form photoactive surfaces with highly tunable and readily modeled plasmon resonances. The devised methods, hence, advance the integration of single-crystal gold nanotriangles into device platforms and provide an overall fabrication strategy that is adaptable to other nanomaterials.

42 ENGINEERING↗

Bicarbonate is a key regulator but not a substrate for O2 evolution in Photosystem II

Abstract Photosystem II (PSII) uses light energy to oxidize water and to reduce plastoquinone in the photosynthetic electron transport chain. O 2 is produced as a byproduct. While most members of the PSII research community agree that O 2 originates from water molecules, alternative hypotheses involving bicarbonate persist in the literature. In this perspective, we provide an overview of the important roles of bicarbonate in regulating PSII activity and assembly. Further, we emphasize that biochemistry, spectroscopy, and structural biology experiments have all failed to detect bicarbonate near the active site of O 2 evolution. While thermodynamic arguments for oxygen-centered bicarbonate oxidation are valid, the claim that bicarbonate is a substrate for photosynthetic O 2 evolution is challenged.

Vinyard, David J.↗

Probing substrate water access through the O1 channel of Photosystem II by single site mutations and membrane inlet mass spectrometry

Abstract Light-driven water oxidation by photosystem II sustains life on Earth by providing the electrons and protons for the reduction of CO 2 to carbohydrates and the molecular oxygen we breathe. The inorganic core of the oxygen evolving complex is made of the earth-abundant elements manganese, calcium and oxygen (Mn 4 CaO 5 cluster), and is situated in a binding pocket that is connected to the aqueous surrounding via water-filled channels that allow water intake and proton egress. Recent serial crystallography and infrared spectroscopy studies performed with PSII isolated fromThermosynechococcus vestitus(T. vestitus) support that one of these channels, the O1 channel, facilitates water access to the Mn 4 CaO 5 cluster during its S 2 →S 3 and S 3 →S 4 →S 0 state transitions, while a subsequent CryoEM study concluded that this channel is blocked in the cyanobacteriumSynechocystis sp.PCC 6803, questioning the role of the O1 channel in water delivery. Employing site-directed mutagenesis we modified the two O1 channel bottleneck residues D1-E329 and CP43-V410 (T. vestitusnumbering) and probed water access and substrate exchange via time resolved membrane inlet mass spectrometry. Our data demonstrates that water reaches the Mn 4 CaO 5 cluster via the O1 channel in both wildtype and mutant PSII. In addition, the detailed analysis provides functional insight into the intricate protein-water-cofactor network near the Mn 4 CaO 5 cluster that includes the pentameric, near planar ‘water wheel’ of the O1 channel.

Plant Sciences↗

In-situ ETEM study of plasma-facing tungsten nanofuzz oxidation at atmospheric pressure: Microstructure evolution and substrate-free oxidation kinetics

To enable sustainable carbon-free fusion energy, managing reactor structural material degradation during normal operation as well as accident scenarios is vital. Tungsten (W) plasma-facing materials (PFMs) are susceptible to aggressive high-temperature oxidation during air-ingress fusion reactor accidents, yet there's a lack of oxidation kinetic data for irradiated tungsten. Here, in this study, we utilize atmospheric environmental transmission electron microscopy (ETEM) to present the first kinetic data for substrate-free W nanofuzz oxidation at 400 ºC and 500 ºC in 1 bar dry air. Comparison with pristine bulk W during the early parabolic stage suggests an irradiationdecelerated oxidation for W nanofuzz. Our time-resolved in-situ characterization reveals a durable amorphous surface oxide, likely promoted by high-flux He + irradiation-induced surface defects, serving as an effective passivating layer that impedes nanofuzz oxidation onset. This surface oxide layer also interfaces well with newly formed orthorhombic WO 3 , facilitated by stress relief through He bubble shrinkage, providing lasting passivating protection throughout the nanofuzz parabolic oxidation. This new finding challenges conventional notions of irradiation's negative impact on metal oxidation, and calls for advanced characterization to enhance our understanding of fusion energy materials degradation, informed by further accident modeling.

36 MATERIALS SCIENCE↗

Mixed Tin-Titanium Oxides by Atomic Layer Deposition on Planar Substrates: Physical and Electronic Structure

Ternary atomic layer deposition of Sn-doped TiO x (Sn:TiO x ) and Ti-doped SnO x (Ti:SnO x ) was performed using tetrakisdimethylamidotitanium (IV) and tin(IV) with water at 150 °C on (1 0 0) Si and quartz substrates. The physical structure of the films was investigated using scanning electron, atomic force, and Kelvin probe force microscopies as well as spectroscopic ellipsometry, Raman spectroscopy, and X-ray diffraction. All as-deposited films are amorphous and possessed flat and conformal topographies with low surface roughness (<1 nm). Annealed Sn:TiO x and Ti:SnO x crystallize into the tetragonal anatase TiO 2 and cassiterite SnO 2 structures, respectively, without large variations to the film topography. The chemical composition of the as-deposited and annealed films was investigated through X-ray photoelectron spectroscopy. While dopants are homogenously mixed, the ternary ALD to form Sn:TiO x and Ti:SnO x surprisingly does not follow the rule of mixtures, despite similarities in both the growth rates of binary SnO x and TiO x and the precursors used. This finding is also supported by spectroscopic ellipsometry. Here, we postulate the deviation from the rule of mixtures is due to non-ideal surface chemistry of the binary ALD of SnO x . The optical bandgap of all films was quantified by the Tauc analysis and the valence band position was investigated by valence band X-ray photoelectron spectroscopy. Intra-bandgap states above the valence band maximum were observed for as-deposited Ti:SnO x and Sn:TiO x and ascribed to 5 s states from Sn 2+ ions. The presence of these intra-bandgap states induces enhanced visible absorption and bathochromic shifts to the apparent bandgap for all as-deposited films. Annealing the films removes the intra-bandgap states and increases the optical bandgap. Simplified band diagrams created using the data available demonstrated that the conduction and valence band positions did not vary between the positions of pure TiO 2 or SnO 2 with monotonic increases to the dopant incorporation.

36 MATERIALS SCIENCE↗

Accommodating a hexagonal ζ- phase Mn 2 N film on a cubic MgO (001) substrate

The thin films of c -plane dominated hexagonal ζ- phase Mn 2 N were successfully grown on a cubic MgO (001) substrate directly using plasma-assisted molecular beam epitaxy. The surface was comprehensively studied through experimental and theoretical approaches. Reflection high energy electron diffraction revealed two pseudo-cubic domains along [100] MgO and [110] MgO , and one hexagonal domain, which is 30° apart from the [100] MgO direction. Scanning tunneling microscopy was used to image and resolve the high-quality surface, revealing a distorted hexagonal surface structure. Furthermore, atomic resolution of the hexagonal domain with a 2 × 2 reconstructed surface is presented. For c-plane surface, theoretical investigations were carried out using first principles studies to determine the surface formation energy for various reconstructed surfaces. The theoretical study shows that the nitrogen terminated 2 × 2 structure with a manganese adatom on the surface as the most stable reconstruction that reproduces the experimental results. A corresponding simulated scanning tunneling microscopy model is also presented, providing strong support for the experimentally observed in-plane lattice structures. Furthermore, the manganese: nitrogen stoichiometry within the bulk and surface is in good agreement with the expected ratio of 2:1.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Identification and characterization of substrate- and product-selective nylon hydrolases

Enzymes can rapidly and selectively hydrolyze diverse natural and anthropogenic polymers, but few have been shown to hydrolyze synthetic polyamides. Here, in this work, we synthesized and characterized a panel of 95 enzymes from the N-terminal nucleophile hydrolase superfamily with 30%–50% pairwise amino acid identity. We found that nearly 40% of the enzymes had substantial nylon hydrolase activity, but there was no relationship between phylogeny and activity, nor any evidence of prior evolutionary selection for nylon hydrolysis. Several newly identified hydrolases showed substrate selectivity, generating up to 20-fold higher product titers with nylon-6,6 versus nylon-6. However, the yield was still less than 1%, necessitating further optimization before potential applications. Finally, we determined the crystal structure and oligomerization state of a nylon-6,6-selective hydrolase to elucidate structural factors that could affect activity and selectivity. These new enzymes provide insights into nylon hydrolase evolution and opportunities for analysis and engineering of improved hydrolases.

nylon↗

Bacterial microcompartment architectures as biomaterials for conversion of gaseous substrates

Bacterial microcompartments (BMCs) are protein shells encapsulating multiple enzymes of a metabolic pathway. Interpretations of early experiments on carboxysomes led to the narrative that transport of small gases (CO 2 , O 2 ) across the shell membrane is restricted. Since then, this notion has been largely contradicted by studies of engineered shells, although these shell constructs lack important proteins present in the native BMCs, altering the synthetic shells’ topology, surface and mechanical properties. Here, we discuss here an updated model of gas permeability that informs the design of engineered shells for catalysis on gas substrates and outline how nonshell suprastructures of BMC shell proteins could be used in formulating sustainable biomaterials for hydrogen generation via methane pyrolysis and for other greenhouse gas mitigations.

Bacterial microcompartment↗

Electrodeposition of Fe–Ni alloy on Au(111) substrate: Metastable BCC growth via hydrogen evolution and interactions

The electrodeposition of Fe–Ni alloy is usually complicated by the effects of anomalous codeposition and hydrogen evolution. Although the influence of the deposition conditions on the alloy composition has been studied extensively, very few works considered the influence of growth conditions on the phase constitution. In this work, various electrodeposition conditions were investigated to grow Fe–Ni alloy films (<30 nm) with similar compositions in the Invar-to-equiatomic range on Au (111) substrate. Highly (110) oriented BCC phase Fe–Ni with a Ni fraction (ca. 40 at.% Ni) well beyond the equilibrium solubility limit (5 at.% Ni) was obtained with a significant alloy deposition partial current. An increase in the fraction of the BCC phase was found to be associated with a higher alloy deposition partial current, but not necessarily with an increase in the hydrogen evolution partial current. Motivated by the findings from this work, the formation of the metastable BCC phase is speculated to depend on the competing kinetics between the inclusion and desorption of hydrogen adatoms at the electrodeposited growth front.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Carbon isotope evidence for the substrates and mechanisms of prebiotic synthesis in the early solar system

Meteorites contain prebiotic, bio-relevant organic compounds including amino acids. Their syntheses could result from diverse sources and mechanisms and provide a window on the conditions and materials present in the early solar system. Here we constrain alanine’s synthetic history in the Murchison meteorite using site-specific 13 C/ 12 C measurements, reported relative to the VPDB standard. The δ 13 C VPDB values of -29 ± 10‰, 142 ± 20‰, and -36 ± 20‰ for the carboxyl, amine-bound, and methyl carbons, respectively, are consistent with Strecker synthesis of interstellar-medium-derived aldehydes, ammonia, and low-δ 13 C nebular or interstellar-medium-derived CN. We report experimentally measured isotope effects associated with Strecker synthesis, and use them to constrain the δ 13 C values of the alanine precursors, which we then use to construct a model that predicts the molecular-average δ 13 C values of 19 other organic compounds of prebiotic significance found in Murchison if they were made by our proposed synthetic network. Finally, most of these predictions agree with previous measurements, suggesting that interstellar-medium-derived aldehydes and nebular and/or pre-solar CN could have served as substrates for synthesis of a wide range of prebiotic compounds in the early solar system.

79 ASTRONOMY AND ASTROPHYSICS↗