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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Structural and Electronic Tuning of Luminescent Zn II Complexes Based on an o -Terphenyl Ligand Motif

Here, the structural and photophysical properties of five chiral Zn complexes incorporating a carbazolate (Cz) donor that is electronically decoupled from a pyridyl acceptor by an ortho -connection to a bridging phenylene group are presented. The bidentate ligand in the unsubstituted bis-ligated parent complex was methylated at key positions to constrain the torsional freedom of the donor/acceptor moieties, resulting in three structurally modified bis-ligated derivatives, all exhibiting energy gaps between the singlet and triplet excited states (ΔE ST ) between 22 and 27 meV. Methylation improves the photoluminescence quantum yield (up to 30% in solution), while the low ΔE ST of these complexes allows for dual-emission properties in all of the bis-ligated derivatives. Structural modification of the Cz/pyridyl ligand was also investigated by linking the unsubstituted bidentate ligand to generate a tetradentate, tetrapodal ligand. The solution-state structure of the tetradentate ligand is similar in its free and ligated forms, featuring a binding site reminiscent of enzymes and metal-sequestering ligands. The resulting tetradentate complex [Zn(N 2 R 2 )] shows enhanced through-bond conjugation, increasing the ΔE ST to 89 meV, thereby eliminating the dual-emission characteristics of the bis-ligated complexes. Furthermore, this complex shows a 50-fold improvement in hydrolytic stability in organic solution relative to the parent complex. These compounds and their analyses are intended to enrich the understanding of compounds exhibiting through-space charge transfer and guide the search for earth-abundant metal complexes for applications in photosensitization and luminescence.

aromatic compounds↗
NASA NTRS2017

Novel Approach to Quantification of Telomere Length with Direct Nanopore Sequencing and PCR Amplification

The ends of human chromosomes contain telomeres, or tandem arrays of repeating DNA sequences capped by multiple associated proteins that protect chromosomal ends from degradation. Telomeres function to preserve genomic stability by preventing natural chromosomal ends from being recognized as broken DNA double-strand breaks and triggering inappropriate DNA damage responses. Mounting evidence shows telomere length is an inherited trait that decreases with cellular division and normal aging. In addition, telomere length also appears to be influenced by other factors such as cellular oxidative stress, radiation and mechanical unloading of tissues as in microgravity. To measure these potential effects of the space environment on telomere lengths and cellular aging and regenerative potential we developed a novel telomere measurement approach based on nanopore sequencing of PCR amplified bar-coded chromosome termini. Specifically, telomeres can be directly enriched using barcode sequences ligated to the end of a free end- repaired telomere using the WetLab-2 facility SmartCycler on ISS. Prior to the ligation and amplification protocol a proteinase K digestion of capping proteins followed by a single 95-degree C heat denaturation of the protease is included. After digestion and bar-code ligation, PCR amplification will initiate with the ligated barcoded sequence, suppressing amplification of intra-genomic fragments and resulting in long read barcoded telomere amplicons including the nanopore motor protein sequences. Purified PCR amplicons are then used for nanopore sequencing library generation by simple addition of motor proteins and sequencing library is loaded into the MinION nanopore DNA-sequencer. Amplicon sequence reads from the nanopore device can be base-called quickly on ISS due to barcoding ligation and subsequent PCR amplification enhancing the telomere sequence resolution. If successfully implemented on ISS this technique will provide a novel means of measuring regenerative ability of somatic stem cells in astronauts, and of determining whether spaceflight in microgravity alters their telomere lengths and causes premature cellular aging.

Ma, Kristin R.↗
DOE OSTI2021

Control of Catalyst Isomers Using an N -Phenyl-Substituted RN(CH 2 CH 2 P i Pr 2 ) 2 Pincer Ligand in CO 2 Hydrogenation and Formic Acid Dehydrogenation

A novel pincer ligand, i Pr PN Ph P [PhN- (CH 2 CH 2 P i Pr 2 ) 2 ], which is an analogue of the versatile MACHO ligand, iPr PN H P [HN(CH 2 CH 2 P i Pr 2 ) 2 ], was synthesized and characterized. The ligand was coordinated to ruthenium, and a series of hydride-containing complexes were isolated and characterized by NMR and IR spectroscopies, as well as X-ray diffraction. Comparisons to previously published analogues ligated by iPr PN H P and iPr PN Me P [CH 3 N(CH 2 CH 2 P i Pr 2 ) 2 ] illustrate that there are large changes in the coordination chemistry that occur when the nitrogen substituent of the pincer ligand is altered. For example, ruthenium hydrides supported by the iPr PN Ph P ligand always form the syn isomer (where syn/anti refer to the relative orientation of the group on nitrogen and the hydride ligand on ruthenium), whereas complexes supported by iPr PN H P form the anti isomer and complexes supported by iPr PN Me P form a mixture of syn and anti isomers. We evaluated the impact of the nitrogen substituent of the pincer ligand in catalysis by comparing a series of iPr PN R P (R = H, Me, Ph)-ligated ruthenium hydride complexes as catalysts for formic acid dehydrogenation and carbon dioxide (CO 2 ) hydrogenation to formate. The iPr PN Ph P-ligated species is the most active for formic acid dehydrogenation, and mechanistic studies suggest that this is likely because there are kinetic advantages for catalysts that operate via the syn isomer. In CO 2 hydrogenation, the iPr PN Ph P-ligated species is again the most active under our optimal conditions, and we report some of the highest turnover frequencies for homogeneous catalysts. Experimental and theoretical insights into the turnover-limiting step of catalysis provide a basis for the observed trends in catalytic activity. Additionally, the stability of our complexes enabled us to detect a previously unobserved autocatalytic effect involving the base that is added to drive the reaction. Overall, by modifying the nitrogen substituent on the MACHO ligand, we have developed highly active catalysts for formic acid dehydrogenation and CO 2 hydrogenation and also provided a framework for future catalyst development.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS1993

Unexpected substrate specificity of T4 DNA ligase revealed by in vitro selection

We have used in vitro selection techniques to characterize DNA sequences that are ligated efficiently by T4 DNA ligase. We find that the ensemble of selected sequences ligates about 50 times as efficiently as the random mixture of sequences used as the input for selection. Surprisingly many of the selected sequences failed to produce a match at or close to the ligation junction. None of the 20 selected oligomers that we sequenced produced a match two bases upstream from the ligation junction.

Harada, Kazuo↗
NASA NTRS2003

Synthesis of substantially monodispersed colloids

A method of forming ligated nanoparticles of the formula Y(Z).sub.x where Y is a nanoparticle selected from the group consisting of elemental metals having atomic numbers ranging from 21-34, 39-52, 57-83 and 89-102, all inclusive, the halides, oxides and sulfides of such metals, and the alkali metal and alkaline earth metal halides, and Z represents ligand moieties such as the alkyl thiols. In the method, a first colloidal dispersion is formed made up of nanoparticles solvated in a molar excess of a first solvent (preferably a ketone such as acetone), a second solvent different than the first solvent (preferably an organic aryl solvent such as toluene) and a quantity of ligand moieties; the first solvent is then removed under vacuum and the ligand moieties ligate to the nanoparticles to give a second colloidal dispersion of the ligated nanoparticles solvated in the second solvent. If substantially monodispersed nanoparticles are desired, the second dispersion is subjected to a digestive ripening process. Upon drying, the ligated nanoparticles may form a three-dimensional superlattice structure.

Klabunde, Kenneth J.↗
DOE OSTI2021

Investigating the non-classical M-H 2 bonding in OsClH 3 (PPh 3 ) 3

Dihydrogen ligation to metal centers results in a wide range of metal-hydrogen interactions. Compounds containing non-classical dihydrogen ligands in which the H-H contacts are significantly longer than the 0.74 A distance found in solid H 2 are classified as Kubas-like compounds, stretched dihydrogen ligands, or compressed dihydrides, depending on the H-H contact length. Compounds containing stretched dihydrogen and compressed dihydride ligands are somewhat rare. Developing a more complete understanding of the metal-hydrogen and hydrogen-hydrogen interactions in these species may provide insights into the mechanisms for the oxidative addition reaction and hydrogen storage. Here, we use diffraction and inelastic neutron scattering (INS) measurements, paired with both molecular and solid-state density functional theory (DFT), to fully characterize the nature of the metal-hydrogen and hydrogen-hydrogen interactions in a previously reported compound, OsClH 3 (PPh 3 ) 3 . In that report, the H-H distance was measured as 1.48(2) A by single-crystal neutron diffraction and was described as a "stretched" dihydrogen. The INS-generated phonon density of states is well described by the DFT calculations, including those normal modes dominated by the vibrational motions of the three Os-ligated hydrogen atoms. Additionally, the resulting calculated electron charge density landscape indicates that there is no remnant bonding character between the Os-ligated hydrogen atoms in the compound. Based on these findings, we update the understanding of the metal-hydrogen bonding in this complex and reclassify it as a compressed dihydride. As such, OsClH 3 (PPh 3 ) 3 represents a rare example of a non-classical compressed dihydride species.

08 HYDROGEN↗
DOE OSTI2024

Shallow Rate-Redox Potential Scaling in Aqueous Molecular Oxygen Reduction Electrocatalysis Across a Family of Iron Macrocycles

Rate-overpotential scaling relationships have been employed widely to understand trends in oxygen reduction reaction (ORR) electrocatalysis by dissolved metal macrocycles in organic electrolytes. Similar scaling relationships remain unknown for surface-adsorbed ORR electrocatalysts in the acidic aqueous environments germane to proton-exchange membrane (PEM) fuel cells. Herein, we examine ORR catalysis in aqueous perchloric acid media for a structurally diverse array of iron macrocycle complexes adsorbed on Vulcan carbon black. The macrocycles encompass Fe– N 4 , Fe–N 2 N' 2 and Fe–N x C 4-x motifs bearing pyrrolic, pyridinic, and N-heterocyclic carbene (NHC) moieties in the primary ligation sphere, giving rise to a 670 mV range in Fe(III/II) redox potentials, E Fe(III/II) . Experimental Tafel data in the micropolarization regime were extrapolated to the E Fe(III/II) to furnish estimated per-site-normalized current density (j per-site ) values that span ~4.6 orders of magnitude across the family of compounds. Despite the structural diversity of this family of compounds, extrapolated j per-site values correlate with the Fe(III/II) redox potentials in a roughly log-linear fashion with a shallow scaling factor of approximately 145 mV/decade. Further, these findings highlight that negative shifts in E Fe(III/II) lead to diminishing returns in catalytic rate promotion and suggest that changes to the primary ligating environment in a macrocycle are insufficient to break fundamental rate-potential scaling relationships in aqueous ORR catalysis. Together these studies motivate the further development of higher-potential iron complexes that employ motifs beyond the equatorial ligation plane to enhance ORR catalysis.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Catalytic Hydrogenation of a Ruthenium Carbonyl to Formyl Enabled by Metal–Ligand Cooperation

Metal formyl complexes are critical intermediates in the reduction of CO to valuable products such as methanol and higher alcohols/hydrocarbons, yet examples of formyl generation via the catalytic hydrogenation of transition metal carbonyl complexes under mild conditions are lacking. The catalytic hydrogenation of a ruthenium carbonyl complex with H 2 to produce a formyl complex is reported here. Two classes of hydrogenation catalysts were compared: bis(diphosphine)-ligated complexes that proceed via termolecular H 2 splitting with an external base and pincer-ligated complexes that proceed via an H 2 splitting mechanism involving metal–ligand cooperativity. The hydride transfer and H 2 splitting steps were evaluated for both classes of catalysts, revealing advantages for catalysts that utilize metal–ligand cooperativity and elucidating conditions to promote formyl generation. Only the pincer-ligated Ir and Ru complexes capable of reacting via pathways involving metal–ligand cooperativity were suitable for catalysis. Using 1–10 mol % of the catalysts (PNP)Ir(H) 2 and (HPNP)Ru(H) 2 (CO) (PNP = ( i Pr 2 PC 2 H 4 ) 2 N – ), which use metal–ligand cooperation to activate H 2 , up to 10 turnovers or up to 71% yield were achieved for the conversion of [Ru(bpy) 2 (CO) 2 ] 2+ (bpy = 2,2′-bipyridine) to the formyl complex [Ru(bpy) 2 (CO)(CHO)] + . The Lewis acid B(C 6 F 5 ) 3 was required as an additive to achieve high yields of the formyl complex using (HPNP)Ru(H) 2 (CO) as a catalyst. In conclusion, the catalytic route avoids the use of expensive stoichiometric reagents, such as borohydride, instead generating metal formyls that are key intermediates in CO reduction schemes with H 2 gas.

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

Can the Rate of a Catalytic Turnover Be Altered by Ligands in the Absence of Direct Binding Interactions?

Second sphere coordination effects ubiquitous in enzymatic catalysis occur through direct interactions, either covalent or non-covalent, with reaction intermediates and transition states. Here, we present herein evidence of indirect second sphere coordination effects in which ligation of water/alkanols far removed from the primary coordination sphere of the active site nevertheless alter energetic landscapes within catalytic redox cycles in the absence of direct physicochemical interactions with surface species mediating catalytic turnovers. Density functional theory, in situ X-ray absorption and infrared spectroscopy, and a wide array of steady-state and transient CO oxidation rate data suggest that the presence of peripheral water renders oxidation half-cycles within two-electron redox cycles over μ m -oxo-bridged trimers in MIL-100(M) more kinetically demanding. Communication between ligated water and the active site appears to occur through the Fe-O-Fe backbone, as inferred from spin density variations on the central μ m -oxygen 'junction'. Evidence is provided for the generality of these second sphere effects in that they influence different types of redox half-cycles or metals, and can be amplified or attenuated through choice of coordinating ligand. Specifically in the case of MIL-100(M) materials, the Cr isostructure can be made to kinetically mimic the Fe variant by disproportionately hindering oxidation half-cycles relative to the reduction half-cycles. Kinetic and spectroscopic inferences presented here significantly expand both the conceptual definition of second sphere effects as well as the palette of synthetic levers available for tuning catalytic redox performance through chemical ligation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Processing of DNA single-strand breaks with oxidatively damaged ends by LIG1

Abstract DNA ligase 1 (LIG1) seals broken strand breaks by joining two adjacent ends during DNA replication and repair transactions. We previously reported atomic-level insight into the strategies that LIG1 uses to discriminate mismatches or ribonucleotides. However, how LIG1 processes strand breaks with oxidatively damaged ends in the absence and presence of a “wrong” sugar remains unknown. Here, we determined the crystal structures of LIG1/nick DNA complexes with 3′-8-oxodG and 3′-8-oxorG templating A or C during the pre- and post-catalytic steps of the ligation reaction. Our structures demonstrated differences in the distances at the +1 and +2 nucleotides relative to the 3′-end of the nick and a shift in the template base position to accommodate the oxidative lesion depending on the dual coding potential of 8-oxoG, which forms Hoogsteen or Watson–Crick base pairing in -syn or -anti conformation. Furthermore, these structural adjustments lead to mutagenic ligation or non-mutagenic end joining of the nick substrates. Overall, our findings provide mechanistic insight into how LIG1 processes nicks harboring oxidative damage and ribonucleotides to ensure fidelity at the final ligation step of DNA repair and replication to maintain genome integrity.

Balu, Kanal E [Department of Biochemistry and Mole↗
DOE OSTI2021

Functional Adaptation of LPS-affected Dentoalveolar Fibrous Joints in Rats

We report the functional interplay between cementum of the root and alveolar bone of the socket is tuned by a uniquely positioned 70–80 µm wide fibrous and lubricious ligament in a dentoalveolar joint (DAJ). In this study, structural and biomechanical properties of the DAJ, periodontal ligament space (PDL-space also known as the joint space), alveolar bone of the socket, and cementum of the tooth root that govern the biomechanics of a lipopolysaccharide (LPS)-affected DAJ were mapped both in space and time. The hemi-maxillae from 20 rats (4 control at 6 weeks of age, 4 control and 4 LPS-affected at 12 weeks of age, 4 control and 4 LPS-affected at 16 weeks of age) were investigated using a hybrid technique; micro-X-ray computed tomography (5 µm resolution) in combination with biomechanical testing in situ. Temporal variations in bone and cementum volume fractions were evaluated. Trends in mineral apposition rates (MAR) in additional six Sprague Dawley rats (3 controls, 3 LPS-affected) were revealed by transforming spatial fluorochrome signals to functional growth rates (linearity factor - RW) of bone, dentin, and cementum using a fast Fourier transform on fluorochrome signals from 100-µm hemi-maxillae sections. An overall change in LPS-affected DAJ biomechanics (a 2.5–4.5X increase in tooth displacement and 2X tooth rotation at 6 weeks, no increase in displacement and a 7X increase in rotation at 12 weeks; 27% increase in bone effective strain at 6 weeks and 11% at 12 weeks relative to control) was associated with structural changes in the coronal regions of the DAJ (15% increase in PDL-space from 0 to 6 weeks but only 5% from 6 to 12 weeks compared to control). A significant increase (p < 0.05) in PDL-space between ligated and age-matched control was observed. The bone fraction of ligated at 12 weeks was significantly lower than its age-matched control, and no significant differences (p > 0.05) between groups were observed at 6 weeks. Cementum in the apical regions grew faster but nonlinearly (11% and 20% increase in cementum fraction (CF) at 6 and 12 weeks) compared to control. Alveolar bone revealed site-specific nonlinear growth with an overall increase in MAR (108.5 µm/week to 126.7 µm/week after LPS treatment) compared to dentin (28.3 µm/week in control vs. 26.1 µm/week in LPS-affected) and cementum (126.5 µm/week in control vs. 119.9 µm/week in LPS-affected). A significant increase in CF (p < 0.05) in ligated specimens was observed at 6 weeks of age. Anatomy-specific responses of cementum and bone to the mechano-chemo stimuli, and their collective temporal contribution to observed changes in PDL-space were perpetuated by altered tooth movement. Data highlight the “resilience” of DAJ function through the predominance of nonlinear growth response of cementum, changes in PDL-space, and bone architecture. Despite the significant differences in bone and cementum architectures, data provided insights into the reactionary effects of cementum as a built-in compensatory mechanism to reestablish functional competence of the DAJ. The spatial shifts in architectures of alveolar bone and cementum, and consequently ligament space, highlight adaptations farther away from the site of insult, which also is another novel insight from this study. These adaptations when correlated within the context of joint function (biomechanics) illustrate that they are indeed necessary to sustain DAJ function albeit being pathological.

60 APPLIED LIFE SCIENCES↗
NASA NTRS2012

A "Warm Formamide" Scenario for the Origins of Life Might not be so Hot: Comment on "Formamide and the Origin of Life"

In this review, Saladino et al. present an intriguing hypothesis surrounding the role of formamide in the origins of life on Earth, backed by experimental results supporting each step from formamide to RNA polymers. The overall premise is that, from formamide and inorganic phosphate, RNA molecules over 100 nucleotides in length can be produced. In addition, many carboxylic acids likely relevant to prebiotic metabolism, are formed along the way. Thus, from a rather simple organic molecule that has been observed in outer space (formamide), you can generate many of the compounds necessary for the origins of life. However, because high temperatures (160 C) are required for the formamide reactions, it remains unclear where the "warm formamide" scenario could have occurred. Low-temperature, aqueous hydrogen cyanide-based prebiotic chemistry that we know actually happened has been shown to produce many of the molecules invoked in the formamide hypothesis: amino acids, carboxylic acids, sugar acids, and nucleobases have all been found in meteorites recovered on Earth, providing a plausible route for their synthesis and delivery. In contrast, a large portion of the formamide hypothesis is based on relatively hightemperature reactions, A plausible milieu for high-temperature reactions with concentrated formamide is yet to be described, and is critical for this hypothesis to be validated. Hydrothermal vents are attractive heat sources, and the higher boiling point of formamide has been invoked as a mechanism to concentrate it from an aqueous solution, Unless the water can actually evaporate, however, there would be no net enrichment. For example, in the context of a deep-sea vent, any water "removed" by heating would be quickly replaced. Some of the individual reactions underpinning the present hypothesis have been met with skepticism because they go against conventional wisdom, To name a few of the surprising results: the observation that nucleosides can be converted to cyclic phosphates when heated in the presence of minerals and inorganie phosphate; that 3'-5' cGMP and cAMP nucleotides polymerize rapidly into RNA oligomers, even in the absence of monovalent counterions and that end-to-end ligation reactions between RNA oligomers occur in essentially pure water, without requiring any activating groups or counterions. Because the polymerization reactions are simply transesterification reactions, that they readily occur in the absence of cations makes one wonder why nearly all ribozyme-catalyzed transesterification reactions are metal-ion dependent; similarly, that the end-to-end ligation reactions do not require activation runs counter to the observation that all protein-catalyzed ligation and polymerization reactions of RNA and DNA require activated substrates. Detailed mechanistic studies of the reported reactions are warranted and could provide important insights for understanding the chemistry behind the origins of life. Because the authors have produced many of the experimental results supporting their hypothesis, they could demonstrate the validity of their hypothesis by converting formamide into approx 100 nucleotide RNA oligomers, using the products of one reaction as the reactants for the next reaction, under specific conditions plausible on the pre-biotic Earth. Such a demonstration would represent a milestone for our understanding of the origins of life.

Burton, Aaron S.↗
NASA NTRS2012

A 'Warm Formamide' Scenario for the Origins of Life Might Not Be so Hot Comment on 'Formamide and the Origin of Life' by E. Di Mauro Et Al.

In this review, Saladino et al. present an intriguing hypothesis surrounding the role of formamide in the originsof life on Earth, backed by experimental results supporting each step from formamide to RNA polymers [1]. The overall premise is that, from formamide and inorganic phosphate, RNA molecules over 100 nucleotides in length canbe produced. In addition, many carboxylic acids likely relevant to prebiotic metabolism are formed along the way. Thus, from a rather simple organic molecule that has been observed in outer space (formamide), you can generatemany of the compounds necessary for the origins of life. However, because high temperatures (160 C) are requiredfor the formamide reactions, it remains unclear where the warm formamide scenario could have occurred.Low-temperature, aqueous hydrogen counter to the observation that all protein-catalyzed ligation and polymerization reactions of RNA and DNA requireactivated substrates. Detailed mechanistic studies of the reported reactions are warranted and could provide important insights for understanding the chemistry behind the origins of life.Because the authors have produced many of the experimental results supporting their hypothesis, they coulddemonstrate the validity of their hypothesis by converting formamide into 100 nucleotide RNA oligomers, usingthe products of one reaction as the reactants for the next reaction, under specific conditions plausible on the pre-bioticEarth. Such a demonstration would represent a milestone for our understanding of the origins of life.cyanide-based prebiotic chemistry that we know actually happened has beenshown to produce many of the molecules invoked in the formamide hypothesis: amino acids, carboxylic acids, sugaracids, and nucleobases have all been found in meteorites recovered on Earth [e.g. [24]], providing a plausible routefor their synthesis and delivery. In contrast, a large portion of the formamide hypothesis is based on relatively high-temperature reactions. A plausible milieu for high-temperature reactions with concentrated formamide is yet to bedescribed, and is critical for this hypothesis to be validated. Hydrothermal vents are attractive heat sources, and the higher boiling point of formamide has been invoked as a mechanism to concentrate it from an aqueous solution.Unless the water can actually evaporate, however, there would be no net enrichment. For example, in the context of a deep-sea vent, any water removed by heating would be quickly replaced.Some of the individual reactions underpinning the present hypothesis [1] have been met with skepticism becausethey go against conventional wisdom. To name a few of the surprising results: the observation that nucleosides can beconverted to cyclic phosphates when heated in the presence of minerals and inorganic phosphate [5]; that 35 cGMPand cAMP nucleotides polymerize rapidly into RNA oligomers, even in the absence of monovalent counterions [6];and that end-to-end ligation reactions between RNA oligomers occur in essentially pure water, without requiring any activating groups or counterions [7,8]. Because the polymerization reactions are simply transesterification reactions,that they readily occur in the absence of cations makes one wonder why nearly all ribozyme-catalyzed transesterification reactions are metal-ion dependent; similarly, that the end-to-end ligation reactions do not require activation runs.

life↗
NASA NTRS2022

Final Report - Hypergravity Effects on Chromatin Conformation and Nuclear Structure in Cultured Cells using High-throughput Sequencing

The conformation of the human genome is known to play an important role in transcriptional control of gene expression. Our aim is to assess whether exposure of cultured human cardiomyocytes to hypergravity can induce changes in chromatin organization as assayed by Hi-C proximity ligation technique. Hi-C is used to analyze chromatin interactions by using formaldehyde to crosslink regions of chromatin that are in close proximity. The DNA is then fragmented using a restriction enzyme and ligated under dilute conditions to favor intramolecular ligation of cross-linked fragments. Finally, the DNA is sequenced, allowing reconstruction of genomic structure. iCell cardiomyocyte cultures will be exposed to 40 g via an engineered device (incu-fuge) that allows for the chemical fixation of cells on a spinning centrifuge. Additionally, we plan on using fluorescence microscopy to analyze the nuclear and actin cytoskeletal conformation of cardiomyocytes post hypergravity exposure. We hypothesize that chromatin will rearrange in hypergravity conditions, both rapidly due to direct mechanical forces, as well as over longer time frames due to changes to structures necessary for transcriptional responses such as the de novo formation of promoter-enhancer loops. A negative result–no change between 1 g and hypergravity conditions–would nevertheless be an important data point in our understanding of the rheology of the nucleus, and how cells and cellular structures respond to different gravity fields. The cellular physiology of hypergravity has clinical relevance for spaceflight, and can further inform our understanding of microgravity physiology.

chromatin↗
DOE OSTI2026

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↗
DOE OSTI2022

DNA Sequence Analysis of an Inversion Hot Spot in Lobeliaceae Plastomes

The evolution of plastid genomes (plastomes) in land plants is typically conservative, with extensive structural rearrangements present in only a few groups. Early Southern blot analysis identified two Lobelia species that minimally required deletion of the plastid gene accD and five inversions to account for their plastome arrangement relative to the ancestral organization. Sixty alternative 5-step inversion scenarios could account for the observed arrangement, but only one scenario was consistent with the criterion of ‘common cause’ attributable to a putative rearrangement hot spot at the accD deletion-site. Plastome sequencing demonstrated that this previously hypothesized inversion order is historically accurate. Detailed reconstructions of the ancestral plastome organization before and after each inversion are presented herein. Stem-loop and disruption-rescue models were evaluated for each inversion. One inversion has an obvious stem-loop basis, but the other four inversions were primarily caused by serial insertion of foreign (extra-plastid) DNA bearing large open-reading frames that disrupted plastome organization at the accD deletion-site, and complete plastomes were rescued by seemingly arbitrary ligation or fortuitous recombination at the other inversion endpoint. Transposed copies of DNA segments from elsewhere in the plastome are frequently inserted at inversion junctions, and four junctions are consistent with the stem-loop ligation model.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Nitric oxide delivery and heme-assisted S-nitrosation by the bedbug nitrophorin

Here, nitrophorins are heme proteins used by blood feeding insects to deliver nitric oxide (NO) to a victim, leading to vasodilation and antiplatelet activity. Cimex lectularius (bedbug) nitrophorin (cNP) accomplishes this with a cysteine ligated ferric (Fe(III)) heme. In the acidic environment of the insect's salivary glands, NO binds tightly to cNP. During a blood meal, cNP-NO is delivered to the feeding site where dilution and increased pH lead to NO release. In a previous study, cNP was shown to not only bind heme, but to also nitrosate the proximal cysteine, leading to Cys-NO (SNO) formation. SNO formation requires oxidation of the proximal cysteine, which was proposed to be metal-assisted through accompanying reduction of ferric heme and formation of Fe(II)-NO. Here, we report the 1.6 Å crystal structure of cNP first chemically reduced and then exposed to NO, and show that Fe(II)-NO is formed but SNO is not, supporting a metal-assisted SNO formation mechanism. Crystallographic and spectroscopic studies of mutated cNP show that steric crowding of the proximal site inhibits SNO formation while a sterically relaxed proximal site enhances SNO formation, providing insight into specificity for this poorly understood modification. Experiments examining the pH dependence for NO implicate direct protonation of the proximal cysteine as the underlying mechanism. At lower pH, thiol heme ligation predominates, leading to a smaller trans effect and 60-fold enhanced NO affinity (K d = 70 nM). Unexpectedly, we find that thiol formation interferes with SNO formation, suggesting cNP-SNO is unlikely to form in the insect salivary glands.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗