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Results for “nucleic acid structure”

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 19 records
All sourcesNASA NTRSDOE OSTI
NASA NTRS1987

Nucleic acid-like structures. II - Polynucleotide analogues as possible primitive precursors of nucleic acids

Activated derivatives of purine-containing deoxynucleoside- diphosphates spontaneously oligomerize to produce pyrophosphate- linked oligodeoxynucleotide analogs. These analogs are of potential interest as models of primitive, polynucleotide precursors. The efficiency of oligomerization (ImpdGpIm and ImpdApIm much greater than ImpdIpIm) appears to reflect a combination of stacking forces and the specific geometric orientations of the stacked units. Under favorable conditions, chain lengths greater than 20 have been obtained for oligomers containing pdGp in the absence of a template. In the presence of a complementary template, the activated derivatives of pdGp and pdAp oligomerize much more extensively. An acyclo-analog of G has also been shown to undergo template-directed oligomerization on poly(C). These observations suggest the possibility that primitive information transfer might have evolved in much simpler systems and that this function was taken over by polynucleotides at a later stage in evolution.

Schwartz, Alan W.↗
NASA NTRS1986

A comparative study of prebiotic and present day translational models

It is generally recognized that the understanding of the molecular basis of primitive translation is a fundamental step in developing a theory of the origin of life. However, even in modern molecular biology, the mechanism for the decoding of messenger RNA triplet codons into an amino acid sequence of a protein on the ribosome is understood incompletely. Most of the proposed models for prebiotic translation lack, not only experimental support, but also a careful theoretical scrutiny of their compatibility with well understood stereochemical and energetic principles of nucleic acid structure, molecular recognition principles, and the chemistry of peptide bond formation. Present studies are concerned with comparative structural modelling and mechanistic simulation of the decoding apparatus ranging from those proposed for prebiotic conditions to the ones involved in modern biology. Any primitive decoding machinery based on nucleic acids and proteins, and most likely the modern day system, has to satisfy certain geometrical constraints. The charged amino acyl and the peptidyl termini of successive adaptors have to be adjacent in space in order to satisfy the stereochemical requirements for amide bond formation. Simultaneously, the same adaptors have to recognize successive codons on the messenger. This translational complex has to be realized by components that obey nucleic acid conformational principles, stabilities, and specificities. This generalized condition greatly restricts the number of acceptable adaptor structures.

Rein, R.↗
DOE OSTI2026

Role of electron correlation on the adenine dimer interaction for non-equilibrium geometries: a benchmark Quantum Monte Carlo study

The accurate description of non-covalent interactions is critical for understanding the structure, dynamics, and eventual function of biomolecules. The adenine dimer serves as a benchmark system for computational methods due to its role in nucleic acid structures and its rich conformational landscape. In this study, we employ benchmark diffusion quantum Monte Carlo (DMC) methods to investigate the relative energies and role of electron correlation on a set of adenine dimer conformations generated via a search of the potential energy landscape using the global optimizer algorithm. Relative DMC energies are compared against a wide range of density functional theory (DFT) approximation results. We find that although most of the DFT functionals perform well for low-energy structures, their accuracy varies significantly for higher-energy conformations, including stacked and T-shaped structures. A large fraction of the variation is due to the treatment of the van der Waals interaction. BLYP, B3LYP, and PBE0 significantly improve with added D4 dispersion, while the recent r2SCAN-D4 and ωB97M-V functionals show the least scatter and closest agreement with the DMC. These findings highlight the delicate nature of these interactions in biomolecular systems and provide guidance for simulations of their structure and dynamics and for the development of machine learned interatomic potentials.

Washburn, Laurel [ORNL] (ORCID:0000000324179335)↗
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↗
NASA NTRS1985

Template-directed synthesis of novel, nucleic acid-like structures

In studying the origins of life, it is important to examine reactions of substrate mixtures that could plausibly have accumulated on the primitive earth. Nucleoside diphosphates would probably have been synthesized along with the standard nucleotides under prebiotic conditions. For these reasons, the template-directed reactions of activated derivatives of these diphosphates, alone or mixed with activated nucleotides, were investigated. An activated derivative of deoxyguanosine 3',5'-didphosphate condensed efficiently on a polycytidylate template to give oligonucleotide analogous in which each 3,5'ophosphodiester bond was replaced by a pyrophosphate linkage. Oligomers were formed even in the absence of a template, but much more slowly. Template-directed condensation occurred also with an analogous deoxadenosine derivative on polyuridylic acid and with an analogous acycloguanosine derivative on polycytidylic acid.

Schwartz, A. W.↗
DOE OSTI2025

Depolymerization as a Design Strategy: Depolymerization Etching of Polymerization-Induced Microphase Separations

Thermally triggered depolymerization has traditionally been viewed through the lens of sustainability and recycling, not as a constructive tool for materials design. Herein, we show that selective, thermally triggered depolymerization to gaseous monomer serves as a solvent-free strategy for generating porosity in nanostructured polymer materials, offering a means to bypass the mass transport limitations inherent in conventional solution-based etching. As a demonstration platform, we employed polymerization-induced microphase separation (PIMS) to generate disordered bicontinuous block copolymer structures with embedded depolymerizable domains. By incorporating a methacrylate block susceptible to thermal depolymerization within a cross-linked, depolymerization-resistant styrenic matrix, we developed a process we term depolymerization etching of polymerization-induced microphase separations (DEPIMS). This approach enables highly selective and efficient domain removal via reversion to monomer to produce mesoporous materials with high surface areas (>200 m 2 /g). Subsequent surface functionalization yielded mesoporous adsorbents with tunable uptake kinetics and among the highest dye adsorption capacities reported for PIMS-derived materials, demonstrating the adaptability of the DEPIMS platform for chemical separations. DEPIMS can also be extended to a gram-scale, one-pot approach to yield mesoporous materials with recoverable monomer in under 12 h. These findings reposition thermal depolymerization from a sustainability tool to a broadly enabling strategy for scalable, on-demand fabrication of functional nanostructured materials.

Depolymerization↗
DOE OSTI2025

Standardized Residue Numbering and Secondary Structure Nomenclature in the Class D β-Lactamases

Over 1370 class D β-lactamases are currently known, and they pose a serious threat to the effective treatment of many infectious diseases, particularly in some pathogenic bacteria where evolving carbapenemase activity has been reported. Detailed understanding of their molecular biology, enzymology, and structural biology are critically important, but the lack of a standardized residue numbering scheme and inconsistent secondary structure annotation has made comparative analyses sometimes difficult and cumbersome. Compounding this, in the post-AlphaFold world where we currently find ourselves, an extraordinary wealth of detailed structural information on these enzymes is literally at our fingertips; therefore it is vitally important that a standard numbering system is in place to facilitate the accurate and straightforward analysis of their structures. In conclusion, here we present a residue numbering and secondary structure scheme for the class D enzymes based on the sequence and structure of OXA-48 and apply it to test targets to demonstrate the ease with which it can be used.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Mechanical Roles of Polysaccharide Assembly and Interactions in Plant Cell Walls

Plants synthesize polysaccharide-based primary cell walls that possess unique microstructures and mechanical properties to accommodate plant growth and provide protection. Here, it remains challenging to assess the role of polysaccharide organization and interactions in the mechanical behavior of primary cell walls owing to their complex microstructure and highly nonlinear mechanical responses. Employing a coarse-grained molecular dynamics model developed for onion epidermal walls, this work explores the conditions under which polysaccharide assembly and interactions might play a significant role in primary cell wall mechanics. Cellulose–cellulose adhesion plays a dominant role in the wall load-bearing capacity, but when cellulose–cellulose adhesion was disrupted computationally, cellulose–xyloglucan adhesion could influence the wall load-bearing capacity. Contrary to the common concept that xyloglucans mechanically tether well-separated cellulose microfibrils, xyloglucans functioned in this case as interfibrillar adhesives capable of transmitting tensile forces between cellulose microfibrils. Our findings may inform design criteria of new materials inspired by plant cell walls.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Molecular Dynamics Simulation and Theoretical Analysis of Structural Relaxation, Bond Exchange Dynamics, and Glass Transition in Vitrimers

Vitrimers are a class of polymer networks featuring dynamic covalent cross-links that can undergo associative bond exchange. There has been recent interest in these materials due to their promise as recyclable thermosets or self-healing polymers because of the ability of vitrimer networks to rearrange at the molecular level and undergo macroscopic flow. However, the practical use of these materials often occurs in the supercooled regime or glassy state, where the implications of dynamic bonds are complicated by the interplay between slow activated segmental dynamics, cross-link (i.e., bond-exchange) kinetics, and ultimately material properties. Here, in this paper, we combine coarse-grained molecular dynamics simulation and microscopic statistical mechanical theory to understand how cross-linking kinetics affect material dynamics and how this couples to segmental relaxation of the polymeric network strands across a spectrum of length and time scales, especially in the supercooled regime. We characterize the Kuhn segmental alpha relaxation time and bond exchange time for vitrimer systems across various cross-link densities, temperatures, and bond exchange rates. Simulation and theory both exhibit a bending-up behavior for bond exchange time upon cooling, suggesting a coupling between bond exchange dynamics and segmental relaxation that intensifies with faster bond exchange kinetics. We also found bond exchange dynamics have an impact on Kuhn segment alpha relaxation time, which is most significant at higher cross-link densities. Both these effects are most prominent when the bond exchange time is similar to the Kuhn segment alpha relaxation time, and the resulting coupling of these two relaxation processes is tied to both the probability of a free end to find a bonded pair and the time scale of the constraints imposed by the dynamic cross-links. This relationship is reflected by a cross-link dependence of a theoretical parameter which represents the quantitative degree of coupling between bond exchange and segmental dynamics. Overall, the combination of simulation and theory clarifies the intricate interaction between bond kinetics and segmental relaxation and demonstrates the ability to provide molecular-level insights into vitrimer dynamics over a wide temperature range.

dynamic relaxation↗
DOE OSTI2024

Incorporation of Thioacetate Pendants on a Polyalkenamer Enables High Extensibility

This study focuses on functionalizing polycyclooctene (PCOE) with thioacetate groups using thiol–ene click chemistry. The ethylene thioacetate (EVSA) copolymers produced vary in thioacetate incorporation (4–25 mol %) via a controlled semibatch addition technique with AIBN dosing. Copolymers with 4–14 mol % thioacetate are semicrystalline, while those with 20–25 mol % are amorphous. Increased functionalization correlates with decreased crystallinity and increased stretchability, with the highest functionalization (25 mol %) showing a modulus of 0.045 MPa and 2000% elongation at break. Here, this behavior is due to the pseudoprecise functionalization of the thioacetate pendants and intrinsic cross-linking that occurs during melt processing. Broadband dielectric spectroscopy (BDS) indicates a low activation energy barrier (16 kJ/mol for the β process), suggesting potential self-healing applications.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Precise Linker Length and Dynamic Bond Exchange Control Penetrant Diffusion in Dense Vitrimers

Polymer networks with dynamic covalent bonds have been investigated for their self-healing ability, recyclability, and potential as more sustainable materials. Recent results have indicated that in some cases, bond exchange can enhance the transport of penetrants in dense networks, pointing to their potential for separations of membranes. Here, imine dynamic bonds in ethylene oxide (EO) networks with precise linker lengths were synthesized to investigate the transport of N,N′-bis(2,5-di-tert-butylphenyl)-3,4,9,10-perylenedicarboximide (BTBP), a large, anisotropic dye molecule. Networks with mesh sizes smaller than, comparable to, and greater than the size of the penetrant axes were investigated to probe the effects of bond exchange and network confinement on transport. Mesh sizes, which ranged from 0.5 to 1.62 nm, were determined from shear rheology, glass transitions by calorimetry, and probe diffusion coefficients by fluorescence recovery after photobleaching. Permanent networks with identical EO chain lengths were prepared as control samples, and up to a 3 orders of magnitude increase in diffusion coefficient is observed in the dynamic systems for short linkers containing 13 backbone atoms. The longest linkers with 71 backbone atoms show no difference between the permanent and dynamic networks. Linkers shorter than 11 backbone atoms, corresponding to a mesh size smaller than the penetrant small axis, diffusion is no longer observable on the experimental time scale, indicating a sharp cutoff attributed to the precise linkers and narrow mesh size distribution. The dynamic imine exchange time scales were compared to the diffusive hopping times of penetrants and indicate that exchange can occur during a diffusive displacement. Furthermore, these findings provide insights into the factors affecting penetrant transport in dense polymers and inspire the development of next-generation selective polymer membranes.

Diffusion↗
DOE OSTI2026

Cross-Linker Selection Controls Glass Transition Elevation or Reduction in Dynamic Covalently Bonded Polymer Networks

Introducing cross-links is a powerful approach to improve polymeric material performance relevant to controlling viscoelasticity, thermal and creep resistance, degradability, and efficient membrane separations. The chemically specific glass transition temperature T g is of fundamental importance in determining the time scales of key dynamical processes and physical state of the material in such applications. Here, we study experimentally how the introduction of relatively large cross-linking molecules in slowly exchanging dynamic bond-forming polymers (vitrimers) impacts vitrification for diverse polymer chemistries and a wide range of cross-link fractions. We find T g can increase, decrease, or even remain essentially unchanged, in qualitative contrast to the generic elevation of T g in traditional permanent polymer networks. We formulate an effective terpolymer network model to understand this rich behavior, which emerges as a consequence of a competition between pure cross-linking and generalized plasticization effects. The latter is associated with the tunable cross-linker size and intrinsic dynamic mobility that can offset slowing down due to traditional permanent cross-linking constraints. Here, a new strategy for functional polymer network design is suggested based on adjusting the relative importance of the two competing physical effects, which potentially can significantly enhance energy savings in applications while retaining other intrinsic properties germane to advanced materials performance.

Copolymers↗
DOE OSTI2026

Integrated Strategies for Overcoming Resolution Limits in Electron Beam Lithography of Chemically Amplified Resists

Electron beam lithography (EBL) of chemically amplified resists (CARs) faces fundamental challenges, including stochastic electron scattering and acid diffusion, that limit resolution and reproducibility. Using SU-8 as a model CAR, this study systematically investigated complementary strategies to address these challenges, combining multipass exposure, proximity effect correction (PEC) with midrange correction factors, base quencher incorporation, and post-exposure bake (PEB) suppression. Monte Carlo simulations and calibrated PEC modeling revealed that extending the point spread function to include a midrange scattering component significantly improved critical dimension (CD) control across varying pattern densities, correcting deviations that conventional two-term PEC failed to capture. Multipass exposure, particularly 4-pass writing with a 25% offset, redistributed the dose to average stochastic beam and scattering fluctuations, reducing line-width roughness by more than 50% and yielding more uniform nanoscale features. Photoacid confinement was investigated by adding urea as a base quencher, which successfully reduced acid diffusion but introduced substantial sensitivity penalties without improving ultimate resolution or Z-factor performance, underscoring the trade-offs of chemical versus physical confinement. Suppressing PEB most directly minimized acid diffusion, resulting in improved Z-factors and reproducible 30 nm half-pitch dense line/space patterns. Overall, these results demonstrated that PEC with midrange correction, multipass strategies, quencher additives, and PEB-free processing addresses different aspects of the EBL process window and that their integration provides a comprehensive framework for managing stochastic scattering, diffusion, and chemical amplification effects. This framework advances dense nanoscale patterning in CARs and establishes guiding principles for optimizing resist design and process strategies in high-resolution EBL and potentially other advanced lithographies, such as extreme ultraviolet (EUV) lithography.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Reactive Modified Epoxy Resin and Its Miscible Blends Based on Recycled Oligomers from Solvolysis

Chemical depolymerization of fully cured epoxy resin with 20% reactive modifier was successfully performed via a solvent-assisted solvolysis process into low molecular weight recyclable oligomers (RO) at 240 °C in a pressure vessel at 650 psi for 4 h. The thermoset epoxy resin was depolymerized into transparent brown viscous fluid with a higher viscosity than the uncured epoxy resin with approximately 93% yield. Different concentrations of the RO were homogeneously mixed with the pure epoxy resin, and their curing kinetics, viscosity, FTIR, mechanical properties, DMA, and cross-link density were investigated. The curing kinetics of the pure reactive modified epoxy resin (baseline) and its mixtures with RO of different concentrations were investigated under both isothermal and nonisothermal conditions using small amplitude oscillatory shear flow. The elastic and viscous moduli (G′ and G″), complex viscosity (η*), and tan δ values were evaluated at different curing times and temperatures. The G′, G″, and η* increased dramatically, while tan δ decreased strongly by several orders of magnitude at the gel point. The zero-shear viscosity (η 0 ) was determined from the angular frequency dependent on η* based on the Cross model for different blend compositions in the liquid state before curing. The composition dependence of η 0 showed a positive deviation from the linear mixing rule and was well described by the Lecyar model. Here, the apparent activation energy of curing (E a ) was also evaluated according to the Arrhenius equation and was found to be 46 ± 2 kJ/mol regardless of the different contents of RO. For all blends up to 40 wt % RO, only one tan δ peak systematically shifting to lower temperatures with increasing content of RO was observed in the DMA measurements, indicating that the epoxy resin and the RO are miscible with up to 40 wt % RO.

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

Topology-Informed Design Rules for Deconstructable Thermoset Copolymer Networks

Existing models of thermoset deconstruction facilitated by incorporating cleavable comonomers rely on a mean-field reverse gel point paradigm, which predicts network dissolution once cleavable bonds reach a critical stoichiometric threshold, but does not account for where those bonds reside within the network architecture. Using reactive coarse-grained molecular dynamics simulations coupled with graph-theoretic analysis, we extend this stoichiometric picture to show that deconstructability is governed by the curing-imprinted network topology rather than stoichiometry alone. This topological organization is hierarchical: at the local scale, the elastic effectiveness of cross-link junctions determines which cross-links constitute the load-bearing scaffold; at the mesoscale, the cross-linking rate kinetically templates that scaffold into topologically modular communities─densely cross-linked clusters connected by sparse bridging strands that sustain network connectivity. Using betweenness centrality to identify nodes that disproportionately lie on intercommunity shortest paths, we demonstrate that effective deconstruction of the network into macromolecular fragments requires cleavable comonomers to intercept these high-centrality bridging strands. We further find that under uniform, disassortative comonomer incorporation, this topological requirement provides a mechanistic basis for extending the reverse gel point to incorporate network topology. We also show that modularity imposes a fundamental limit on fragment uniformity that persists even when the centrality requirement is met. Finally, we demonstrate that chain stiffness provides a nearly independent lever to suppress mechanically redundant cross-links and raise the glass transition temperature without significantly altering the deconstruction outcome. Together, these findings reframe the thermoset design space around network topology and provide actionable guidelines for engineering thermoset copolymers with predictable deconstructability and targeted thermomechanical performance.

coarse-grained molecular dynamics↗