Search NASA⌕ Search

SEARCH · Search NASA

Results for “ENCODE”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2026

B -Alkyl-borabicyclo[3.3.1]nonane Reagents Promote Closed-Shell Nickel-Catalyzed Alkylarylation Toward Encoded Cyclooctene Monomers

Access to new tailored monomers is essential to explore unprecedented polymer structures and modulate their properties. In previous work, we disclosed an iteroselective diarylation of 1,5-cyclooctadiene as an attractive platform for preparing diverse cyclooctene monomers; however, it was limited to C(sp 2 ) coupling partners. Established difunctionalization methods with C(sp 3 ) fragments rely on carbon-based radical formation, which is incompatible with 1,5-cyclooctadiene. This work describes a two-electron redox manifold for the nickel-catalyzed alkylarylation of 1,5-cyclooctadiene and discloses B -alkyl-borabicyclo[3.3.1]nonane (alkyl-9-BBN) as an effective transmetalating reagent for maintaining a polar reaction mechanism. The method provides 5,6-alkylarylated cyclooctenes suitable for ring-opening metathesis polymerization to obtain new materials. The properties of these polymers are benchmarked and fine-tuned by variation of coupling partners in the nickel catalysis. Density functional theory calculations revealed that destabilization of the pretransmetalation complex promotes the reactivity of alkyl-9-BBN in transmetalation compared to alkylboronic esters.

alkyls↗
DOE OSTI2021

Nanoparticle Superlattices through Template-Encoded DNA Dendrimers

The chemical interactions that lead to the emergence of hierarchical structures are often highly complex and difficult to program. In this paper, the synthesis of a series of superlattices based upon 30 different structurally reconfigurable DNA dendrimers is reported, each of which presents a well-defined number of single-stranded oligonucleotides (i.e., sticky ends) on its surface. Such building blocks assemble with complementary DNA-functionalized gold nanoparticles (AuNPs) to yield five distinct crystal structures, depending upon choice of dendrimer and defined by phase symmetry. These DNA dendrimers can associate to form micelle-dendrimers, whereby the extent of association can be modulated based upon surfactant concentration and dendrimer length to produce a low-symmetry Ti5Ga4-type phase that has yet to be reported in the field of colloidal crystal engineering. Taken together, colloidal crystals that feature three different types of particle bonding interactions.template-dendron, dendrimer-dendrimer, and DNA-modified AuNP-dendrimer.are reported, illustrating how sequence-defined recognition and dynamic association can be combined to yield complex hierarchical materials.

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

Encoding multistate charge order and chirality in endotaxial heterostructures

Abstract High-density phase change memory (PCM) storage is proposed for materials with multiple intermediate resistance states, which have been observed in 1 T -TaS 2 due to charge density wave (CDW) phase transitions. However, the metastability responsible for this behavior makes the presence of multistate switching unpredictable in TaS 2 devices. Here, we demonstrate the fabrication of nanothick verti-lateral H -TaS 2 /1 T -TaS 2 heterostructures in which the number of endotaxial metallic H -TaS 2 monolayers dictates the number of resistance transitions in 1 T -TaS 2 lamellae near room temperature. Further, we also observe optically active heterochirality in the CDW superlattice structure, which is modulated in concert with the resistivity steps, and we show how strain engineering can be used to nucleate these polytype conversions. This work positions the principle of endotaxial heterostructures as a promising conceptual framework for reliable, non-volatile, and multi-level switching of structure, chirality, and resistance.

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

Chromophore carbonyl twisting in fluorescent biosensors encodes direct readout of protein conformations with multicolor switching

Fluorescent labeling of proteins is a powerful tool for probing structure-function relationships with many biosensing applications. Structure-based rules for systematically designing fluorescent biosensors require understanding ligand-mediated fluorescent response mechanisms which can be challenging to establish. We installed thiol-reactive derivatives of the naphthalene-based fluorophore Prodan into bacterial periplasmic glucose-binding proteins. Glucose binding elicited paired color exchanges in the excited and ground states of these conjugates. X-ray structures and mutagenesis studies established that glucose-mediated color switching arises from steric interactions that couple protein conformational changes to twisting of the Prodan carbonyl relative to its naphthalene plane. Mutations of residues contacting the carbonyl can optimize color switching by altering fluorophore conformational equilibria in the apo and glucose-bound proteins. A commonly accepted view is that Prodan derivatives report on protein conformations via solvatochromic effects due to changes in the dielectric of their local environment. Here we show that instead Prodan carbonyl twisting controls color switching. These insights enable structure-based biosensor design by coupling ligand-mediated protein conformational changes to internal chromophore twists through specific steric interactions between fluorophore and protein.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Ni-catalysed dicarbofunctionalization for the synthesis of sequence-encoded cyclooctene monomers

The properties of polymeric materials can be modulated by factors such as sequence control or functional group modifications. However, the synthesis of new macromolecular scaffolds is limited by the accessibility of structurally diverse monomers. This work describes a one-step, nickel-catalysed synthesis of 5,6-diaryl cyclooctene monomers from the feedstock chemical 1,5-cyclooctadiene. The reaction proceeds in a modular, regio- and diastereoselective fashion, granting access to both homo- and hetero-diaryl cyclooctene monomers that smoothly undergo ring-opening metathesis polymerization (ROMP). The resulting 1,2-diaryl-substituted polymers possess sequences with head-to-head styrene dyads that have not been previously explored, giving rise to unique and tunable properties. Density functional theory calculations highlight mechanistic aspects of the nickel-catalysed diarylation reaction and the ruthenium-catalysed ROMP process, revealing a previously unappreciated role of the boronic ester in promoting migratory insertion, which was leveraged to provide enantioinduction.

Catalytic mechanisms↗
DOE OSTI2024

An essential and highly selective protein import pathway encoded by nucleus-forming phage

Targeting proteins to specific subcellular destinations is essential in prokaryotes, eukaryotes, and the viruses that infect them. Chimalliviridae phages encapsulate their genomes in a nucleus-like replication compartment composed of the protein chimallin (ChmA) that excludes ribosomes and decouples transcription from translation. These phages selectively partition proteins between the phage nucleus and the bacterial cytoplasm. Currently, the genes and signals that govern selective protein import into the phage nucleus are unknown. Here, we identify two components of this protein import pathway: a species-specific surface-exposed region of a phage intranuclear protein required for nuclear entry and a conserved protein, PicA (Protein importer of chimalliviruses A), that facilitates cargo protein trafficking across the phage nuclear shell. We also identify a defective cargo protein that is targeted to PicA on the nuclear periphery but fails to enter the nucleus, providing insight into the mechanism of nuclear protein trafficking. Using CRISPRi-ART protein expression knockdown of PicA, we show that PicA is essential early in the chimallivirus replication cycle. Together, our results allow us to propose a multistep model for the Protein Import Chimallivirus pathway, where proteins are targeted to PicA by amino acids on their surface and then licensed by PicA for nuclear entry. The divergence in the selectivity of this pathway between closely related chimalliviruses implicates its role as a key player in the evolutionary arms race between competing phages and their hosts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Peripheral positions encode transport specificity in the small multidrug resistance exporters

In secondary active transporters, a relatively limited set of protein folds have evolved diverse solute transport functions. Because of the conformational changes inherent to transport, altering substrate specificity typically involves remodeling the entire structural landscape, limiting our understanding of how novel substrate specificities evolve. In the current work, we examine a structurally minimalist family of model transport proteins, the small multidrug resistance (SMR) transporters, to understand the molecular basis for the emergence of a novel substrate specificity. We engineer a selective SMR protein to promiscuously export quaternary ammonium antiseptics, similar to the activity of a clade of multidrug exporters in this family. Using combinatorial mutagenesis and deep sequencing, we identify the necessary and sufficient molecular determinants of this engineered activity. Using X-ray crystallography, solid-supported membrane electrophysiology, binding assays, and a proteoliposome-based quaternary ammonium antiseptic transport assay that we developed, we dissect the mechanistic contributions of these residues to substrate polyspecificity. We find that substrate preference changes not through modification of the residues that directly interact with the substrate but through mutations peripheral to the binding pocket. Our work provides molecular insight into substrate promiscuity among the SMRs and can be applied to understand multidrug export and the evolution of novel transport functions more generally.

Science & Technology - Other Topics↗