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DNA Crystals as a Template for Patterned Functional Materials

DNA nanotechnology offers a wide toolkit of molecular functionalities and scales, including intricate motifs less than 10 nm and periodic structures exceeding 100 µm. At larger scales, however, there are often significant tradeoffs for DNA structures, namely stability and mechanical strength. This work describes the design, synthesis, and characterization of a functionalized DNA crystal. Using a ligated DNA crystal grants significant freedom for various functional materials to be applied, in this case, semiconducting cadmium sulfide and palladium metal. Properties investigated in this study include stability, mechanical strength, and optoelectronic properties such as photoluminescence (PL) and electric conductivity. Significant changes are observed based on the functional material applied to DNA crystals. The Young's modulus of the crystal varies by about five orders of magnitude when functionalized with palladium. PL and semiconductive behaviors were observed when cadmium sulfide was attached. These crystals represent an expansion of the capabilities of DNA structures at these length scales, and additionally a platform for future studies exchanging the materials or altering the ligation scheme.

CdS

Diffraction-quality, ultraflexible protein single crystals engineered with DNA

DNA-functionalized colloidal nanoparticles assemble through flexible, nanoscale DNA hybridization interactions that limit atomic-level structural order. Here, we report a valence-centric strategy that enables DNA-bonded, protein single crystals with unconventional mechanical properties. An octameric enzyme, glutarate L-2-hydroxylase, was site- and number-selectively conjugated with eight self-complementary single-stranded DNA, yielding octavalent molecular bonds. The resulting conjugate assembled into the designed body-centered tetragonal crystals that diffracted to 1.42- to 2.61-angstrom resolution, with contacts mediated by B-form DNA helices spanning 17 to 25 angstroms. Increasing oligonucleotide length induces anisotropic lattice expansion while preserving atomic periodicity, even with partial DNA occupancy. Mechanistic studies suggest that the dynamic motion of unhybridized DNA facilitates crystallization, analogous to fluctuating electron clouds in atomic bonding. Compared with native protein crystals, DNA-hybridized crystals are 23-fold softer. These results challenge the assumption that flexibility is incompatible with structural order and establish a programmable framework for biomolecular crystallization and nanomaterials engineering with atomic precision.

Han, Zhenyu [Department of Chemistry, Northwestern

Effect of Thermodynamic and Environmental Factors on Crystallization of DNA‐Origami Superlattices

The directed self‐assembly of nanoscale materials into ordered superlattices presents a powerful strategy for creating next‐generation materials with programmable mechanical, optical, and photonic properties. Deoxyribonucleic acid (DNA) origami has emerged as a versatile scaffold for encoding nanoscale geometry and guiding the crystallization of complex 3D architectures. However, a systematic understanding of the parameters that govern the efficiency and quality of superlattice formation remains limited. In this study, we utilize octahedral DNA nanoscale frames as a model system to investigate the relative influence of key factors, including buffer composition, ionic strength, frame concentration, and thermal annealing protocols, on the size, order, and reproducibility of the resulting superlattices. Our findings provide a quantitative framework to rationally optimize DNA‐based assembly pathways. Structural characterization via small‐angle x‐ray scattering (SAXS), scanning electron microscopy (SEM), and optical microscopy validates the quality and fidelity of the assembled lattices. Moreover, by templating these DNA frameworks into inorganic replicas, we establish general design principles that extend beyond biomolecular systems, providing a foundation for the synthesis of programmable materials in broader nanofabrication contexts.

77 NANOSCIENCE AND NANOTECHNOLOGY

An enzyme-based approach for highly efficient self-replication of DNA origami dimers

Self-replication and exponential growth are essential to all living things, the driving force for Darwinian evolution, and potentially useful in nanotechnology for large-scale production of nanoscopic materials. An artificial (nonliving) self-replication system has been shown to exhibit exponential growth and selection using DNA monomer origami tiles templated on a dimer seed. That system purposefully avoided the use of enzymes to get a hint of how self-replication might have evolved in a prebiotic world by using CNV K and UV light to crosslink complementary DNA single strands. For further investigations into competition and extinction and for potential applications involving biocompatibility, we wanted to investigate enzymatic ligation to replace the chemical photo crosslinking step. Here, we present a system which uses thermotolerant T4 DNA ligase and no UV. This system has several additional advantages including a much faster cycling time, yielding 2,000,000 amplifications in 12 h. We also introduce competition to study the possibility of Darwinian-like evolution. Two pairs of DNA origami tiles compete for the same connection strands and show different growth rates under different connection strand concentrations. This system has the potential to combine with other enzymes, such as RNA polymerase to support feedback, allowing us to fine-tune replication dynamics and achieve sophisticated, life-like behaviors. The highly efficient self-replication and exponential growth of DNA origami dimers demonstrated in this work not only enhances our understanding of Darwinian evolution in nature but also opens the door to applications ranging from synthetic biology to smart materials.

Science & Technology - Other Topics

Does the International Space Station Leak DNA? Preliminary Results from the ISS External Microorganisms Payload

Existing crewed spacecraft like the ISS (International Space Station) leak by design. The ISS routinely releases gas to maintain life support systems and when astronauts exit the station to perform space walks. The chemical component of this leakage is well characterized, but the biological components are not. The ISS is not subject to planetary protection requirements, but planned missions to Mars will use similar systems and will be subject to planetary protection requirements. If detectable microorganisms are escaping through vents and or airlocks we may need to redesign our crewed habitats to minimize this type of contamination. To test the hypothesis that microorganisms from inside ISS are detectable on exterior surfaces an astronaut used the ISS External Microorganisms sampling kit (Rucker et al. 2018) to sample exterior surfaces of the ISS during an EVA (Extra Vehicular Activity) in January of 2025. These samples were returned to Earth for DNA extraction and sequencing. We successfully, extracted and sequenced bacterial, fungal and viral DNA from these samples that was not present in the negative controls. These results should help NASA refine the planetary protection requirements for crewed missions. Methods: The samples were collected using sterile, DNA free, buccal swabs (23 mm. diameter) housed in custom canisters. Each canister uses a 0.2 μm Teflon filter to maintain sterility as the caddy, holding 8 swabs moves in and out of vacuum. The astronaut sampled the: 1) airlock vestibule, 2) airlock thermal cover, 3) a gap in the micrometeorite shielding near the airlock, 4) a handrail near the airlock, 5) the Carbon Dioxide Removal Assembly vent, and 6) the Vacuum Exhaust System vent. The seventh swab was exposed to vacuum during the EVA without touching it to a surface. The eighth swab, a negative control, was not opened until the caddy returned to Earth. DNA was extracted from the swabs using a QIamp UCP Pathogen kit and prepared for sequencing on an Aviti (Element Biosciences) sequencer (Arslan et al. 2024). The resulting sequences were analyzed using the EDGE Bioinformatics platform (Li et al. 2017). The sequences were analyzed individually using tools like BLAST, GOTTCHA2, Kraken2, and PanGIA. The data were also assembled into metagenome assembled genomes) using tools like CONCOCT, MaxBin2 and MetaBAT2. Results: We successfully extracted and sequenced bacterial, archaeal, fungal and viral DNA from all seven samples. The handrail swab had the lowest number of reads (768,651) and the airlock thermal cover had the highest number of reads (8,819,230). These samples contain DNA from human associated bacteria (e.g. Crynebacterium riegelii ), fungi (.e.g. Penicillium rubens ), and viruses (e.g Alphapapillomavirus ). Conclusion: Preliminary interpretation suggest that the airlock and the space suits themselves are the largest sources of contaminant DNA. Most if not all of the DNA is from organisms known to be present inside the ISS. Vents attached to life support systems may be a lesser source of biological contamination. Further analysis should help NASA address planetary protection knowledge gaps for crewed missions.

Aaron B Regberg

Assembly of catalytic complexes from randomized oligonucleotides

The early evolution of life relied on catalytic RNAs (ribozymes) for central functions. To test whether early catalysts could have assembled from multiple short nucleic acid fragments in random sequence environments, we performed an in vitro selection from a short RNA library in the presence of 256 different DNA 20-nucleotide oligomers. High-throughput sequencing and biochemical analysis showed that most of the selected 1331 RNA sequences required at least one DNA for activity. Representatives for four of six RNA clusters that depended on DNA cofactors were active even when the 256 DNAs were replaced by completely random DNA 20-nucleotide oligomers. The formation of these catalytic complexes and the recruitment of oligonucleotide cofactors from completely random libraries demonstrate an important principle for the emergence of the earliest oligonucleotide catalysts.

Xu Han

Integration of ultra-low coverage whole-genome sequences for reconstructing the evolutionary history of Galapagos giant tortoises

Genomic data from contemporary and historical samples often need to be coupled for evolutionary reconstructions of multitaxon complexes. However, the genetic data recovered from historical samples may result only in ultra-low coverage whole-genome sequences (ulcWGS; <0.15× depth), leading to inaccurate evolutionary inferences given a preponderance of missing data. Using the Galapagos giant tortoise radiation as a study system (Chelonoidis spp., composed of 13 extant and four extinct lineages), we assembled a novel methodological pipeline that removes potential noise introduced by the missing data and enhances the evolutionary signal from ulcWGS samples. We leveraged existing tools for phylogenomic placement (EPA-ng), population genomic structure (smartsnp) and admixture (Admixfrog, NGSadmix) to demonstrate that the evolutionary history of samples can be uncovered with sequencing depths as low as 0.008–0.139×. Importantly, these approaches do not use genotype imputation of the ulcWGS samples, which would require extensive reference datasets. Our application to two cases of extinct lineages of Galapagos giant tortoises, with and without references from the same lineage, demonstrates the general value of the approach. We confirm where the extinct lineages from San Cristóbal and Santa Fe islands fit into the Galapagos giant tortoise radiation, and that these lineages were evolutionarily distinct entities.

ancient DNA

Crystal Growth Scale-Up and Stability of RbSr 2 X 5 :Eu Scintillators

The discovery and development of new scintillation materials support national security needs. In these applications, large volumes of scintillator crystals are needed to achieve efficient screening for contraband. Therefore, one important step in the discovery of new scintillator compositions is testing their feasibility for scale-up and their stability. In this work, high-quality Ø22 mm crystals of two new scintillators RbSr 2 Br 5 :Eu and RbSr 2 I 5 :Eu were grown via the Vertical Bridgman method, and their scintillation properties were characterized. Here, the Ø22 mm RbSr 2 I 5 :Eu crystals could be grown with fast translation rates up to 3.5 mm/h. Both RbSr 2 Br 5 :Eu and RbSr 2 I 5 :Eu had high scintillation performance, including light yields of 46,000 and 61,000 ph/MeV, respectively, for Ø22 × 35 mm crystals. Additionally, properties related to physical stability were investigated, including the coefficients of thermal expansion via high-temperature X-ray diffraction (HTXRD) as well as moisture sensitivity. HTXRD confirmed the absence of solid–solid phase transitions and showed that RbSr 2 Br 5 had minimal thermal expansion anisotropy compared to RbSr 2 I 5 and some other inorganic metal halide scintillators, which favors the growth of large-sized crystals.

36 MATERIALS SCIENCE

Crystal Growth of Selected II-VI Semiconducting Alloys By Directional Solidification

A Hg 0.84 Zn 0.16 Te alloy crystal was back-melted and partially resolidified during the first United States Microgravity Laboratory (USML-1) mission in the Marshall Space Flight Center's Crystal Growth Furnace. The experiment was inadvertently terminated at about 30% of planned completion. Nonetheless, it was successfully demonstrated that HgZnTe alloy ingots partially grown and quenched on the ground can be back-melted and regrown in space under nearly steady state growth conditions. An identical 'ground-truth' experiment was performed following the mission. Preliminary results are presented for both crystals, as well as for a series of other crystals grown prior to the mission for the purposes of optimizing in-flight growth conditions.

S L Lehoczky

Reconfigurable structural color by reversible switching of colloidal discoid liquid crystal alignment

Combining the effects of alternating-current (AC) electric fields and sedimentation reconfigures colloidal discoids between planar and homeotropic orientational alignments, thereby controlling the material’s structural color. Here, we self-assemble micrometer-size polystyrene discoids in an isopropanol-water mixture. After sedimentation, the discoids adopt a homeotropic alignment, with the minor axis perpendicular to the substrate. Adding an AC electric field (1 kHz) of ≥0.50 V switches the discoids to planar alignment—with the minor axis parallel to the substrate—within ∼100 s. Removing the field switches them back to homeotropic alignment within ∼300 s. Kinetic modeling of the field-induced torques yields good agreement with these measurements. The peak wavelength and intensity of the crystal’s diffraction response shift significantly upon reconfiguration; scattering simulation predicts these shifts. The reconfiguration is maintained for at least 10 cycles. This method is a simple, scalable avenue to reconfigure the optical properties of colloidal crystals produced from simple dielectric spheroids.

colloidal crystals

Ion Transport and Crystal Rotation in Plastic Crystal Electrolytes Under Applied Electric Fields

Organic ionic plastic crystal electrolytes, containing a plastic crystal and lithium salt, offer a potential balance between mechanical and electrochemical properties for solid state lithium-ion battery electrolytes. These electrolytes contain multiple mobile ionic species (three or four), resulting in complex transport mechanisms which have not yet been established. Plastic crystals are defined by long-range positional order and short-range rotational disorder. It is therefore necessary to quantify changes in the local crystal structure of the electrolyte as current flows through it. Herein, we examine the electrochemical properties of pyrrolidinium-based plastic crystal electrolytes containing lithium salt and zwitterion additives, including measurements of current fraction and limiting current. We obtain species-specific insight into electrolyte transport using pulsed-field gradient nuclear magnetic resonance spectroscopy and find that, while the zwitterion additive increases ionic conductivity, it decreases lithium diffusivity with respect to other ionic components. With operando spatiotemporally resolved wide-angle X-ray scattering we observe location-specific crystal rotations due to the passage of ionic current. In conclusion, we posit that reducing energy dissipation due to rotation is essential for using plastic crystal electrolytes in practical applications.

Yap, Kyra M. K. [University of California, Berkele

Tautomerism induces bending and twisting of biogenic crystals

Understanding and exploiting material flexibility through phenomena such as the bending and twisting of molecular crystals has been a subject of increased interest owing to the number of applications that benefit from these properties, such as optoelectronics, mechanophotonics, soft robotics, and smart sensors. Here, we report the growth of spontaneously bent and twisted ammonium urate crystals induced by the keto–enol tautomerism of the urate molecule. The major tautomer is native to biogenic crystals, whereas the minor tautomer functions as an effective crystal growth modifier to induce naturally bent and twisted ammonium urate crystals. We show that the degree of curvature can be tailored based on the judicious selection of growth conditions. A combination of state-of-the-art microscopy and spectroscopy techniques are used to characterize the origin of bending. Spatially resolved nano-electron diffraction and high-resolution electron microscopy of naturally bent crystals show nearly single crystallinity with local lattice deformations generated by a combination of screw and edge dislocations. These observations are consistent with photoinduced force microscopy and contact resonance atomic force microscopy, which confirmed spatially resolved changes in the intermolecular interactions and the mechanical properties throughout the cross-sectional and axial regions of bent crystals. A mechanism of bending involving the generation of regionally specific dislocations is proposed as an alternative to more commonly reported models. These findings highlight a unique characteristic of tautomeric crystals that may have broader implications for other biogenic materials.

Science & Technology - Other Topics

Protein Crystal Growth Results From the United States Microgravity Laboratory-1 Mission

Protein crystal growth experiments have been performed by this laboratory on 18 Space Shuttle missions since April, 1985. In addition, a number of microgravity experiments also have been performed and reported by other investigators. These Space Shuttle missions have been used to grow crystals of a variety of proteins using vapor diffusion, liquid diffusion, and temperature-induced crystallization techniques. The United States Microgravity Laboratory - 1 mission (USML-1, June 25 - July 9, 1992) was a Spacelab mission dedicated to experiments involved in materials processing. New protein crystal growth hardware was developed to allow in orbit examination of initial crystal growth results, the knowledge from which was used on subsequent days to prepare new crystal growth experiments. In addition, new seeding hardware and techniques were tested as well as techniques that would prepare crystals for analysis by x-ray diffraction, a capability projected for the planned Space Station. Hardware that was specifically developed for the USML-1 mission will be discussed along with the experimental results from this mission.

L J Delucas