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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 1,009 records · Page 56
All sourcesNASA NTRSDOE OSTI
DOE OSTI2015

Structural impact of complete CpG methylation within target DNA on specific complex formation of the inducible transcription factor Egr-1

The inducible transcription factor Egr–1 binds specifically to 9–bp target sequences containing two CpG sites that can potentially be methylated at four cytosine bases. Although it appears that complete CpG methylation would make an unfavorable steric clash in the previous crystal structures of the complexes with unmethylated or partially methylated DNA, our affinity data suggest that DNA recognition by Egr–1 is insensitive to CpG methylation. We have determined, at a 1.4–Å resolution, the crystal structure of the Egr–1 zinc–finger complex with completely methylated target DNA. In conclusion, structural comparison of the three different methylation states reveals why Egr–1 can recognize the target sequences regardless of CpG methylation.

5-methylcytosine↗
DOE OSTI2013

Detection and Repair of Ionizing Radiation-Induced DNA Double Strand Breaks: New Developments in Nonhomologous End Joining

DNA damage can occur as a result of endogenous metabolic reactions and replication stress or from exogenous sources such as radiation therapy and chemotherapy. DNA double strand breaks are the most cytotoxic form of DNA damage, and defects in their repair can result in genome instability, a hallmark of cancer. The major pathway for the repair of ionizing radiation-induced DSBs in human cells is nonhomologous end joining. Here we review recent advances on the mechanism of nonhomologous end joining, as well as new findings on its component proteins and regulation.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

Time-Lapse Monitoring of DNA Damage Colocalized With Particle Tracks in Single Living Cells

Purpose: Understanding the DNA damage and repair induced by hadron therapy (HT) beams is crucial for developing novel strategies to maximize the use of HT beams to treat cancer patients. However, spatiotemporal studies of DNA damage and repair for beam energies relevant to HT have been challenging. We report a technique that enables spatiotemporal measurement of radiation-induced damage in live cells and colocalization of this damage with charged particle tracks over a broad range of clinically relevant beam energies. The technique uses novel fluorescence nuclear track detectors with fluorescence confocal laser scanning microscopy in the beam line to visualize particle track traversals within the subcellular compartments of live cells within seconds after injury. Methods and Materials: We designed and built a portable fluorescence confocal laser scanning microscope for use in the beam path, coated fluorescence nuclear track detectors with fluorescent-tagged live cells (HT1080 expressing enhanced green fluorescent protein tagged to XRCC1, a single-strand break repair protein), placed the entire assembly into a proton therapy beam line, and irradiated the cells with a fluence of ∼1 × 10{sup 6} protons/cm{sup 2}. Results: We successfully obtained confocal images of proton tracks and foci of DNA single-strand breaks immediately after irradiation. Conclusions: This technique represents an innovative method for analyzing biological responses in any HT beam line at energies and dose rates relevant to therapy. It allows precise determination of the number of tracks traversing a subcellular compartment and monitoring the cellular damage therein, and has the potential to measure the linear energy transfer of each track from therapeutic beams.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2016

Dlx5 Homeodomain: DNA Complex: Structure, Binding and Effect of Mutations Related to Split Hand and Foot Malformation Syndrome

The Dlx5 homeodomain is a transcription factor related to the Drosophila Distal-less gene that is associated with breast and lung cancer, lymphoma, Rett syndrome and osteoporosis in humans. Mutations in the DLX5 gene have been linked to deficiencies in craniofacial and limb development in higher eukaryotes, including Split Hand and Foot Malformation-1 (SHFM-1) in humans. Our characterization of a Dlx5 homeodomain–(CGACTAATTAGTCG) 2 complex by NMR spectroscopy paved the way for determination of its crystal structure at 1.85 Å resolution that enabled rationalization of the effects of disease-related mutations on the protein function. A remarkably subtle mutation, Q186H, is linked to SHFM-1; this change likely affects affinity of DNA binding by disrupting water-mediated interactions with the DNA major groove. A more subtle effect is implicated for the Q178P mutation, which is not in direct contact with the DNA. Our data indicate that these mutations diminish the ability of the Dlx5 homeodomain to recognize and bind target DNAs, and likely destabilize the formation of functional complexes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Metabolic changes and DNA hypomethylation in cerebellum are associated with behavioral alterations in mice exposed to trichloroethylene postnatally

Previous studies demonstrated that low-level postnatal and early life exposure to the environmental contaminant, trichloroethylene (TCE), in the drinking water of MRL +/+ mice altered glutathione redox homeostasis and increased biomarkers of oxidative stress indicating a more oxidized state. Plasma metabolites along the interrelated transmethylation pathway were also altered indicating impaired methylation capacity. Here we extend these findings to further characterize the impact of TCE exposure in mice exposed to water only or two doses of TCE in the drinking water (0, 2, and 28 mg/kg/day) postnatally from birth until 6 weeks of age on redox homeostasis and biomarkers of oxidative stress in the cerebellum. In addition, pathway intermediates involved in methyl metabolism and global DNA methylation patterns were examined in cerebellar tissue. Because the cerebellum is functionally important for coordinating motor activity, including exploratory and social approach behaviors, these parameters were evaluated in the present study. Mice exposed to 28 mg/kg/day TCE exhibited increased locomotor activity over time as compared with control mice. In the novel object exploration test, these mice were more likely to enter the zone with the novel object as compared to control mice. Similar results were obtained in a second test when an unfamiliar mouse was introduced into the testing arena. The results show for the first time that postnatal exposure to TCE causes key metabolic changes in the cerebellum that may contribute to global DNA methylation deficits and behavioral alterations in TCE-exposed mice. - Highlights: • We exposed male mice to low-level trichloroethylene from postnatal days 1 through 42. • This exposure altered redox potential and increased oxidative stress in cerebellum. • This exposure altered metabolites important in cellular methylation in cerebellum. • This exposure promoted DNA hypomethylation in cerebellum. • This exposure enhanced locomotor activity and exploratory behavior.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2013

Sustained induction of cytochrome P4501A1 in human hepatoma cells by co-exposure to benzo[a]pyrene and 7H-dibenzo[c,g]carbazole underlies the synergistic effects on DNA adduct formation

To gain a deeper insight into the potential interactions between individual aromatic hydrocarbons in a mixture, several benzo[a]pyrene (B[a]P) and 7H-dibenzo[c,g]carbazole (DBC) binary mixtures were studied. The biological activity of the binary mixtures was investigated in the HepG2 and WB-F344 liver cell lines and the Chinese hamster V79 cell line that stably expresses the human cytochrome P4501A1 (hCYP1A1). In the V79 cells, binary mixtures, in contrast to individual carcinogens, caused a significant decrease in the levels of micronuclei, DNA adducts and gene mutations, but not in cell survival. Similarly, a lower frequency of micronuclei and levels of DNA adducts were found in rat liver WB-F344 cells treated with a binary mixture, regardless of the exposure time. The observed antagonism between B[a]P and DBC may be due to an inhibition of Cyp1a1 expression because cells exposed to B[a]P:DBC showed a decrease in Cyp1a1 mRNA levels. In human liver HepG2 cells exposed to binary mixtures for 2 h, a reduction in micronuclei frequency was also found. However, after a 24 h treatment, synergism between B[a]P and DBC was determined based on DNA adduct formation. Accordingly, the up-regulation of CYP1A1 expression was detected in HepG2 cells exposed to B[a]P:DBC. Our results show significant differences in the response of human and rat cells to B[a]P:DBC mixtures and stress the need to use multiple experimental systems when evaluating the potential risk of environmental pollutants. Our data also indicate that an increased expression of CYP1A1 results in a synergistic effect of B[a]P and DBC in human cells. As humans are exposed to a plethora of noxious chemicals, our results have important implications for human carcinogenesis. - Highlights: • B[a]P:DBC mixtures were less genotoxic in V79MZh1A1 cells than B[a]P and DBC alone. • An antagonism between B[a]P and DBC was determined in rat liver WB-F344 cells. • The inhibition of CYP1a1 expression by B[a]P:DBC mixture underlies this antagonism. • A synergism between B[a]P and DBC was detected in human liver HepG2 cells. • The up-regulation of CYP1A1 expression was found in B[a]P:DBC-exposed HepG2 cells.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Differential DNA methylation profile of key genes in malignant prostate epithelial cells transformed by inorganic arsenic or cadmium

Previous work shows altered methylation patterns in inorganic arsenic (iAs)- or cadmium (Cd)-transformed epithelial cells. Here, the methylation status near the transcriptional start site was assessed in the normal human prostate epithelial cell line (RWPE-1) that was malignantly transformed by 10 μM Cd for 11 weeks (CTPE) or 5 μM iAs for 29 weeks (CAsE-PE), at which time cells showed multiple markers of acquired cancer phenotype. Next generation sequencing of the transcriptome of CAsE-PE cells identified multiple dysregulated genes. Of the most highly dysregulated genes, five genes that can be relevant to the carcinogenic process (S100P, HYAL1, NTM, NES, ALDH1A1) were chosen for an in-depth analysis of the DNA methylation profile. DNA was isolated, bisulfite converted, and combined bisulfite restriction analysis was used to identify differentially methylated CpG sites, which was confirmed with bisulfite sequencing. Four of the five genes showed differential methylation in transformants relative to control cells that was inversely related to altered gene expression. Increased expression of HYAL1 (> 25-fold) and S100P (> 40-fold) in transformants was correlated with hypomethylation near the transcriptional start site. Decreased expression of NES (> 15-fold) and NTM (> 1000-fold) in transformants was correlated with hypermethylation near the transcriptional start site. ALDH1A1 expression was differentially expressed in transformed cells but was not differentially methylated relative to control. In conclusion, altered gene expression observed in Cd and iAs transformed cells may result from altered DNA methylation status. - Highlights: • Cd and iAs are known human carcinogens, yet neither appears directly mutagenic. • Prior data suggest epigenetic modification plays a role in Cd or iAs induced cancer. • Altered methylation of four misregulated genes was found in Cd or iAs transformants. • The resulting altered gene expression may be relevant to cellular transformation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

Zebrafish embryos as a screen for DNA methylation modifications after compound exposure

Modified epigenetic programming early in life is proposed to underlie the development of an adverse adult phenotype, known as the Developmental Origins of Health and Disease (DOHaD) concept. Several environmental contaminants have been implicated as modifying factors of the developing epigenome. This underlines the need to investigate this newly recognized toxicological risk and systematically screen for the epigenome modifying potential of compounds. In this study, we examined the applicability of the zebrafish embryo as a screening model for DNA methylation modifications. Embryos were exposed from 0 to 72 h post fertilization (hpf) to bisphenol-A (BPA), diethylstilbestrol, 17α-ethynylestradiol, nickel, cadmium, tributyltin, arsenite, perfluoroctanoic acid, valproic acid, flusilazole, 5-azacytidine (5AC) in subtoxic concentrations. Both global and site-specific methylation was examined. Global methylation was only affected by 5AC. Genome wide locus-specific analysis was performed for BPA exposed embryos using Digital Restriction Enzyme Analysis of Methylation (DREAM), which showed minimal wide scale effects on the genome, whereas potential informative markers were not confirmed by pyrosequencing. Site-specific methylation was examined in the promoter regions of three selected genes vasa, vtg1 and cyp19a2, of which vasa (ddx4) was the most responsive. This analysis distinguished estrogenic compounds from metals by direction and sensitivity of the effect compared to embryotoxicity. In conclusion, the zebrafish embryo is a potential screening tool to examine DNA methylation modifications after xenobiotic exposure. The next step is to examine the adult phenotype of exposed embryos and to analyze molecular mechanisms that potentially link epigenetic effects and altered phenotypes, to support the DOHaD hypothesis. - Highlights: • Compound induced effects on DNA methylation in zebrafish embryos • Global methylation not an informative biomarker • Minimal genome wide site specific changes as detected with DREAM • Compound/class specific effects suggested by pyrosequence of specific targets • Zebrafish embryo may be a screening model for epigenetic effects.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2014

The RXL motif of the African cassava mosaic virus Rep protein is necessary for rereplication of yeast DNA and viral infection in plants

Geminiviruses, single-stranded DNA plant viruses, encode a replication-initiator protein (Rep) that is indispensable for virus replication. A potential cyclin interaction motif (RXL) in the sequence of African cassava mosaic virus Rep may be an alternative link to cell cycle controls to the known interaction with plant homologs of retinoblastoma protein (pRBR). Mutation of this motif abrogated rereplication in fission yeast induced by expression of wildtype Rep suggesting that Rep interacts via its RXL motif with one or several yeast proteins. The RXL motif is essential for viral infection of Nicotiana benthamiana plants, since mutation of this motif in infectious clones prevented any symptomatic infection. The cell-cycle link (Clink) protein of a nanovirus (faba bean necrotic yellows virus) was investigated that activates the cell cycle by binding via its LXCXE motif to pRBR. Expression of wildtype Clink and a Clink mutant deficient in pRBR-binding did not trigger rereplication in fission yeast. - Highlights: • A potential cyclin interaction motif is conserved in geminivirus Rep proteins. • In ACMV Rep, this motif (RXL) is essential for rereplication of fission yeast DNA. • Mutating RXL abrogated viral infection completely in Nicotiana benthamiana. • Expression of a nanovirus Clink protein in yeast did not induce rereplication. • Plant viruses may have evolved multiple routes to exploit host DNA synthesis.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2015

Novel DNA packaging recognition in the unusual bacteriophage N15

Phage lambda's cosB packaging recognition site is tripartite, consisting of 3 TerS binding sites, called R sequences. TerS binding to the critical R3 site positions the TerL endonuclease for nicking cosN to generate cohesive ends. The N15 cos (cos{sup N15}) is closely related to cos{sup λ}, but whereas the cosB{sup N15} subsite has R3, it lacks the R2 and R1 sites and the IHF binding site of cosB{sup λ}. A bioinformatic study of N15-like phages indicates that cosB{sup N15} also has an accessory, remote rR2 site, which is proposed to increase packaging efficiency, like R2 and R1 of lambda. N15 plus five prophages all have the rR2 sequence, which is located in the TerS-encoding 1 gene, approximately 200 bp distal to R3. An additional set of four highly related prophages, exemplified by Monarch, has R3 sequence, but also has R2 and R1 sequences characteristic of cosB–λ. The DNA binding domain of TerS-N15 is a dimer. - Highlights: • There are two classes of DNA packaging signals in N15-related phages. • Phage N15's TerS binding site: a critical site and a possible remote accessory site. • Viral DNA recognition signals by the λ-like bacteriophages: the odd case of N15.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Engineered Silicon Carbide Three-Dimensional Frameworks through DNA-Prescribed Assembly

The ability to create nanoengineered silicon carbide (SiC) architectures is important for the diversity of optical, electronic, and mechanical applications. Here, we report a fabrication of periodic three-dimensional (3D) SiC nanoscale architectures using a self-assembled and designed 3D DNA-based framework. The assembly is followed by the templating into silica and subsequent conversion into SiC using a lower temperature pathway (<700 °C) via magnesium reduction. The formed SiC framework lattice has a unit size of about 50 nm and domains over 5 μm, and it preserves the integrity of the original 3D DNA lattice. The spectroscopic and electron microscopy characterizations reveal SiC crystalline morphology of 3D nanoarchitectured lattices, whereas electrical probing shows 2 orders of magnitude enhancements of electrical conductivity over the precursor silica framework. The reported approach offers a versatile methodology toward creating highly structured and spatially prescribed SiC nanoarchitectures through the DNA-programmable assembly and the combination of templating processes.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2020

Reconfigurable Liquids Stabilized by DNA Surfactants

Polyelectrolyte microcapsules can be produced either by the layer-by-layer assembly technique or the formation of polyelectrolyte complexes at the liquid-liquid interface. In this work, we describe the design and construction of DNA microcapsules using the cooperative assembly of DNA and amine-functionalized polyhedral oligomeric silsesquioxane (POSS-NH 2 ) at the oil-water interface. "Janus-like" DNA surfactants (DNASs) assemble in situ at the interface, forming an elastic film. By controlling the jamming and unjamming behavior of DNASs, the interfacial assemblies can assume three different physical states: solid-like, elastomer-like, and liquid-like, similar to that seen with thermoplastics upon heating, that change from a glassy to a rubbery state, and then to a viscous liquid. By the interfacial jamming of DNASs, the liquid structures can be locked-in and reconfigured, showing promising potentials for drug delivery, biphasic reactors, and programmable liquid constructs.

36 MATERIALS SCIENCE↗
DOE OSTI2022

Programmable Photoluminescence via Intrinsic and DNA-Fluorophore Association in a Mixed Cluster Heterometallic MOF

In this report a rapid and facile design strategy to create a highly complex optical tag with programmable, multimodal photoluminescent properties is described. This was achieved via intrinsic and DNA-fluorophore hidden signatures. As a first covert feature of the tag, an intricate novel heterometallic near-infrared (NIR)-emitting mesoporous metal–organic framework (MOF) was designed and synthesized. The material is constructed from two chemically distinct, homometallic hexanuclear clusters based on Nd and Yb. Uniquely, the Nd-based cluster is observed here for the first time in a MOF and consists of two staggered Nd μ3-oxo trimers. To generate controlled, multimodal, and tailorable emission with difficult to counterfeit features, the NIR-emissive MOF was post-synthetically modified via a fluorescent DNA oligo labeling design strategy. The surface attachment of several distinct fluorophores, including the simultaneous attachment of up to three distinct fluorescently labeled oligos was achieved, with excitation and emission properties across the visible spectrum (480-800 nm). The DNA inclusion as a secondary covert element in the tag was demonstrated via the detection of SYBR Gold dye association. Importantly, the approach implemented here serves as a rapid and tailorable way to encrypt distinct information in a facile and modular fashion and provides an innovative technology in the quest toward complex optical tags.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Antibacterial Drug Leads: DNA and Enzyme Multitargeting

Here, we report the results of an investigation of the activity of a series of amidine and bisamidine compounds against Staphylococcus aureus and Escherichia coli. The most active compounds bound to an AT-rich DNA dodecamer (CGCGAATTCGCG) 2 and using DSC were found to increase the melting transition by up to 24 °C. Several compounds also inhibited undecaprenyl diphosphate synthase (UPPS) with IC 50 values of 100–500 nM, and we found good correlations (R 2 = 0.89, S. aureus; R 2 = 0.79, E. coli) between experimental and predicted cell growth inhibition by using DNA ΔT m and UPPS IC 50 experimental results together with one computed descriptor. Finally, we also solved the structures of three bisamidines binding to DNA as well as three UPPS structures. Overall, the results are of general interest in the context of the development of resistance-resistant antibiotics that involve multitargeting.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2016

Self-organized architectures from assorted DNA-framed nanoparticles

The science of self-assembly has undergone a radical shift from asking questions about why individual components self-organize into ordered structures, to manipulating the resultant order. However, the quest for far-reaching nanomanufacturing requires addressing an even more challenging question: how to form nanoparticle (NP) structures with designed architectures without explicitly prescribing particle positions. Here we report an assembly concept in which building instructions are embedded into NPs via DNA frames. The integration of NPs and DNA origami frames enables the fabrication of NPs with designed anisotropic and selective interactions. Using a pre-defined set of different DNA-framed NPs, we show it is possible to design diverse planar architectures, which include periodic structures and shaped meso-objects that spontaneously emerge on mixing of the different topological types of NP. Even objects of non-trivial shapes, such as a nanoscale model of Leonardo da Vinci's Vitruvian Man, can be self-assembled successfully.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2016

Lattice engineering through nanoparticle–DNA frameworks

Advances in self-assembly over the past decade have demonstrated that nano- and microscale particles can be organized into a large diversity of ordered three-dimensional (3D) lattices. However, the ability to generate different desired lattice types from the same set of particles remains challenging. Here, we show that nanoparticles can be assembled into crystalline and open 3D frameworks by connecting them through designed DNA-based polyhedral frames. The geometrical shapes of the frames, combined with the DNA-assisted binding properties of their vertices, facilitate the well-defined topological connections between particles in accordance with frame geometry. With this strategy, different crystallographic lattices using the same particles can be assembled by introduction of the corresponding DNA polyhedral frames. As a result, this approach should facilitate the rational assembly of nanoscale lattices through the design of the unit cell.

77 NANOSCIENCE AND NANOTECHNOLOGY↗
DOE OSTI2025

Realizing mechanical frustration at the nanoscale using DNA origami

Structural designs inspired by physical and biological systems have been previously utilized to develop mechanical metamaterials with enhanced properties based on clever geometric arrangement of constituent building blocks. Here, we use the DNA origami method to realize a nanoscale metastructure exhibiting mechanical frustration, a counterpart of the well-known phenomenon of magnetic frustration. By selectively actuating reconfigurable struts, it adopts either frustrated or non-frustrated states, each characterized by distinct free energy profiles. While the non-frustrated state distributes the strain homogeneously, the frustrated mode concentrates it at a specific location. Molecular dynamics simulations reconcile the contrasting behaviors and provide insights into underlying mechanics. We explore the design space further by tailoring responses through structural modifications. Our work combines programmable DNA self-assembly with mechanical design principles to overcome engineering limitations encountered at the macroscale to design dynamic, deformable nanostructures with potential applications in elastic energy storage, nanomechanical computation, and allosteric mechanisms in DNA-based nanomachinery.

DNA nanostructures↗
DOE OSTI2016

Engineering a trifunctional proline utilization A chimaera by fusing a DNA-binding domain to a bifunctional PutA

Proline utilization A (PutA) is a bifunctional flavoenzyme with proline dehydrogenase (PRODH) and Δ1-pyrroline-5-carboxylate (P5C) dehydrogenase (P5CDH) domains that catalyses the two-step oxidation of proline to glutamate. Trifunctional PutAs also have an N-terminal ribbon–helix–helix (RHH) DNA-binding domain and moonlight as autogenous transcriptional repressors of the put regulon. A unique property of trifunctional PutA is the ability to switch functions from DNA-bound repressor to membrane-associated enzyme in response to cellular nutritional needs and proline availability. In the present study, we attempt to construct a trifunctional PutA by fusing the RHH domain of Escherichia coli PutA (EcRHH) to the bifunctional Rhodobacter capsulatus PutA (RcPutA) in order to explore the modular design of functional switching in trifunctional PutAs. The EcRHH–RcPutA chimaera retains the catalytic properties of RcPutA while acquiring the oligomeric state, quaternary structure and DNA-binding properties of EcPutA. Furthermore, the EcRHH–RcPutA chimaera exhibits proline-induced lipid association, which is a fundamental characteristic of functional switching. Unexpectedly, RcPutA lipid binding is also activated by proline, which shows for the first time that bifunctional PutAs exhibit a limited form of functional switching. Altogether, these results suggest that the C-terminal domain (CTD), which is conserved by trifunctional PutAs and certain bifunctional PutAs, is essential for functional switching in trifunctional PutAs.

59 BASIC BIOLOGICAL SCIENCES↗