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At least 73 records · Page 4

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DOE OSTI2021

Reconfigurable Two‐Dimensional DNA Lattices: Static and Dynamic Angle Control

Abstract Branched DNA motifs serve as the basic construction elements for all synthetic DNA nanostructures. However, precise control of branching orientation remains a key challenge to further heighten the overall structural order. In this study, we use two strategies to control the branching orientation. The first one is based on immobile Holliday junctions which employ specific nucleotide sequences at the branch points which dictate their orientation. The second strategy is to use angle‐enforcing struts to fix the branching orientation with flexible spacers at the branch points. We have also demonstrated that the branching orientation control can be achieved dynamically, either by canonical Watson–Crick base pairing or non‐canonical nucleobase interactions (e.g., i‐motif and G‐quadruplex). With precise angle control and feedback from the chemical environment, these results will enable novel DNA nanomechanical sensing devices, and precisely‐ordered three‐dimensional architectures.

Wang, Wen↗

DOE OSTI2022

Catalytic DNA Polymerization Can Be Expedited by Active Product Release**

Abstract The sequence‐specific hybridization of DNA facilitates its use as a building block for designer nanoscale structures and reaction networks that perform computations. However, the strong binding energy of Watson–Crick base pairing that underlies this specificity also causes the DNA dehybridization rate to depend sensitively on sequence length and temperature. This strong dependency imposes stringent constraints on the design of multi‐step DNA reactions. Here we show how an ATP‐dependent helicase, Rep‐X, can drive specific dehybridization reactions at rates independent of sequence length, removing the constraints of equilibrium on DNA hybridization and dehybridization. To illustrate how this new capacity can speed up designed DNA reaction networks, we show that Rep‐X extends the range of conditions where the primer exchange reaction, which catalytically adds a domain provided by a hairpin template to a DNA substrate, proceeds rapidly.

Moerman, Pepijn G.↗

DOE OSTI2023

Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles

Abstract Non‐canonical interactions in DNA remain under‐explored in DNA nanotechnology. Recently, many structures with non‐canonical motifs have been discovered, notably a hexagonal arrangement of typically rhombohedral DNA tensegrity triangles that forms through non‐canonical sticky end interactions. Here, we find a series of mechanisms to program a hexagonal arrangement using: the sticky end sequence; triangle edge torsional stress; and crystallization condition. We showcase cross‐talking between Watson–Crick and non‐canonical sticky ends in which the ratio between the two dictates segregation by crystal forms or combination into composite crystals. Finally, we develop a method for reconfiguring the long‐range geometry of formed crystals from rhombohedral to hexagonal and vice versa. These data demonstrate fine control over non‐canonical motifs and their topological self‐assembly. This will vastly increase the programmability, functionality, and versatility of rationally designed DNA constructs.

Lu, Brandon↗

DOE OSTI2021

Reconfigurable Two-Dimensional DNA Lattices: Static and Dynamic Angle Control

Branched DNA motifs serve as the basic construction elements for all synthetic DNA nanostructures. However, precise control of branching orientation remains a key challenge to further heighten the overall structural order. Here in this study, we use two strategies to control the branching orientation. The first one is based on immobile Holliday junctions which employ specific nucleotide sequences at the branch points which dictate their orientation. The second strategy is to use angle-enforcing struts to fix the branching orientation with flexible spacers at the branch points. We have also demonstrated that the branching orientation control can be achieved dynamically, either by canonical Watson–Crick base pairing or non-canonical nucleobase interactions (e.g., i-motif and G-quadruplex). With precise angle control and feedback from the chemical environment, these results will enable novel DNA nanomechanical sensing devices, and precisely-ordered three-dimensional architectures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Catalytic DNA Polymerization Can Be Expedited by Active Product Release**

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Programmable 3D Hexagonal Geometry of DNA Tensegrity Triangles

Non-canonical interactions in DNA remain under-explored in DNA nanotechnology. Recently, many structures with non-canonical motifs have been discovered, notably a hexagonal arrangement of typically rhombohedral DNA tensegrity triangles that forms through non-canonical sticky end interactions. Here, in this study, we find a series of mechanisms to program a hexagonal arrangement using: the sticky end sequence; triangle edge torsional stress; and crystallization condition. We showcase cross-talking between Watson–Crick and non-canonical sticky ends in which the ratio between the two dictates segregation by crystal forms or combination into composite crystals. Finally, we develop a method for reconfiguring the long-range geometry of formed crystals from rhombohedral to hexagonal and vice versa. These data demonstrate fine control over non-canonical motifs and their topological self-assembly. This will vastly increase the programmability, functionality, and versatility of rationally designed DNA constructs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers

ABSTRACT Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building, and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular complexes containing nucleic acids. Here, we report a quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs; however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non‐canonical regions where, for example, the nucleic‐acid backbone bends, deviating from an A‐form helix geometry, or a base forms a non‐standard hydrogen bond (not a Watson‐Crick base pair). These bends and non‐canonical interactions are integral to forming functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life cycle, posing a future challenge for the community.

Biochemistry & Molecular Biology↗

DOE OSTI2023

Synthesis and Structural Characterization of 2′‐Deoxy‐2′‐Methoxy‐ L ‐Cytidine Nucleic Acids

Abstract We report here for the first time the synthesis of a novel 2′‐methoxy‐modified L‐cytidine analog and its phosphoramidite, as well as its incorporation into oligonucleotides via solid‐phase synthesis. Our measure the thermostability of the modified L‐nucleic acids by UV‐melting studies, and find out the 2′‐methoxy‐derivatization enhances the thermostability of the L‐duplexes. Consistent with the thermostability result, our X‐ray crystal structure study reveals that the 2′‐methoxy‐L‐deoxycytidine forms the Watson‐Crick base pair with L‐guanosine virtually as the mirror‐image fashion of native pair. This novel chemically modified L‐cytidine provides a useful biochemical and structural strategy to create mirror‐image nucleic acid molecules with expanded functionalities.

2′-Methoxy↗

DOE OSTI2021

Perseverance’s Scanning Habitable Environments with Raman and Luminescence for Organics and Chemicals (SHERLOC) Investigation

The Scanning Habitable Environments with Raman and Luminescence for Organics and Chemicals (SHERLOC) is a robotic arm-mounted instrument on NASA’s Perseverance rover. SHERLOC has two primary boresights. The Spectroscopy boresight generates spatially resolved chemical maps using fluorescence and Raman spectroscopy coupled to microscopic images (10.1 μm/pixel). The second boresight is a Wide Angle Topographic Sensor for Operations and eNgineering (WATSON); a copy of the Mars Science Laboratory (MSL) Mars Hand Lens Imager (MAHLI) that obtains color images from microscopic scales (~13 μm/pixel) to infinity. SHERLOC Spectroscopy focuses a 40 μs pulsed deep UV neon-copper laser (248.6 nm), to a ~100 μm spot on a target at a working distance of ~48 mm. Fluorescence emissions from organics, and Raman scattered photons from organics and minerals, are spectrally resolved with a single diffractive grating spectrograph with a spectral range of 250 to ~370 nm. Because the fluorescence and Raman regions are naturally separated with deep UV excitation (<250 nm), the Raman region ~ 800 – 4000 cm -1 (250 to 273 nm) and the fluorescence region (274 to ~370 nm) are acquired simultaneously without time gating or additional mechanisms. SHERLOC science begins by using an Autofocus Context Imager (ACI) to obtain target focus and acquire 10.1 μm/pixel greyscale images. Chemical maps of organic and mineral signatures are acquired by the orchestration of an internal scanning mirror that moves the focused laser spot across discrete points on the target surface where spectra are captured on the spectrometer detector. ACI images and chemical maps (< 100 μm/mapping pixel) will enable the first Mars in situ view of the spatial distribution and interaction between organics, minerals, and chemicals important to the assessment of potential biogenicity (containing CHNOPS). Single robotic arm placement chemical maps can cover areas up to 7x7 mm in area and, with the < 10 min acquisition time per map, larger mosaics are possible with arm movements. This microscopic view of the organic geochemistry of a target at the Perseverance field site, when combined with the other instruments, such as Mastcam-Z, PIXL, and SuperCam, will enable unprecedented analysis of geological materials for both scientific research and determination of which samples to collect and cache for Mars sample return.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

Tighter reformulations using classical Dawson and Sankoff bounds for approximating two-stage chance-constrained programs

We extend and improve recent results given by Singh and Watson on using classical bounds on the union of sets in a chance-constrained optimization problem. Specifically, we revisit the so-called Dawson and Sankoff bound that provided one of the best approximations of a chance constraint in the previous analysis. Next, we show that our work is a generalization of the previous work, and in fact the inequality employed previously is a very relaxed approximation with assumptions that do not generally hold. Computational results demonstrate on average over a 43% improvement in the bounds. As a byproduct, we provide an exact reformulation of the floor function in optimization models.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Information theory optimization of signals from small-angle scattering measurements

Small-angle X-ray scattering (SAXS) of particles in solution informs on the conformational states and assemblies of biological macromolecules (bioSAXS) outside of cryo- and solid-state conditions. In bioSAXS, the SAXS measurement under dilute conditions is resolution limited, and through an inverse Fourier transform, the measured SAXS intensities directly relate to the physical space occupied by the particles via the P (r)-distribution. Yet, this inverse transform of SAXS data has been historically cast as an ill-posed, ill-conditioned problem requiring an indirect approach. Here, we show that through the applications of matrix and information theories, the inverse transform of SAXS intensity data is a well-conditioned problem. The so-called ill-conditioning of the inverse problem is directly related to the Shannon number. By exploiting the oversampling enabled by modern detectors, a direct inverse Fourier transform of the SAXS data is possible, provided the recovered information does not exceed the Shannon number. The Shannon limit corresponds to the maximum number of significant singular values that can be recovered in a SAXS experiment, suggesting this relationship is a fundamental property of band-limited inverse integral transform problems. This correspondence reduces the complexity of the inverse problem to the Shannon limit and maximum dimension. We propose a hybrid scoring function using an information theory framework that assesses both the quality of the model-data fit as well as the quality of the recovered P (r)-distribution. The hybrid score utilizes the Akaike information criteria and Durbin-Watson statistic that considers parameter-model complexity, i.e., degrees of freedom, and the randomness of the model-data residuals. The described tests and findings extend the boundaries for bioSAXS by completing the information theory formalism initiated by Peter B. Moore to enable a quantitative measure of resolution in SAXS, robustly determine maximum dimension, and more precisely define the best parameter model appropriately representing the observed scattering data.

Rambo, Robert P. [Science and Technology Facilitie↗

DOE OSTI2026

Kinetic model development for single step ethanol to butene rich olefin process over Cu-Y/Beta catalysts

Here, this study presents the first intrinsic kinetic model for the single-step conversion of ethanol to butene-rich olefins over bifunctional Cu-Y/Beta catalysts, addressing a critical gap in the design and scale-up of Sustainable Aviation Fuel (SAF) processes. The reaction network comprises ten global steps involving dehydrogenation, aldol condensation, hydrogenation, and dehydration reactions, distributed across Cu and rare-earth (Y) active sites. The model incorporates dual-site functionality (Cu and Y site) and explicitly accounts for key intermediates such as crotonaldehyde and butanal. Reaction rates are formulated using Langmuir–Hinshelwood–Hougen–Watson (LHHW) kinetics. Kinetic parameters are extracted by fitting the model to lab-scale packed-bed reactor data across a wide range of temperatures and space velocities, demonstrating strong agreement in ethanol conversion and product selectivity. The reaction kinetics developed in this work provide a foundational basis for constructing reactor models that enable process optimization and scale-up of ethanol-to-jet fuel technologies.

Cu-Y/Beta catalyst↗

DOE OSTI2021

Fatigue behavior of fine-grained magnesium under tension-tension loading at 0 °C

Here, this study investigated low-temperature fatigue behavior of fine-grained magnesium through tension–tension fatigue testing at the temperature of 0 °C. The applied stress profiles of fatigue testing were selected to cover a wide range of loading conditions including low, medium, and high loading stresses. Even when the maximum applied stress of fatigue testing was as high as 88% of the ultimate tensile strength of the material, the corresponding fatigue life was long, i.e., 3973 cycles. Deformation accumulation per loading cycle reduced with the progression of fatigue testing for all studied loading conditions. Fatigue life analyses were performed using both Smith-Watson-Topper (SWT) model and Jahed-Varvani energy-based (JV) model. The fatigue life predictions through both models agree well with the experimental data.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Computational and Experimental Mechanistic Insights into the Ethanol-to-Butanol Upgrading Reaction over MgO

The mechanism of ethanol upgrading to higher products is still under debate, especially regarding intermediate species and hydrogenation and dehydrogenation steps. In this work, we conducted a combined theoretical and experimental approach to contribute to this discussion. For such, detailed electronic structure density functional theory calculations (aiming at probing density of states, infrared spectra, geometric parameters, charge densities, and reaction energetics) and diffuse reflectance infrared Fourier transform spectroscopy experiments were carried out revealing the relevance of an appropriate combination of reactive surface sites to support the formation of several intermediates that are formed in the C-C coupling over MgO. The roles of Mg and O sites were also studied under an electronic perspective and different geometrical arrangements. We found that a kink configuration was the most adequate for ethanol to 1-butanol upgrading. Our calculations also gave us arguments to propose distinct reaction routes, whose mutual predominance would depend upon reaction temperature. At temperatures up to 573 K, the so-called β-route, which goes through scission of a Cβ-H bond and formation of an oxametallacycle-like intermediate, would dominate the coupling, whereas at higher temperatures, up to 673 K, a more usual Guerbet mechanism, via an aldol coupling step and then consecutive hydrogenations, would be expected. Here, the theoretical conclusions were followed by a careful experimental strategy using sequential experimental planning techniques in order to estimate accurate parameters with the lowest possible experimental load. Information from these different sources were coupled to develop a mathematical model for the rate of the ethanol upgrading reaction, using a Langmuir-Hinshelwood-Hougen-Watson approach. The developed and statistically validated model adequately described the experimental data at 673 K and 1.1 bar total pressure for ethanol partial pressures in the range from 0 to 20 kPa.

09 BIOMASS FUELS↗

DOE OSTI2024

RNA-Puzzles Round V: blind predictions of 23 RNA structures

RNA-Puzzles is a collective endeavor dedicated to the advancement and improvement of RNA three-dimensional structure prediction. With agreement from structural biologists, RNA structures are predicted by modeling groups before publication of the experimental structures. We report a large-scale set of predictions by 18 groups for 23 RNA-Puzzles: 4 RNA elements, 2 Aptamers, 4 Viral elements, 5 Ribozymes and 8 Riboswitches. We describe automatic assessment protocols for comparisons between prediction and experiment. Our analyses reveal some critical steps to be overcome to achieve good accuracy in modeling RNA structures: identification of helix-forming pairs and of non-Watson–Crick modules, correct coaxial stacking between helices and avoidance of entanglements. Three of the top four modeling groups in this round also ranked among the top four in the CASP15 contest.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Probing remdesivir nucleotide analogue insertion to SARS-CoV-2 RNA dependent RNA polymerase in viral replication

Remdesivir (RDV) prodrug can be metabolized into a triphosphate form nucleotide analogue (RDV-TP) to bind and insert into the active site of viral RNA dependent RNA polymerase (RdRp) to further interfere with viral genome replication. Here in this work, we computationally studied how RDV-TP binds and inserts to the SARS-CoV-2 RdRp active site, in comparison with natural nucleotide substrate adenosine triphosphate (ATP). To do that, we first constructed atomic structural models of an initial binding complex (active site open) and a substrate insertion complex (active site closed), based on high-resolution cryo-EM structures determined recently for SARS-CoV-2 RdRp or non-structural protein (nsp) 12, in complex with accessory protein factors nsp7 and nsp8. By conducting all-atom molecular dynamics simulation with umbrella sampling strategies on the nucleotide insertion between the open and closed state RdRp complexes, our studies show that RDV-TP can initially bind in a comparatively stabilized state to the viral RdRp active site, as it primarily forms base stacking with the template uracil nucleotide (nt +1), which under freely fluctuations supports a low free energy barrier of the RDV-TP insertion (~1.5 kcal mol -1 ). In comparison, the corresponding natural substrate ATP binds initially to the RdRp active site in Watson–Crick base pairing with the template nt, and inserts into the active site with a medium low free energy barrier (~2.6 kcal mol -1 ), when the fluctuations of the template nt are well quenched. The simulations also show that the initial base stacking of RDV-TP with the template can be specifically stabilized by motif C-S759, S682 (near motif B) with the base, and motif G-K500 with the template backbone. Although the RDV-TP insertion can be hindered by motif F-R555/R553 interaction with the triphosphate, the ATP insertion seems to be facilitated by such interactions. The inserted RDV-TP and ATP can be further distinguished by specific sugar interaction with motif B-T687 and motif A-D623, respectively.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Catalytic production of tetrahydropyran (THP): a biomass-derived, economically competitive solvent with demonstrated use in plastic dissolution

Tetrahydropyran (THP) is a five-carbon heterocyclic ether that is non-carcinogenic, non-peroxide forming, biodegradable, and economically competitive with tetrahydrofuran (THF) as a solvent. In this work, THP has been synthesized from renewable biomass at >99.8% selectivity and 98% yield via hydrogenation of furfural-derived 3,4-dihydropyran (DHP) over Ni/SiO 2 in a continuous flow reactor at 150–200 °C. The apparent activation energy of THP formation is 31 kJ mol -1 , and the reaction orders with respect to the partial pressures of H 2 , DHP, and THP are: 2, 1, and -0.3. The kinetic data has been fitted to a Hougen–Watson model where the rate limiting step is the hydrogenation of adsorbed DHP. Ni/SiO 2 is shown to have a low deactivation rate constant of 0.012 h -1 over 100 h time on stream and can be regenerated in situ. As a performance advantage, THP is shown to be resistant to ring opening polymerization under strongly acidic conditions that THF is not, revealing it to be a superior solvent. Further, the minimum selling price of THP is competitive with the market price of THF ($$900 – 1400 per ton ) at a DHP feedstock cost of $1000 per ton. Conductor-like Screening Model for Real Solvents (COSMO-RS) and molecular dynamics (MD) simulations with 1008 solvents and 8 common plastics have demonstrated that THP can serve as an alternative solvent to THF, 2-methyltetrahydrofuran (MeTHF), and cyclopentyl methyl ether (CPME) for plastic dissolution, especially low-density polyethylene (LDPE), polypropylene (PP), polystyrene (PS) and polyvinyl chloride (PVC). This work establishes THP as a green solvent with excellent thermal, chemical and peroxidative stability that can be used for numerous applications, including waste plastic recycling.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

High-resolution infrared spectroscopy of jet cooled CH 2 Br radicals: The symmetric CH stretch manifold and absence of nuclear spin cooling

Direct laser absorption of a slit supersonic discharge expansion provides the first high-resolution spectroscopic results on the symmetric CH stretch excitation (ν 1 ) of the bromomethyl (CH 2 Br) radical in the ground electronic state. Narrowband (<1 MHz) mid-infrared radiation is produced by difference-frequency generation of two visible laser beams, with the open shell halohydrocarbon radical generated by electron dissociative attachment of CH 2 Br 2 in a discharge and rapidly cooled to T rot = 18 ± 1 K in the subsequent slit-jet supersonic expansion. A rovibrational structure in the radical spectrum is fully resolved, as well as additional splittings due to spin-rotation effects and 79 Br/ 81 Br isotopologues in natural abundance. Spectroscopic constants and band origins are determined by fitting the transition frequencies to a non-rigid Watson Hamiltonian, yielding results consistent with a vibrationally averaged planar radical and an unpaired electron in the out-of-plane p π orbital. Additionally, extensive satellite band structure from a vibrational hot band is observed and analyzed. The hot band data is compared to CFOUR/VPT2 (CCSD(T)cc-pVQZ) ab initio anharmonic predictions of the vibration rotation alpha matrix, which permits unambiguous assignment to CH 2 symmetric-stretch excitation built on the singly excited CH 2 out-of-plane bending mode (ν 1 + ν 4 ← ν 4 ). Longitudinal cooling of the Doppler width in the slit-jet expansion geometry also reveals partially resolved hyperfine structure on transitions out of the lowest angular momentum states in excellent agreement with predictions based on microwave studies. High level ab initio MOLPRO calculations [CCSD(T)-f12b/VnZ-f12 (n = 3, 4, CBS)] are also performed with explicitly correlated f12 electron methods for the out-of-plane CH 2 bending mode over the halogen series CH 2 X (X = F, Cl, Br, I), which clearly reveals a non-planar geometry for X = F (with a ΔE ≈ 0.3 kcal/mol barrier) and yet planar equilibrium geometries for X = Cl, Br, and I. Finally, a detailed Boltzmann analysis of the transition intensities provides support for negligible collisional equilibration of the entangled H atom nuclear spin states on the few hundred microsecond time scale and high collision densities of a slit supersonic expansion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗