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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 253 records · Page 14
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Intrinsically Bifunctional and Tunable Tungsten Carbide Catalysts Enable Efficient PVC-Compatible Polyolefin Hydrocracking

Hydrocracking is a promising route for the chemical recycling of polyolefins (PO), converting them into short hydrocarbons over bifunctional catalysts with metal sites for hydrogenation and dehydrogenation, and Brønsted acid sites (BAS) for isomerization and C–C bond cleavage. However, PO feedstocks containing polyvinyl chloride (PVC) can release chlorine (Cl) under reaction conditions, deactivating conventional noble metal/zeolite catalysts. Moreover, the lack of site intimacy and the presence of micropores within conventional catalysts create challenges around the transport of high-molecular-weight, sterically encumbered polymer intermediates. Here, in this study, we report tungsten carbides (W x C) as a novel type of bifunctional catalysts that address these challenges. W/W 2 C phases on W x C offer “metal” sites, and −OH on WO x species introduces BAS in close proximity. The “metal”:BAS ratio can be tuned through carburization temperature, leading to a volcano-shaped activity trend reflecting the requirement for metal–BAS balance. Kinetic data demonstrate that each PO chain undergoes sequential cleavage, while trends in cracking ideality and selectivity follow those in short-alkane hydrocracking. On the per-BAS basis, W x C is more efficient than conventional bifunctional catalysts by more than an order of magnitude, due to enhanced polymer transport. They maintain or show increased activity with 10 wt % PVC in the substrate. This work establishes transition-metal carbides as earth-abundant bifunctional catalysts with unique site proximity and heteroatom compatibility. These features, along with the broad structure space for rational tuning, make them promising options to tackle specific challenges that polymer feedstocks present in hydrocracking.

Nwachukwu, Uchenna C. [Univ. of Akron, OH (United ↗
DOE OSTI2026

A Mesopore-Confined and Graphene Oxide-Localized Ruthenium Catalyst Increases Rates of Mid-Chain Polyolefin Hydrogenolysis

A catalyst architecture with mesoporous silica coating Ru nanoparticles on reduced graphene oxide (mSiO 2 /Ru/rGO) localizes the 2 nm Ru solely at the closed bottoms of 2.9 nm diameter mesopores. mSiO 2 /Ru/rGO catalyzes the rapid, selective hydrogenolysis of polyolefins at wax formation rates (ν wax ) up to 1700 g wax ·g Ru –1 ·h –1 and a turnover frequency (TOF) for C–C bond cleavage of 130 ± 8 min –1 . The ν wax and TOF for mSiO 2 /Ru/rGO are 23× and 16× those of nonporous Ru/rGO, respectively, indicating that faster chain cleavage is also more selective inside mesopores. The methane yield from mSiO 2 /Ru/rGO is ca. 30% of the value obtained from Ru/rGO. Methane decreases, and wax selectivity improves with narrow-pore (2.3 nm) mSiO 2 /Ru/rGO. The reaction rate decreases at lower and higher H 2 pressures from its maximum at 37 bar. Log(TOF)-log(P H2 ) plots reveal rates ∝ [P H2 ] 2.8 or [P H2 ] −2.0 in the lower or higher pressure ranges, respectively. Corresponding plots for Ru/C give rates ∝ [P H2 ] 1 or [P H2 ] −2.4 . Ru is hydrocarbon-covered at low pressure; thus, the higher H 2 order for mSiO 2 /Ru/rGO indicates that mesopores increase the density of cleavable unsaturated moieties on the Ru surface. The lower H 2 order on Ru/C implies a lower density of cleavable groups because saturated segments occupy a larger fraction of the Ru surface. Higher surface occupancy by the hydrocarbon reactant correlates with more methane formation. Therefore, pore confinement, narrower pore diameter in mSiO 2 /Ru/rGO, or higher H 2 pressure leads to lower methane yields. Ru nanoparticles in mSiO 2 /Ru/rGO maintain equivalent activity and selectivity over five recycling tests.

Catalysts↗
DOE OSTI2026

Heterobimetallic Iridium-Niobia Catalyst for Efficient and Selective Methane Ammonia Reforming

A Surface OrganoMetallic Chemistry (SOMC) approach, leveraging a molecularly defined heterobimetallic niobium–iridium complex, was used to prepare a mesoporous SBA-15 silica-supported Ir-NbOx catalyst. The resulting Ir-NbOx/SiO2 catalyst exhibited excellent catalytic performance in selective methane/ammonia reforming. Specifically, the Ir-NbOx/SiO2 catalyst showed significantly higher activity (turnover frequency 8.5 s–1), selectivity (75%), and stability than the Ir/SiO2 analog, whereas the NbOx/SiO2 counterpart was almost inactive. This contrasts with ethane/ammonia reforming via C–C cleavage, for which the bimetallic Ir-NbOx/SiO2 was less active than Ir/SiO2, demonstrating tuned selectivity toward C–H activation rather than C–C cleavage due to the Ir/NbOx synergy. Importantly, an Ir-NbOx/SiO2 reference catalyst, prepared by conventional impregnation/calcination/reduction steps, was found to be inactive, highlighting the value of the SOMC catalyst preparation approach using well-defined heterobimetallic precursors. These results represent a significant advance over existing catalysts due to the atomic-scale synergy between Ir and NbOx sites, enabling access to activity and selectivity regimes inaccessible to monometallic analogs.

Wu, Jiachun↗
DOE OSTI2020

Internal Fragments Generated by Electron Ionization Dissociation Enhance Protein Top-Down Mass Spectrometry

Top-down proteomics by mass spectrometry (MS) involves the mass measurement of an intact protein followed by subsequent activation of the protein to generate product ions. Electron-based fragmentation methods like electron capture dissociation and electron transfer dissociation are widely used for these types of analyses. Recently, electron ionization dissociation (EID), which utilizes higher energy electrons (>20 eV) has been suggested to be more efficient for top-down protein fragmentation compared to other electron-based dissociation methods. In this paper, we demonstrate that the use of EID enhances protein fragmentation and subsequent detection of protein fragments. Protein product ions can form by either single cleavage events, resulting in terminal fragments containing the C-terminus or N-terminus of the protein, or by multiple cleavage events to give rise to internal fragments that include neither the C-terminus nor the N-terminus of the protein. Conventionally, internal fragments have been disregarded, as reliable assignments of these fragments were limited. Here, we demonstrate that internal fragments generated by EID can account for ~20–40% of the mass spectral signals detected by top-down EID-MS experiments. By including internal fragments, the extent of the protein sequence that can be explained from a single tandem mass spectrum increases from ~50 to ~99% for 29 kDa carbonic anhydrase II and 8.6 kDa ubiquitin. When searching for internal fragments during data analysis, previously unassigned peaks can be readily and accurately assigned to confirm a given protein sequence and to enhance the utility of top-down protein sequencing experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Structural basis for Ca2+-dependent activation of a plant metacaspase

Abstract Plant metacaspases mediate programmed cell death in development, biotic and abiotic stresses, damage-induced immune response, and resistance to pathogen attack. Most metacaspases require Ca 2+ for their activation and substrate processing. However, the Ca 2+ -dependent activation mechanism remains elusive. Here we report the crystal structures of Metacaspase 4 from Arabidopsis thaliana ( At MC4) that modulates Ca 2+ -dependent, damage-induced plant immune defense. The At MC4 structure exhibits an inhibitory conformation in which a large linker domain blocks activation and substrate access. In addition, the side chain of Lys225 in the linker domain blocks the active site by sitting directly between two catalytic residues. We show that the activation of At MC4 and cleavage of its physiological substrate involve multiple cleavages in the linker domain upon activation by Ca 2+ . Our analysis provides insight into the Ca 2+ -dependent activation of At MC4 and lays the basis for tuning its activity in response to stresses for engineering of more sustainable crops for food and biofuels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A unique Co@CoO catalyst for hydrogenolysis of biomass-derived 5-hydroxymethylfurfural to 2,5-dimethylfuran

The development of precious-metal-free catalysts to promote the sustainable production of fuels and chemicals from biomass remains an important and challenging target. Here, we report the efficient hydrogenolysis of biomass-derived 5-hydroxymethylfurfural to 2,5-dimethylfuran over a unique core-shell structured catalyst, Co@CoO that affords the highest productivity among all catalysts, including noble-metal-based catalysts, reported to date. Surprisingly, we find that the catalytically active sites reside on the shell of CoO with oxygen vacancies rather than the metallic Co. The combination of various spectroscopic experiments and computational modelling reveals that the CoO shell incorporating oxygen vacancies not only drives the heterolytic cleavage, but also the homolytic cleavage of H 2 to yield more active H δ- species, resulting in the exceptional catalytic activity. Co@CoO also exhibits excellent activity toward the direct hydrodeoxygenation of lignin model compounds. This study unlocks, for the first time, the potential of simple metal-oxide-based catalysts for the hydrodeoxygenation of renewable biomass to chemical feedstocks.

09 BIOMASS FUELS↗
DOE OSTI2022

Proteolytic processing induces a conformational switch required for antibacterial toxin delivery

Many Gram-negative bacteria use CdiA effector proteins to inhibit the growth of neighboring competitors. CdiA transfers its toxic CdiA-CT region into the periplasm of target cells, where it is released through proteolytic cleavage. The N-terminal cytoplasm-entry domain of the CdiA-CT then mediates translocation across the inner membrane to deliver the C-terminal toxin domain into the cytosol. Here, we show that proteolysis not only liberates the CdiA-CT for delivery, but is also required to activate the entry domain for membrane translocation. Translocation function depends on precise cleavage after a conserved VENN peptide sequence, and the processed ΔVENN entry domain exhibits distinct biophysical and thermodynamic properties. By contrast, imprecisely processed CdiA-CT fragments do not undergo this transition and fail to translocate to the cytoplasm. These findings suggest that CdiA-CT processing induces a critical structural switch that converts the entry domain into a membrane-translocation competent conformation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Tuning hydrogenation chemistry of Pd-based heterogeneous catalysts by introducing homogeneous-like ligands

Abstract Noble metals have been extensively employed in a variety of hydrotreating catalyst systems for their featured functionality of hydrogen activation but may also bring side reactions such as undesired deep hydrogenation. It is crucial to develop a viable approach to selectively inhibit side reactions while preserving beneficial functionalities. Herein, we present modifying Pd with alkenyl-type ligands that forms homogeneous-like Pd-alkene metallacycle structure on the heterogeneous Pd catalyst to achieve the selective hydrogenolysis and hydrogenation. Particularly, a doped alkenyl-type carbon ligand on Pd-Fe catalyst is demonstrated to donate electrons to Pd, creating an electron-rich environment that elongates the distance and weakens the electronic interaction between Pd and unsaturated C of the reactants/products to control the hydrogenation chemistry. Moreover, high H 2 activation capability is maintained over Pd and the activated H is transferred to Fe to facilitate C-O bond cleavage or directly participate in the reaction on Pd. The modified Pd-Fe catalyst displays comparable C-O bond cleavage rate but much higher selectivity (>90%) than the bare Pd-Fe (<50%) in hydrotreating of diphenyl ether (DPE, modelling the strongest C-O linkage in lignin) and enhanced ethene selectivity (>90%) in acetylene hydrogenation. This work sheds light on the controlled synthesis of selective hydrotreating catalysts via mimicking homogeneous analogues.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Plutonium(III) versus uranium(III) and samarium(III) in small molecule activation chemistry

We report the PuIII complex, [PuIII(CpMe4)3] (1-Pu), and demonstrate its differences in small molecule reactivity compared to the UIII and SmIII analogs, [UIII(CpMe4)3] (1-U) and [SmIII(CpMe4)3] (1-Sm), respectively. 1-Pu reductively cleaves the small molecule (PhS)2, affording a PuIII complex, [{PuIII(CpMe4)2}2(μ-SPh)2] (2-Pu), while retaining the PuIII center and eliminating (CpMe4)2 as a by-product, a fingerprint of a sterically induced reduction (SIR) reaction. Sm is often used as a surrogate for Pu, but the analogous [SmIII(CpMe4)3], (1-Sm), is unreactive. The (PhS)2 cleavage by 1-U proceeds solely via a metal-based oxidation (i.e., UIII → UIV), to form [UIV(CpMe4)3(SPh)] (3-U). Only 1-U reacts with (PhHN)2, affording the reductive cleavage product, [UIV(CpMe4)3(NHPh)] (4-U). The difference in reactivity of 1-Pu compared to complexes 1-Sm and 1-U was unexpected, and since SIR chemistry can enable complexes to participate in otherwise impossible reductive transformation of substrates, this reinforces the importance of studying small molecule reactivity with the transuranic elements.

Keener, Megan↗
DOE OSTI2025

Cross-kingdom comparative genomics reveal the metabolic potential of fungi for lignin turnover in deadwood

Deadwood is a major carbon source in forests, and yet the fate of this carbon remains a gap in our understanding of global carbon cycling. Lignin, the most recalcitrant biopolymer in wood, is mainly decayed through extracellular enzymatic and chemical processes initiated by white-rot fungi. However, the intracellular conversion of lignin decay products has been overlooked in the fungal kingdom. Here we integrate comparative genomic and phylogenetic analyses to understand the distribution and evolution of enzymes responsible for modifying lignin-related aromatic compounds—such as decarboxylases, hydroxylases, dioxygenases and other downstream ring-cleavage enzymes—that funnel carbon to central metabolism across the bacterial and the fungal kingdoms. We demonstrate that specific fungal lineages conserve these enzyme families, and that the abilities to enzymatically depolymerize lignin and catabolize lignin-related aromatic compounds are not necessarily coupled. Our analyses also reveal an expanded substrate specificity of aromatic ring-cleavage enzymes during fungal evolution, as well as a clade of extracellular enzymes among them, broadening the spatial range of these biochemical capabilities. Together, our results highlight a large diversity of fungal enzymes and hosts that warrant further investigation for inclusion into carbon cycling models and biotechnological applications for the conversion of aromatic compounds.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Cofactorless oxygenases guide anthraquinone-fused enediyne biosynthesis

The anthraquinone-fused enediynes (AFEs) combine an anthraquinone moiety and a ten-membered enediyne core capable of generating a cytotoxic diradical species. AFE cyclization is triggered by opening the F-ring epoxide, which is also the site of the most structural diversity. Previous studies of tiancimycin A, a heavily modified AFE, have revealed a cryptic aldehyde blocking installation of the epoxide, and no unassigned oxidases could be predicted within the tnm biosynthetic gene cluster. Here, in this study, we identify two consecutively acting cofactorless oxygenases derived from methyltransferase and α/β-hydrolase protein folds, TnmJ and TnmK2, respectively, that are responsible for F-ring tailoring in tiancimycin biosynthesis by comparative genomics. Further biochemical and structural characterizations reveal that the electron-rich AFE anthraquinone moiety assists in catalyzing deformylation, epoxidation and oxidative ring cleavage without exogenous cofactors. These enzymes therefore fill important knowledge gaps for the biosynthesis of this class of molecules and the underappreciated family of cofactorless oxygenases. Cofactorless oxygenases are rare in nature and natural product biosynthesis. Here the authors describe the biochemical and structural characterization of two such oxygenases catalyzing deformylation, ring cleavage and epoxidation in the biosynthesis of the enediyne natural product tiancimycin A.

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

Ultrasmall amorphous zirconia nanoparticles catalyse polyolefin hydrogenolysis

Carbon–carbon bond cleavage reactions, adapted to deconstruct aliphatic hydrocarbon polymers and recover the intrinsic energy and carbon value in plastic waste, have typically been catalysed by metal nanoparticles or air-sensitive organometallics. Metal oxides that serve as supports for these catalysts are typically considered to be inert. Here we show that Earth-abundant, non-reducible zirconia catalyses the hydrogenolysis of polyolefins with activity rivalling that of precious metal nanoparticles. To harness this unusual reactivity, our catalytic architecture localizes ultrasmall amorphous zirconia nanoparticles between two fused platelets of mesoporous silica. Macromolecules translocate from bulk through radial mesopores to the highly active zirconia particles, where the chains undergo selective hydrogenolytic cleavage into a narrow, C18-centred distribution. Calculations indicated that C–H bond heterolysis across a Zr–O bond of a Zr(O) 2 adatom model for unsaturated surface sites gives a zirconium hydrocarbyl, which cleaves a C–C bond via β-alkyl elimination.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

A plant host, Nicotiana benthamiana, enables the production and study of fungal lignin-degrading enzymes

Abstract Lignin has significant potential as an abundant and renewable source for commodity chemicals yet remains vastly underutilized. Efforts towards engineering a biochemical route to the valorization of lignin are currently limited by the lack of a suitable heterologous host for the production of lignin-degrading enzymes. Here, we show that expression of fungal genes in Nicotiana benthamiana enables production of members from seven major classes of enzymes associated with lignin degradation (23 of 35 tested) in soluble form for direct use in lignin activity assays. We combinatorially characterized a subset of these enzymes in the context of model lignin dimer oxidation, revealing that fine-tuned coupling of peroxide-generators to peroxidases results in more extensive C-C bond cleavage compared to direct addition of peroxide. Comparison of peroxidase isoform activity revealed that the extent of C-C bond cleavage depends on peroxidase identity, suggesting that peroxidases are individually specialized in the context of lignin oxidation. We anticipate the use of N. benthamiana as a platform to rapidly produce a diverse array of fungal lignin-degrading enzymes will facilitate a better understanding of their concerted role in nature and unlock their potential for lignin valorization, including within the plant host itself.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Binding of saturated and unsaturated C 6 -hydrocarbons to the electrophilic anion [B 12 Br 11 ] – : a systematic mechanistic study

The highly reactive gaseous ion [B 12 Br 11 ] – is a metal-free closed-shell anion which spontaneously forms covalent bonds with hydrocarbon molecules, including alkanes. Herein, we systematically investigate the reaction mechanism for binding of [B 12 Br 11 ] – to the five hexane isomers yielding [B 12 Br 11 (C 6 H 14 )] – , as well as to cyclohexane and several hexene isomers (yielding [B 12 Br 11 (C 6 H 12 )] – ) using collision-induced dissociation (CID), infrared photodissociation spectroscopy (IRPD) and computational methods. CID of the different [B 12 Br 11 (C 6 H 14 )] – ions results in distinct fragmentation patterns dependent on the structure of the hexane isomer. Further, the observed fragmentation reactions provide insights into the addition mechanism of [B 12 Br 11 ] – to hexane. Based on the observed CID patterns, we identified that either B–C bond formation through heterolytic C–C or C–H bond cleavages or B–H bond formation through heterolytic C–H cleavage occur dependent on the structure of the hexane isomer. Meanwhile, we observe identical CID spectra of adducts originating from isomers of C 6 H 12 . Spectroscopic investigations of adducts of 1-hexene and cyclohexane indicate the same product structure with an open C 6 chain. Computational investigations evidenced that low lying transition states are present, which enable a ring opening reaction of cyclohexane when binding to [B 12 Br 11 ] – .

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Controlled monodefluorination and alkylation of C(sp 3 )–F bonds by lanthanide photocatalysts: importance of metal–ligand cooperativity

The controlled functionalization of a single fluorine in a CF 3 group is difficult and rare. Photochemical C–F bond functionalization of the sp 3 -C–H bond in trifluorotoluene, PhCF 3 , is achieved using catalysts made from earth-abundant lanthanides, (Cp Me4 ) 2 Ln(2-O-3,5- t Bu 2 -C 6 H 2 )(1-C{N(CH) 2 N( i Pr)}) (Ln = La, Ce, Nd and Sm, Cp Me4 = C 5 Me 4 H). The Ce complex is the most effective at mediating hydrodefluorination and defluoroalkylative coupling of PhCF 3 with alkenes; addition of magnesium dialkyls enables catalytic C–F bond cleavage and C–C bond formation by all the complexes. Mechanistic experiments confirm the essential role of the Lewis acidic metal and support an inner-sphere mechanism of C–F activation. Computational studies agree that coordination of the C–F substrate is essential for C–F bond cleavage. The unexpected catalytic activity for all members is made possible by the light-absorbing ability of the redox non-innocent ligands. The results described herein underscore the importance of metal–ligand cooperativity, specifically the synergy between the metal and ligand in both light absorption and redox reactivity, in organometallic photocatalysis.

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

Theoretical assessments of Pd–PdO phase transformation and its impacts on H 2 O 2 synthesis and decomposition pathways

The direct synthesis of H 2 O 2 from O 2 and H 2 provides a green pathway to produce H 2 O 2 , a popular industrial oxidant. Here, in this study, we theoretically investigate the effects of Pd oxidation states, coordination environments, and particle sizes on primary H 2 O 2 selectivities, assessed by calculating the ratio of rate constants for the formation of H 2 O 2 (via OOH* reduction; k O–H ) and the decomposition of OOH* (via O–O cleavage; k O–O ). For Pd metals, the k O–H /k O–O ratio decreased from 10 -4 for Pd(111) to 10 -10 for the Pd 13 cluster at 300 K, indicating poorer H 2 O 2 selectivity as Pd particle size decreases and low primary selectivities for H 2 O 2 overall. As the oxygen chemical potential increases and metals form surface and bulk oxides, the perturbation of Pd–Pd ensemble sites by lattice O atoms results in selectivities that become dramatically higher than unity. For instance, at 300 K, the k O–H /k O–O ratio increases significantly from 10 -4 to 10 9 to 10 16 as Pd(111) oxidizes to Pd 5 O 4 /Pd(111) and to PdO(100), respectively. In contrast, such selectivity enhancements are not observed for surface and bulk oxides that persistently contain rows of more metallic, undercoordinated Pd–Pd ensemble sites, such as PdO(101)/Pd(100) and PdO(101). These Pd–Pd ensembles are also absent when smaller Pd nanoparticles fully oxidize, indicating that smaller PdO clusters can be more selective for H 2 O 2 synthesis. These trends for primary H 2 O 2 selectivities were found to inversely correlate with trends for H 2 O 2 decomposition rates via O–O bond cleavage, demonstrating that catalysts with high primary H 2 O 2 selectivity can also hinder H 2 O 2 decomposition. Ab initio thermodynamic calculations are used to estimate the thermodynamically favored phase among Pd, PdO/Pd and PdO in O 2 , H 2 O 2 /H 2 O, and O 2 /H 2 environments. These results are combined to show that smaller Pd nanoparticles are more prone to be oxidized at lower oxygen chemical potentials, upon which they become more selective than larger Pd particles for H 2 O 2 synthesis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling

The CRISPR-Cas9 nuclease has been widely repurposed as a molecular and cell biology tool for its ability to programmably target and cleave DNA. Cas9 recognizes its target site by unwinding the DNA double helix and hybridizing a 20-nucleotide section of its associated guide RNA to one DNA strand, forming an R-loop structure. A dynamic and mechanical description of R-loop formation is needed to understand the biophysics of target searching and develop rational approaches for mitigating off-target activity while accounting for the influence of torsional strain in the genome. Here we investigate the dynamics of Cas9 R-loop formation and collapse using rotor bead tracking (RBT), a single-molecule technique that can simultaneously monitor DNA unwinding with base-pair resolution and binding of fluorescently labeled macromolecules in real time. By measuring changes in torque upon unwinding of the double helix, we find that R-loop formation and collapse proceed via a transient discrete intermediate, consistent with DNA:RNA hybridization within an initial seed region. Using systematic measurements of target and off-target sequences under controlled mechanical perturbations, we characterize position-dependent effects of sequence mismatches and show how DNA supercoiling modulates the energy landscape of R-loop formation and dictates access to states competent for stable binding and cleavage. Consistent with this energy landscape model, in bulk experiments we observe promiscuous cleavage under physiological negative supercoiling. The detailed description of DNA interrogation presented here suggests strategies for improving the specificity and kinetics of Cas9 as a genome engineering tool and may inspire expanded applications that exploit sensitivity to DNA supercoiling.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Potent CRISPR-Cas9 inhibitors from Staphylococcus genomes

Anti-CRISPRs (Acrs) are small proteins that inhibit the RNA-guided DNA targeting activity of CRISPR-Cas enzymes. Encoded by bacteriophage and phage-derived bacterial genes, Acrs prevent CRISPR-mediated inhibition of phage infection and can also block CRISPR-Cas-mediated genome editing in eukaryotic cells. To identify Acrs capable of inhibiting Staphylococcus aureus Cas9 (SauCas9), an alternative to the most commonly used genome editing protein Streptococcus pyogenes Cas9 (SpyCas9), we used both self-targeting CRISPR screening and guilt-by-association genomic search strategies. Here we describe three potent inhibitors of SauCas9 that we name AcrIIA13, AcrIIA14, and AcrIIA15. These inhibitors share a conserved N-terminal sequence that is dispensable for DNA cleavage inhibition and have divergent C termini that are required in each case for inhibition of SauCas9-catalyzed DNA cleavage. In human cells, we observe robust inhibition of SauCas9-induced genome editing by AcrIIA13 and moderate inhibition by AcrIIA14 and AcrIIA15. We also find that the conserved N-terminal domain of AcrIIA13–AcrIIA15 binds to an inverted repeat sequence in the promoter of these Acr genes, consistent with its predicted helix-turn-helix DNA binding structure. These data demonstrate an effective strategy for Acr discovery and establish AcrIIA13–AcrIIA15 as unique bifunctional inhibitors of SauCas9.

59 BASIC BIOLOGICAL SCIENCES↗