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At least 487 records · Page 27
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

The effects of in-situ emulsion formation and superficial velocity on foam performance in high-permeability porous media

Foam has been considered as a mobility control agent for Enhanced Oil Recovery (EOR) applications in heterogeneous and fractured reservoirs. Foam enhances sweep efficiency by enabling the injected gas to flow from high-permeability to low-permeability regions. The foam injection velocity is an essential factor affecting foam mobility control and flow behavior. Furthermore, the presence of remaining oil adversely impacts foam generation leading to a failure in governing mobility control. In this study, foam performance in establishing mobility control effect and favorable apparent viscosity was experimentally investigated under a range of total superficial velocities in the presence and absence of crude oil during foam propagation in high permeability sand packs representing a propped fracture network. In the absence of oil, a pronounced effect of total superficial velocity on the mobility control performance was observed at the transition foam quality regime. Co-injection of oil and foam led to noticeable foam destabilization, as expected. However, a further increase in oil fractional flow resulted in larger overall flow resistance. We found that the formation of in-situ surfactant/oil emulsion contributed to the high apparent viscosity exhibited at the steady-state condition. These findings suggest that the steady-state flow resistance established during foam flooding at high oil saturations should be interpreted as the mobility control effect resulting from emulsion formation rather than the development of strong foam.

02 PETROLEUM↗
DOE OSTI2016

Modern water/rock reactions in Oman hyperalkaline peridotite aquifers and implications for microbial habitability

The Samail ophiolite in Oman is undergoing modern hydration and carbonation of peridotite and may host a deep subsurface biosphere. Previous investigations of hyperalkaline fluids in Oman have focused on fluids released at surface seeps, which quickly lose their reducing character and precipitate carbonates upon contact with the O 2 /CO 2 -rich atmosphere. In this study, geochemical analysis of rocks and fluids from the subsurface provides new insights into the operative reactions in serpentinizing aquifers. Serpentinite rock and hyperalkaline fluids (pH > 10), which exhibit millimolar concentrations of Ca 2+ , H 2 and CH 4 , as well as variable sulfate and nitrate, were accessed from wells situated in mantle peridotite near Ibra and studied to investigate their aqueous geochemistry, gas concentrations, isotopic signatures, mineralogy, Fe speciation and microbial community composition.The bulk mineralogy of drill cuttings is dominated by olivine, pyroxene, brucite, serpentine and magnetite. At depth, Fe-bearing brucite is commonly intermixed with serpentine, whereas near the surface, olivine and brucite are lost and increased magnetite and serpentine is detected. Micro-Raman spectroscopy reveals at least two distinct generations of serpentine present in drill cuttings recovered from several depths from two wells. Fe K-edge X-ray absorption near-edge spectroscopy (XANES) analysis of the lizardite shows a strong tetrahedral Fe coordination, suggesting a mixture of both Fe(II) and Fe(III) in the serpentine. Magnetite veins are also closely associated with this second generation serpentine, and 2-10 μm magnetite grains overprint all minerals in the drill cuttings. Thus we propose that the dissolved H 2 that accumulates in the subsurface hyperalkaline fluids was evolved through low temperature oxidation and hydration of relict olivine, as well as destabilization of pre-existing brucite present in the partially serpentinized dunites and harzburgites. In particular, we hypothesize that Fe-bearing brucite is currently reacting with dissolved silica in the aquifer fluids to generate late-stage magnetite, additional serpentine and dissolved H 2 . Dissolved CH 4 in the fluids exhibits the most isotopically heavy carbon in CH 4 reported in the literature thus far. The CH 4 may have formed through abiotic reduction of dissolved CO 2 or through biogenic pathways under extreme carbon limitation. The methane isotopic composition may have also been modified by significant methane oxidation. 16S rRNA sequencing of DNA recovered from filtered hyperalkaline well fluids reveals an abundance of Meiothermus, Thermodesulfovibrionaceae (sulfate-reducers) and Clostridia (fermenters). The fluids also contain candidate phyla OP1 and OD1, as well as Methanobacterium (methanogen) and Methylococcus sp. (methanotroph). Finally, the composition of these microbial communities suggests that low-temperature hydrogen and methane generation, coupled with the presence of electron acceptors such as nitrate and sulfate, sustains subsurface microbial life within the Oman ophiolite.

58 GEOSCIENCES↗
DOE OSTI2020

Bio-reduction of ferrihydrite-montmorillonite-organic matter complexes: Effect of montmorillonite and fate of organic matter

Organic matter (OM) is often associated with Fe (hydr)oxides such as ferrihydrite (Fh) in soils and sediments, forming binary Fh-OM complexes. Microbial reduction of Fh results in destabilization of the complexes and mineral/OM transformation. However, little is known about the role of clay minerals in such processes, despite their common co-existence with Fh and OM in natural environments. Here Fh-OM complexes were synthesized in the presence of montmorillonite (SWy-2), forming ternary Fh-(SWy-2)-OM complexes. A metal-reducing bacterium Geobacter sulfurreducens was used to reduce Fh in the complexes under circumneutral pH and anoxic conditions with or without H 2 as extra electron donor. Various spectroscopy and mass spectrometry methods were used to monitor the progress of Fh bio-reduction and mineral/OM transformation. Results showed that G. sulfurreducens utilized mineral-bound OM as electron donor and/or carbon source to couple with Fh reduction. Relative to Fh-OM complex, Addition of SWy-2 to Fh-OM complex enhanced the bio-reduction extent of Fh by increasing the proportion of bioavailable OM that was weakly bound to SWy-2. However, its effect on the bio-reduction rate was variable. SWy-2 initially decreased the rate, because it spatially separated OM (electron donor) from Fh (electron acceptor). During later incubation, SWy-2 increased the reduction rate by sorbing biogenic Fe 2+ that would otherwise passivate the Fh and cell surfaces. Bio-reduction transformed mineral-bound OM to microbial products (e.g. necromass, extracellular polymeric substances), but organic compounds with aromatic structures, carboxyl groups and large molecular weight were more resistant to desorption and oxidation. The persistence of these compounds against bio-reduction induced transformation is likely due to their stronger binding with minerals and/or lower nominal oxidation states of carbon relative to other compounds. Our results provide new insights into the role of clay minerals in regulating biogeochemical cycling of solid-phase Fe and transformation of mineral-associated OM in anoxic soil environments.

58 GEOSCIENCES↗
DOE OSTI2026

Composition and persistence of soil organic matter along eroding and depositional transects in buried vs. modern soil layers: A case of the Brady paleosol at Wauneta, Nebraska

Paleosols form when soils are buried through deposition by aeolian, colluvial, alluvial or other processes. Burial of former topsoil isolates soil organic matter (SOM) from surface conditions, allowing carbon to accumulate and potentially remain stable for millennia. In this study, SOM composition, distribution, and persistence were analyzed in the Brady Soil of Nebraska, USA to compare SOM spatial variability in modern and buried soils, as well as the impact of erosional exposure on SOM stability. The Brady Soil, formed as a surface soil during the Pleistocene-Holocene transition and now a paleosol buried up to 6 m deep (or more) by loess deposition during the Holocene, was sampled along burial (up to 5.8 m depth) and erosional (up to 1.8 m depth) transects to compare SOM dynamics in different geomorphic settings. Fourier Transform Infrared Spectroscopy (FTIR) and Fourier Transform ion cyclotron resonance mass spectrometry (FTICR-MS) were used to analyze SOM composition, while δ 13 C isotope analyses identified SOM sources and radiocarbon values were used to estimate turnover rates. Results confirmed a vegetation shift from C3 to C4 plants after Brady Soil formation, reflecting warming climatic conditions. Increasing SOM age and decreasing δ 13 C and δ 15 N values with depth indicated slowing of decomposition rate in buried soils. Higher pH in the Brady Soil suggested greater base cation content, supporting SOM stabilization through organo-mineral associations and aggregate formation. However, exposure of the Brady Soil due to surface erosion caused faster SOM turnover. This result suggested susceptibility of buried SOM to losses via decomposition upon erosional exposure, possibly accelerated by priming in response to modern SOM inputs. These findings highlight the potential loss of carbon stocks in buried soils under future climate change, as shifts in soil physicochemical properties may destabilize long-preserved SOM.

Environmental sciences↗
DOE OSTI2020

Redox-active dinuclear oxorhenium(V) pyrazolate complexes

Four new structurally similar dinuclear oxorhenium(V) complexes, [{Re(O)X(PPh 3 )} 2 (μ-O)(μ-4-x'-pz) 2 ], where pz = pyrazolate anion, X = X' = Cl (1) and Br (4), X = Cl, X' = Br (2), and X = Br, X' = Cl (3), have been synthesized and characterized. Little variation in spectroscopic features – 1 H NMR, IR, UV–Vis – exists among the four complexes. All complexes possess a bent Re-O-Re core as well as distorted octahedral coordination geometry around the rhenium centers. Finally, a reversible one-electron electrochemical process is observed at approximately 0.84 V vs. Fc + /Fc in all four complexes; however, changing the terminal halide from chloride to bromide slightly destabilizes the oxidized Re(VI) center.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Causal control design for wave energy converters with finite stroke

Control design is of central importance in the optimization of power generation from ocean wave energy converters (WECs). The problem is made challenging by the fact that the resource is vibratory and stochastic, with a low quality factor. It has recently been shown that when constrained to causality, the optimal feedback controller for a WEC is solvable in closed-form as a sign-indefinite LQG problem, for the case in which the WEC exhibits linear dynamics and quadratic power transmission dissipation. However, most WECs exhibit stroke limits, which must be explicitly accounted for in control design to avoid end-stop collisions. This is important because such collisions lead to damage, and also because the introduction of unmodeled stroke limits can actually destabilize the otherwise-optimal closed loop. We illustrate a control design technique to address this issue, which consists of two design steps. In the first step, LMI techniques are used to optimize the mean power harvested from waves with a known power spectral density, subject to several competing objectives. In the second step, the controller is augmented via a nonlinear passivity-based outer-loop design which guarantees to prevent stroke saturation while also guaranteeing to preserve closed-loop stability. Furthermore, the technique is illustrated using a model of a simple heaving point absorber, and verified in simulation.

16 TIDAL AND WAVE POWER↗
DOE OSTI2021

The influence of LiH and TiH 2 on hydrogen storage in MgB 2 II. XPS study of surface and near-surface phenomena

We report that Mg(BH 4 ) 2 is a promising solid-state hydrogen storage material, releasing 14.9 wt% hydrogen upon conversion to MgB 2 . The rehydrogenation of MgB 2 is particularly challenging, requiring prolonged exposure to high pressures of hydrogen at high temperature. Here we report an XPS study probing the influence of LiH and TiH 2 on the hydrogen storage properties of MgB 2 in the surface and near-surface regions, as a complementary investigation to a preceding study of the bulk properties. Surface and near-surface properties are important considerations for nanoscale and bulk hydrogen storage materials. If there are reactions occurring at the surface that modify the chemical composition in the near-surface region, species diffusion can alter the chemical composition even deep into the bulk of the material. For LiH/MgB 2 , metastable LiH–B and LiH–Mg species are produced that are more reactive than Bulk MgB 2 . With prolonged glovebox storage, the LiH/MgB 2 material shows increased reactivity towards O and C and enriched levels of Li and B in the near-surface region. In addition, Li induces the growth of Li 2 CO 3 in the surface and near surface regions. Exposing LiH/MgB 2 to hydrogen at 700 bar and 280 °C for 24 h produces borohydride at a temperature 100 °C below the threshold for bulk MgB 2 hydrogenation. In a specifically surface process with macroscopic implications, the hydrogenation conditions also cause Li 2 CO 3 to react with boron hydroxide in the sample to form a Li-deficient glassy lithium borate melt at the interfaces of the particles, bonding them together. Subsequent heating to 380 °C dehydrogenates the borohydride and eliminates the Li-deficient glassy lithium borate. The LiH/MgB 2 material is not reversible because desorption does not lead back to LiH/MgB 2 , but rather to elemental B and Mg metal in the near-surface region. In contrast to LiH, TiH 2 does not react with MgB 2 , despite the favorable thermodynamics for destabilization via TiB 2 formation. Furthermore, high pressure hydrogenation yields only unreacted TiH 2 and MgB 2 in the surface and near-surface regions. Thus, added TiH 2 provides no benefit to MgB 2 hydrogenation, in agreement with the findings of the preceding bulk study.

08 HYDROGEN↗
DOE OSTI2012

Energy and Entropy Effects in Dissociation of Peptide Radical Anions

Time- and collision energy-resolved surface-induced dissociation (SID) of peptide radical anions was studied for the first time using a Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS) configured for SID experiments. Peptide radical cations and anions were produced by gas-phase fragmentation of CoIII(salen)-peptide complexes. The effect of the charge, radical, and the presence of a basic residue on the energetics and dynamics of dissociation of peptide ions was examined using RVYIHPF (1) and HVYIHPF (2) as model systems. Comparison of the survival curves for of [M+H]{sup +}, [M-H]{sup -}, M{sup +{sm_bullet}}, and [M-2H]{sup -{sm_bullet}} ions of these precursors demonstrated that even-electron ions are more stable towards fragmentation than their odd-electron counterparts. RRKM modeling of the experimental data demonstrated that the lower stability of the positive radicals is mainly attributed to lower dissociation thresholds while entropy effects are responsible the relative instability of the negative radicals. Substitution of arginine with less basic histidine residue has a strong destabilizing effect on the [M+H]{sup +} ions and a measurable stabilizing effect on the odd-electron ions. Lower threshold energies for dissociation of both positive and negative radicals of 1 are attributed to the presence of lower-energy dissociation pathways that are most likely promoted by the presence of the basic residue.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Frozen storage of proteins: Use of mannitol to generate a homogenous freeze-concentrate

Therapeutic proteins may be subjected to several freeze–thaw cycles throughout manufacturing and storage. The protein solution composition and the freezing conditions may lead to incomplete ice crystallization in the frozen state. This can also result in freeze-concentrate heterogeneity characterized by multiple glass transition temperatures and protein destabilization. The overall objective was to investigate the potential advantages of including a crystallizing excipient (mannitol) along with a sugar (sucrose or trehalose) for frozen storage. Here, this study showed that the addition of mannitol, a readily crystallizing excipient, facilitated ice crystallization. Inclusion of an isothermal hold during cooling (annealing) maximized the mannitol crystallization and resulted in a homogenous freeze-concentrate of a constant composition characterized by a single glass transition temperature. The role of freezing rate and annealing on both mannitol and ice crystallization were discerned using high intensity synchrotron radiation. The addition of sucrose or trehalose, at an appropriate concentration, stabilized the protein. The mannitol to sugar ratio (3:1 or 1:1, 5 % w/v) was optimized to selectively cause maximal crystallization of mannitol while retaining the sugar amorphous. Human serum albumin (1 mg/mL) in these optimized and annealed compositions did not show any meaningful aggregation, even after multiple freeze–thaw cycles. Thus, in addition to a sugar as a stabilizer, the use of a crystallizing excipient coupled with an annealing step can provide an avenue for frozen storage of proteins.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Coupled geomechanical investigation of depletion-induced fault reactivation

Fault reactivation during subsurface fluid production pose significant challenges to safe and sustainable resource extraction. Here, this study presents a three-dimensional coupled geomechanical framework to investigate the processes driving fault reactivation, capturing the interactions between reservoir dynamics and geomechanical responses. Verification against theoretical estimations based on linear poroelasticity confirms the model's capacity in representing reservoir background stress responses. However, the study reveals that relying solely on background stress states can underestimate or overestimate fault reactivation potential, emphasizing the importance of including localized stress perturbations such as differential compaction and stress redistribution. Applied to a fault (M1) inspired by the geological characteristics of the Groningen field, the model shows slip initiation at 2965 m depth with 16.0 MPa depletion, aligning with field observations where seismicity occurred at approximately 3 km depth after 15.8 MPa depletion. Parametric studies reveal: (1) inelastic reservoir compaction delays fault reactivation and mitigates fault slip by reducing stress concentration, (2) higher intermediate in-situ stress magnitudes decrease the Coulomb Failure Stress (CFS) increase rate and reduce fault slip, (3) larger fault offsets amplify shear stress near the offset zone, promoting earlier reactivation and longer rupture propagation, and (4) fault permeability significantly influences pressure diffusion, with low-permeability faults leading to sharper stress changes and earlier fault destabilization. These insights highlight the critical role of geological and mechanical parameters in fault reactivation and provide a predictive framework for mitigating induced seismicity risks.

Coupled geomechanical modeling↗
DOE OSTI2025

Resilient information and inference networks under mixed-trust sensing

With ubiquitous digitization, sensing, and computational intelligence deployed in increasingly more and broader domains, including critical infrastructure, potentially misleading and destabilizing effects of multimodal anomalies and adversarial behavior are growing in importance. Here, we develop randomized and reinforcement learning-based strategies for strategically recruiting and utilizing deployed (and, thus, vulnerable and potentially faulty and/or compromised) nodes from information and inference networks, while defending against adversaries that attempt to misguide assessments of inferred variables. Recognizing that, besides communication and other costs, sampling from any observable node can either provide true data or dangerously expose our inference to misinformation (without being easily distinguishable what actually happens), the proposed strategies proceed by progressively recruiting nodes and cautiously scaling their information contribution based on assumed, or, in our reinforcement learning approach, intelligently weighed trustworthiness, with the learning approach also considering network-wide, threat-inclusive risk/value tradeoffs. While avoiding the hardware, communication, analytical and computational burden of explicit redundancy, the proposed defensive schemes enable on-the-fly assessments of underlying processes, and system-wide situational awareness with demonstrable resilience against adversarial activities.

97 - MATHEMATICS AND COMPUTING↗
DOE OSTI2022

The effect of 10 at.% Al addition on the hydrogen storage properties of the Ti 0.33 V 0.33 Nb 0.33 multi-principal element alloy

We report here a thorough study on the effect of 10 at.% Al addition into the ternary equimolar Ti 0.33 V 0.33 Nb 0.33 alloy on the hydrogen storage properties. Despite a decrease of the storage capacity by 20%, several other properties are enhanced by the presence of Al. The hydride formation is destabilized in the quaternary alloy as compared to the pristine ternary composition, as also confirmed by machine learning approach. The hydrogen desorption occurs at lower temperature in the Al-containing alloy relative to the initial material. Moreover, the Al presence improves the stability during hydrogen absorption/desorption cycling without significant loss of the capacity and phase segregation. Finally, this study proves that Al addition into multi-principal element alloys is a promising strategy for the design of novel materials for hydrogen storage.

36 MATERIALS SCIENCE↗
DOE OSTI2020

High susceptibility to adiabatic shear banding and high dynamic strength in tungsten heavy alloys with a high-entropy alloy matrix

The susceptibility to adiabatic shear banding (ASB) of tungsten heavy alloys (WHAs) is a key factor to determine their penetration performance for kinetic energy penetrators (KEPs). This work reports a novel WHA with strong susceptibility to ASB that uses a precipitation-hardening high-entropy alloy (HEA) as the binding phase of W particles. The results find that nanoscale L12 precipitates and high dislocation density in the matrix contribute a high dynamic yield strength of ~2300 MPa. Also, a narrow ASB with a width of ~12 μm forms in the novel WHA, which is only 6% of the width of ASB in traditional WHAs like W-NiFe, exhibiting a great susceptibility to ASB. The redissolution of precipitates into the matrix because of temperature rise during shearing could sharply soften the shearing location, which is suggested to be a very important factor of destabilizing mechanism to promote the development of ASB.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Phase stabilization and oxidation of a continuous composition spread multi-principal element (AlFeNiTiVZr) 1-x Cr x alloy

Multi-Principal Element Alloys (MPEA) have been hypothesized to maintain a stable single alloy phase and resist corrosion at high temperatures, which are desirable in various functional applications, including material of turbine blades. However, studies into oxidation resistant alloys have been constrained to individual MPEA systems or a limited selection of compositions within those systems. Here, High-Throughput Experimental (HTE) techniques were utilized to rapidly assess phase stability and resistance to oxidation of an (AlFeNiTiVZr) 1-x Cr x continuous composition spread (CCS) thin-film alloy system. High-throughput synchrotron diffraction and Raman spectroscopy were used to identify phases, especially high symmetry structures and oxides, as a function of annealing time and composition. The formation of two distinct phase regions, R 1 and R 2 , across the CCS was observed. One of these phase regions, R 2 , exhibited a stable high symmetry BCC-like phase at Cr concentrations greater than 25.4 at%, and grew a passivating mixed metal surface oxide; whereas, the R 1 phase region, decomposed on oxidation to multiple oxides and reacted with the substrate to form silicides. The passivating mixed metal oxide layer appears to prevent destabilization of the (AlFeNiTiVZr) 1-x Cr x MPEA BCC solid solution. Furthermore, at longer annealing times the passivating phase was seen only above 29.2 at% Cr. High Cr-doped (AlFeNiTiVZr) 1-x Cr x appear to be a good candidate for high temperature, oxidation-resistant structural alloys.

36 MATERIALS SCIENCE↗
DOE OSTI2022

The orbital effect on the anomalous magnetism and evolution in La $x$ Y 1-$x$ VO 3 (0 ≤ $x$ ≤ 0.2) single crystals

The orbital effect on the anomalous magnetism and evolution of single crystals with low La doping, La $x$ Y 1-$x$ VO 3 ($x$ = 0, 0.1, and 0.2), has been studied using single-crystal X-ray diffraction, specific heat, magnetization, and Raman-scattering techniques. It is found that substituting Y 3+ by La 3+ increases the degeneracy of the $yz/zx$ orbitals and decreases the Jahn-Teller distortion. These weakens the G-type (antiphase ordering along the c axis) orbital ordering phase. Meanwhile, the substituting decreases the magnetism entropy, indicating the shrinking of the t 2g and e g orbital hybridization, eventually destabilizing the C-type (in-phase ordering along the c axis) antiferromagnetic ordering phase. In addition, the mechanism for the shrinking of the diamagnetism with increasing $x$ is analyzed. In conclusion, it may attribute to the competition between the antisymmetric Dzyaloshinsky–Moriya interaction and the single-ion anisotropy.

36 MATERIALS SCIENCE↗
DOE OSTI2026

Characterization of γ′/γ″ compact and sandwich type precipitates during long-term high-temperature exposure in Ni-based superalloys

Here, the formation of γ′/γ″ co-precipitates is investigated in Ni-based superalloys with a varying Ti/Al ratio and Ta content and their stability is studied using long-term high-temperature exposure. Transmission electron microscopy and atom probe tomography analyses demonstrate that both higher Ti/Al ratios and increased Ta promote γ″ phase formation, leading to sandwich and compact structures. The compact co-precipitation significantly reduces γ′ precipitate coarsening during 10,000 h exposure at 700°C by restricting elemental diffusion, particularly of aluminum, from the γ matrix to the γ′ phase. For the alloy without a compact structure, and only γʹ precipitates, at the beginning of the exposure, the coarsening rate over 10,000 h was 3.5 times faster than for the alloy with compact γʹ/γʺ precipitates. Evidence of destabilization of the compact morphology was found to occur between 5,000 and 10,000 h exposure and originated from the extensive formation and growth of δ platelets that extended throughout the grains. Thus, the outer layer of the compact, which consists of γʺ, was subjected to the γ″ to δ phase transformation.

gamma double prime↗
DOE OSTI2022

Stabilization of glucose-6-phosphate dehydrogenase oligomers enhances catalytic activity and stability of clinical variants

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is a genetic trait that can cause hemolytic anemia. To date, over 150 nonsynonymous mutations have been identified in G6PD, with pathogenic mutations clustering near the dimer and/or tetramer interface and the allosteric NADP + -binding site. Recently, our lab identified a small molecule that activates G6PD variants by stabilizing the allosteric NADP + and dimer complex, suggesting therapeutics that target these regions may improve structural defects. Here, we elucidated the connection between allosteric NADP + binding, oligomerization, and pathogenicity to determine whether oligomer stabilization can be used as a therapeutic strategy for G6PD deficiency (G6PD def ). We first solved the crystal structure for G6PD K403Q , a mutant that mimics the physiological acetylation of wild-type G6PD in erythrocytes and demonstrated that loss of allosteric NADP + binding induces conformational changes in the dimer. These structural changes prevent tetramerization, are unique to Class I variants (the most severe form of G6PD def ), and cause the deactivation and destabilization of G6PD. We also introduced nonnative cysteines at the oligomer interfaces and found that the tetramer complex is more catalytically active and stable than the dimer. Furthermore, stabilizing the dimer and tetramer improved protein stability in clinical variants, regardless of clinical classification, with tetramerization also improving the activity of G6PD K403Q and Class I variants. These findings were validated using enzyme activity and thermostability assays, analytical size-exclusion chromatography (SEC), and SEC coupled with small-angle X-ray scattering (SEC-SAXS). Taken together, our findings suggest a potential therapeutic strategy for G6PD def and provide a foundation for future drug discovery efforts.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Primer terminal ribonucleotide alters the active site dynamics of DNA polymerase η and reduces DNA synthesis fidelity

DNA polymerases catalyze DNA synthesis with high efficiency, which is essential for all life. Extensive kinetic and structural efforts have been executed in exploring mechanisms of DNA polymerases, surrounding their kinetic pathway, catalytic mechanisms, and factors that dictate polymerase fidelity. Recent time-resolved crystallography studies on DNA polymerase η (Pol η) and β have revealed essential transient events during the DNA synthesis reaction, such as mechanisms of primer deprotonation, separated roles of the three metal ions, and conformational changes that disfavor incorporation of the incorrect substrate. DNA-embedded ribonucleotides (rNs) are the most common lesion on DNA and a major threat to genome integrity. While kinetics of rN incorporation has been explored and structural studies have revealed that DNA polymerases have a steric gate that destabilizes ribonucleotide triphosphate binding, the mechanism of extension upon rN addition remains poorly characterized. Using steady-state kinetics, static and time-resolved X-ray crystallography with Pol η as a model system, we showed that the extra hydroxyl group on the primer terminus does alter the dynamics of the polymerase active site as well as the catalysis and fidelity of DNA synthesis. During rN extension, Pol η error incorporation efficiency increases significantly across different sequence contexts. Finally, our systematic structural studies suggest that the rN at the primer end improves primer alignment and reduces barriers in C2'-endo to C3'-endo sugar conformational change. Overall, our work provides further mechanistic insights into the effects of rN incorporation on DNA synthesis.

59 BASIC BIOLOGICAL SCIENCES↗