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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 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Nanopore Activity Assays for Detection of Biomarker Protease Activity: Design and Testing of Substrates for Both Nanopore Sequencing and PCR-Based Detection Methods

The work performed in this project has demonstrated the ability to construct proteolytic enzyme substrates that are PCR and sequencing-readable reporter molecules. Specifically, the goal was to detect those reporter molecules via PCR and Oxford Nanopore Technologies MinION sequencing methods following exposure to the biomarker protease thrombin. The assay development focused on binding the constructed peptide-oligonucleotide chimera to immobilized streptavidin. The action of thrombin on the peptide portion of the molecule released the oligonucleotide for detection. Detection of protease activity was demonstrated in a concentration-dependent manner using MALDI-MS, RT-PCR and DNA sequencing. Additional steps to remove background release of reporter molecules during the assay was used to improve the difference in detected oligonucleotide reporter following protease activity. Additional steps in assay development will be to (1) test the assay in an appropriate matrix, (2) investigate detection using additional DNA sequencing platforms and (3) demonstrate multiplexed detection of multiple protease markers in a single reaction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Targeted self-assembly of functionalized carbon nanotubes on tumors

Provided herein is the two component self-assembly single wall nanotube system and the single wall nanotube construct that is the second component. The two component self-assembly single wall nanotube system has a morpholino oligonucleotide with a targeting moiety followed by a single wall nanotube construct with second morpholino oligonucleotides complementary to the first morpholino oligonucleotides and one or both of a therapeutic or diagnostic payload molecule linked to the single wall nanotube construct.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2021

Structured sequences emerge from random pool when replicated by templated ligation

The central question in the origin of life is to understand how structure can emerge from randomness. The Eigen theory of replication states, for sequences that are copied one base at a time, that the replication fidelity has to surpass an error threshold to avoid that replicated specific sequences become random because of the incorporated replication errors [M. Eigen, Naturwissenschaften 58 (10), 465–523 (1971)]. Here, we showed that linking short oligomers from a random sequence pool in a templated ligation reaction reduced the sequence space of product strands. We started from 12-mer oligonucleotides with two bases in all possible combinations and triggered enzymatic ligation under temperature cycles. Surprisingly, we found the robust creation of long, highly structured sequences with low entropy. At the ligation site, complementary and alternating sequence patterns developed. However, between the ligation sites, we found either an A-rich or a T-rich sequence within a single oligonucleotide. Our modeling suggests that avoidance of hairpins was the likely cause for these two complementary sequence pools. What emerged was a network of complementary sequences that acted both as templates and substrates of the reaction. This self-selecting ligation reaction could be restarted by only a few majority sequences. The findings showed that replication by random templated ligation from a random sequence input will lead to a highly structured, long, and nonrandom sequence pool. This is a favorable starting point for a subsequent Darwinian evolution searching for higher catalytic functions in an RNA world scenario.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Structural insights into the substrate specificity of the endonuclease activity of the influenza virus cap-snatching mechanism

Abstract The endonuclease activity within the influenza virus cap-snatching process is a proven therapeutic target. The anti-influenza drug baloxavir is highly effective, but is associated with resistance mutations that threaten its clinical efficacy. The endonuclease resides within the N-terminal domain of the PA subunit (PAN) of the influenza RNA dependent RNA polymerase, and we report here complexes of PAN with RNA and DNA oligonucleotides to understand its specificity and the structural basis of baloxavir resistance mutations. The RNA and DNA oligonucleotides bind within the substrate binding groove of PAN in a similar fashion, explaining the ability of the enzyme to cleave both substrates. The individual nucleotides occupy adjacent conserved pockets that flank the two-metal active site. However, the 2′ OH of the RNA ribose moieties engage in additional interactions that appear to optimize the binding and cleavage efficiency for the natural substrate. The major baloxavir resistance mutation at position 38 is at the core of the substrate binding site, but structural studies and modeling suggest that it maintains the necessary virus fitness via compensating interactions with RNA. These studies will facilitate the development of new influenza therapeutics that spatially match the substrate and are less likely to elicit resistance mutations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Early events in G-quadruplex folding captured by time-resolved small-angle X-ray scattering

Abstract Time-resolved small-angle X-ray experiments are reported here that capture and quantify a previously unknown rapid collapse of the unfolded oligonucleotide as an early step in the folding of hybrid 1 and hybrid 2 telomeric G-quadruplex structures. The rapid collapse, initiated by a pH jump, is characterized by an exponential decrease in the radius of gyration from 24.3 to 12.6 Å. The collapse is monophasic and is complete in <600 ms. Additional hand-mixing pH-jump kinetic studies show that slower kinetic steps follow the collapse. The folded and unfolded states at equilibrium were further characterized by SAXS studies and other biophysical tools, showing that G4 unfolding was complete at alkaline pH, but not in LiCl solution as is often claimed. The SAXS Ensemble Optimization Method analysis reveals models of the unfolded state as a dynamic ensemble of flexible oligonucleotide chains with a variety of transient hairpin structures. These results suggest a G4 folding pathway in which a rapid collapse, analogous to molten globule formation seen in proteins, is followed by a confined conformational search within the collapsed particle to form the native contacts ultimately found in the stable folded form.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Chymotrypsin-like Elastase-1 Mediates Progressive Emphysema in Alpha-1 Antitrypsin Deficiency

Alpha-1 antitrypsin (AAT) deficiency is a rare disease affecting approximately 1 in 2000 White individuals with approximately 10% of these individuals developing AATD lung disease. This lung disease is marked by progressive alveolar loss despite the withdrawal of triggering agents such as cigarette smoke. Although the PiZZ genotype is the most common mutation, there are over 100 described variants making true population estimates difficult and AAT deficiency is typically diagnosed by reduced levels of AAT in the blood. Typically developing in the fourth and fifth decades of life, AAT-deficient lung disease is marked by progressive emphysema and is the fourth leading indication for lung transplantation. AAT augmentation therapy does not prevent disease progression making the development of new therapeutic approaches critical. Chymotrypsin-like elastase 1 (CELA1) is a serine protease synthesized and secreted by alveolar type 2 cells with a physiologic role in reducing postnatal lung elastance. At a molecular level, CELA1 binds and cleaves non-crosslinked, hydrophobic domains of tropoelastin, and its binding to lung elastin fibers is increased with strain—similar to other pancreatic elastases. CELA1 is neutralized by covalent binding with AAT, and Cela1 -/- mice were completely protected from emphysema in an antisense oligonucleotide model of AAT-deficient emphysema. This model, however, did not include any injury apart from administration of the antisense oligonucleotide with levels of emphysema exceeding that seen in mice with genetic ablation of 5 Serpina1 paralogues and subjected to tracheal lipopolysacharide or cigarette smoke. Here, we use this murine genetic model of AAT deficiency to test the role of the CELA1 gene in AAT-deficient emphysema using multiple models to show that CELA1 has a role in progressive airspace enlargement in AAT-deficiency independent of inflammation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Nucleic Acid-Based Detection Protease Activity

Proteases include clinically relevant markers for clotting disorders, certain cancers as well as toxins. Assays for protease activity often use designed peptides mimicking natural substrates and detection with colorometric and fluorescence-based detection that is difficult to multiplex without expensive and resource demanding instruments. This work demonstrates detection of proteolytic activity using PCR and sequencing-readable reporter molecules. The assay development focused on binding the constructed peptide-oligonucleotide chimera to immobilized streptavidin. Thrombin, an essential component of the clotting cascade, was used as a model system for testing peptide substrate recognition and release of a designed oligonucleotide for detection. Detection of protease activity was demonstrated in a concentration-dependent manner using MALDI-MS, RT-PCR and DNA sequencing.

Wunschel, David S [Pacific Northwest National Labo↗
DOE OSTI2023

Scar-less multi-part DNA assembly design automation

The present invention provides a method of a method of designing an implementation of a DNA assembly. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding flanking homology sequences to each of the DNA oligos. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding optimized overhang sequences to each of the DNA oligos.

Hillson, Nathan J.↗
DOE OSTI2021

The role of SAXS and molecular simulations in 3D structure elucidation of a DNA aptamer against lung cancer

Aptamers are short, single-stranded DNA or RNA oligonucleotide molecules that function as synthetic analogs of antibodies and bind to a target molecule with high specificity. Aptamer affinity entirely depends on its tertiary structure and charge distribution. Therefore, length and structure optimization are essential for increasing aptamer specificity and affinity. Here, we present a general optimization procedure for finding the most populated atomistic structures of DNA aptamers. Based on the existed aptamer LC-18 for lung adenocarcinoma, a new truncated LC-18 (LC-18t) aptamer LC-18t was developed. A three-dimensional (3D) shape of LC-18t was reported based on small-angle X-ray scattering (SAXS) experiments and molecular modeling by fragment molecular orbital or molecular dynamic methods. Molecular simulations revealed an ensemble of possible aptamer conformations in solution that were in close agreement with measured SAXS data. The aptamer LC-18t had stronger binding to cancerous cells in lung tumor tissues and shared the binding site with the original larger aptamer. The suggested approach reveals 3D shapes of aptamers and helps in designing better affinity probes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural Insight into a Sixteen Cyanine Dye Construct via Exciton–Exciton Annihilation

Molecular (dye) aggregates play a prominent role in light harvesting and are of interest in quantum information science; however, there are limited reports hat programmably assemble many (>4) dye aggregates featuring strong coupling and exciton delocalization. Using oligonucleotides with four Cy5s covalently linked in series along the phosphate backbone, we bring four, eight, and sixteen Cy5s in close proximity by assembling four-armed junctions. We elucidate their structure via gel electrophoresis and steady-state and transient optical spectroscopy. We find that Cy5 has a strong propensity to form tetramer clusters, where the exciton is delocalized over all four Cy5s, that the exciton is not delocalized beyond tetramer clusters in the eight and sixteen Cy5 constructs, and that the sixteen Cy5 construct may consist of pairs of tetramer clusters that are isolated from one another. Many-dye aggregates such as these may serve useful as antennae for their intense light absorption and spatially directed energy transfer.

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

Targeted mutagenesis and high-throughput screening of diversified gene and promoter libraries for isolating gain-of-function mutations

Targeted mutagenesis of a promoter or gene is essential for attaining new functions in microbial and protein engineering efforts. In the burgeoning field of synthetic biology, heterologous genes are expressed in new host organisms. Similarly, natural or designed proteins are mutagenized at targeted positions and screened for gain-of-function mutations. Here, we describe methods to attain complete randomization or controlled mutations in promoters or genes. Combinatorial libraries of one hundred thousands to tens of millions of variants can be created using commercially synthesized oligonucleotides, simply by performing two rounds of polymerase chain reactions. With a suitably engineered reporter in a whole cell, these libraries can be screened rapidly by performing fluorescence-activated cell sorting (FACS). Within a few rounds of positive and negative sorting based on the response from the reporter, the library can rapidly converge to a few optimal or extremely rare variants with desired phenotypes. Library construction, transformation and sequence verification takes 6–9 days and requires only basic molecular biology lab experience. Screening the library by FACS takes 3–5 days and requires training for the specific cytometer used. Further steps after sorting, including colony picking, sequencing, verification, and characterization of individual clones may take longer, depending on number of clones and required experiments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Expanding Structural Space for Immunomodulatory Nucleic Acid Nanoparticles via Spatial Arrangement of Their Therapeutic Moieties

Different therapeutic nucleic acids (TNAs) can be unified in a single structure by their elongation with short oligonucleotides designed to self-assemble into nucleic acid nanoparticles (NANPs). With this approach, therapeutic cocktails with precisely controlled composition and stoichiometry of active ingredients can be delivered to the same diseased cells for enhancing pharmaceutical action. In this study, an additional nanotechnology-based therapeutic option that enlists a biocompatible NANP-encoded platform for their controlled patient-specific immunorecognition is explored. For this, a set of representative functional NANPs is extensively characterized in vitro, ex vivo, and in vivo and then further analyzed for immunostimulation of human peripheral blood mononuclear cells freshly collected from healthy donor volunteers. The results of the study present the advancement of the current TNA approach toward personalized medicine and offer a new strategy to potentially address top public health challenges related to drug overdose and safety through the biodegradable nature of the functional platform with immunostimulatory regulation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2022

Harnessing Particle Size‐Control and DNA‐Oligo Functionalization in ZIF‐76 for Biological Applications

Abstract Advanced therapeutics require novel nanocarriers to ensure their functionality is preserved during transit. Zeolitic imidazolate frameworks (ZIFs) have emerged as promising materials in this field owing to their combined biocompatibility, high porosity, and tunable chemistry. While a diverse family of ZIFs has been reported, few have been explored beyond the prototypical ZIF‐8. Herein, the size‐controlled synthesis of three distinct ZIF‐76 analogs is demonstrated, overcoming the unique synthetic challenges intrinsic to the lta topology and complex crystallization kinetics associated with the mixed linker approach. This assesses the materials’ platform effectiveness for intracellular delivery first by exploring the structural and colloidal stability in biologically relevant media. To circumvent particle aggregation, fluorescently labeled DNA oligonucleotides are post‐synthetically attached to the ZIF surface. This modification significantly improves the colloidal stability in media and facilitates particle internalization tracking. Finally, the particle‐cell interactions are assessed, revealing rapid cell membrane association with macrophages, but not lung epithelial cells, and ZIF accumulation within macrophages which increased over time. Importantly, this study outlines a generalized approach toward expanding the available library of ZIFs for biological applications, enabling the potential for targeted therapeutic delivery for intracellular infections treatment.

Deneff, Jacob I.↗
DOE OSTI2021

Superstructured Biomaterials Formed by Exchange Dynamics and Host–Guest Interactions in Supramolecular Polymers

Dynamic and reversible assembly of molecules is ubiquitous in the hierarchical superstructures of living systems and plays a key role in cellular functions. Recent work from the laboratory reported on the reversible formation of such superstructures in systems of peptide amphiphiles conjugated to oligonucleotides and electrostatically complimentary peptide sequences. Here, a supramolecular system is reported upon where exchange dynamics and host–guest interactions between β-cyclodextrin and adamantane on peptide amphiphiles lead to superstructure formation. Superstructure formation with bundled nanoribbons generates a mechanically robust hydrogel with a highly porous architecture that can be 3D printed. Functionalization of the porous superstructured material with a biological signal results in a matrix with significant in vitro bioactivity toward neurons that could be used as a supramolecular model to design novel biomaterials.

36 MATERIALS SCIENCE↗
DOE OSTI2020

DNA Reaction–Diffusion Attractor Patterns

Abstract Living systems can form and recover complex chemical patterns with precisely sized features in the ranges of tens or hundreds of microns. We show how designed reaction–diffusion processes can likewise produce precise patterns, termed attractor patterns, that reform their precise shape after being perturbed. We use oligonucleotide reaction networks, photolithography, and microfluidic delivery to form precisely controlled attractor patterns and study the responses of these patterns to different localized perturbations. Linear and “hill”‐shaped patterns formed and stabilized into shapes and at time scales consistent with reaction–diffusion models. When patterns were perturbed in particular locations with UV light, they reliably reformed their steady‐state profiles. Recovery also occurred after repeated perturbations. By designing the far‐from‐equilibrium dynamics of a chemical system, this study shows how it is possible to design spatial patterns of molecules that are sustained and regenerated by continually evolving towards a specific steady state configuration.

Dorsey, Phillip James↗
DOE OSTI2020

DNA Reaction–Diffusion Attractor Patterns

Living systems can form and recover complex chemical patterns with precisely sized features in the ranges of tens or hundreds of microns. We show how designed reaction-diffusion processes can likewise produce precise patterns, termed attractor patterns, that reform their precise shape after being perturbed. We use oligonucleotide reaction networks, photolithography and microfluidic delivery to form precisely controlled attractor patterns and study the responses of these patterns to different localized perturbations. Linear and ‘hill’-shaped patterns formed and stabilized into shapes and at time scales consistent with reaction-diffusion models. When patterns were perturbed in particular locations with UV light, they reliably reformed their steady state profiles. Recovery also occurred after repeated perturbations. As a result, by designing the far-from-equilibrium dynamics of a chemical system, this study shows how it is possible to design spatial patterns of molecules that are sustained and regenerated by continually evolving towards a specific steady state configuration

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

Improved two–stage protein expression and purification via autoinduction of both autolysis and auto DNA/RNA hydrolysis conferred by phage lysozyme and DNA/RNA endonuclease

We report improved release of recombinant proteins in Escherichia coli, which relies on combined cellular autolysis and DNA/RNA autohydrolysis, conferred by the tightly controlled autoinduction of both phage lysozyme and the nonspecific DNA/RNA endonuclease from Serratia marcescens. Autoinduction occurs in a two–stage process wherein heterologous protein expression and autolysis enzymes are induced upon entry into stationary phase by phosphate depletion. Cytoplasmic lysozyme and periplasmic endonuclease are kept from inducing lysis until membrane integrity is disrupted. After cell harvest, the addition of detergent (0.1% Triton X–100) and a single 30 min freeze–thaw cycle results in >90% release of protein, green fluorescent protein. Here, this cellular lysis is accompanied by complete oligonucleotide hydrolysis. The approach has been validated for shake flask cultures, high–throughput cultivation in microtiter plates, and larger scale stirred–tank bioreactors. This tightly controlled system enables robust growth and resistance to lysis in routine media when cells are propagated and autolysis/hydrolysis genes are only induced upon phosphate depletion

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Derivatization of Mirror-Image L -Nucleic Acids with 2'-OMe Modification for Thermal and Structural Stabilization

To further expand the functionality and enhance the stability of mirror-image nucleic acids as advanced agents for basic research and therapeutic design, we have synthesized 2'-deoxy-2'-methoxy- L -uridine phosphoramidite and incorporated it into L -DNA and L -RNA by solid-phase synthesis quantitatively. We found that the thermostability of L -nucleic acids is dramatically improved after introducing the modifications. Moreover, we successfully crystallized both L -DNA and L -RNA duplexes containing the 2'-OMe modifications and sharing identical sequences. Crystal structure determination and analysis revealed the overall structures of the mirror-image nucleic acids, and for the first time it was possible to interpret the structural deviations caused by 2'-OMe and 2'-OH groups in the oligonucleotides, which are very similar. In conclusion, this novel chemical nucleic acid modification has the potential to be used to design nucleic acid-based therapeutics and materials in the future.

2'-OMe-modifications↗