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At least 1,171 records · Page 65
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Self-assembly and condensation of intermolecular poly(UG) RNA quadruplexes

Abstract Poly(UG) or ‘pUG’ dinucleotide repeats are highly abundant sequences in eukaryotic RNAs. In Caenorhabditis elegans, pUGs are added to RNA 3′ ends to direct gene silencing within Mutator foci, a germ granule condensate. Here, we show that pUG RNAs efficiently self-assemble into gel condensates through quadruplex (G4) interactions. Short pUG sequences form right-handed intermolecular G4s (pUG G4s), while longer pUGs form left-handed intramolecular G4s (pUG folds). We determined a 1.05 Å crystal structure of an intermolecular pUG G4, which reveals an eight stranded G4 dimer involving 48 nucleotides, 7 different G and U quartet conformations, 7 coordinated potassium ions, 8 sodium ions and a buried water molecule. A comparison of the intermolecular pUG G4 and intramolecular pUG fold structures provides insights into the molecular basis for G4 handedness and illustrates how a simple dinucleotide repeat sequence can form complex structures with diverse topologies.

Biochemistry & Molecular Biology↗
DOE OSTI2025

Cryo-EM structure of AAV2 Rep68 bound to integration site AAVS1: insights into the mechanism of DNA melting

Abstract The Rep68 protein from Adeno-Associated Virus (AAV) is a multifunctional SF3 helicase that performs most of the DNA transactions necessary for the viral life cycle. During AAV DNA replication, Rep68 assembles at the origin of replication, catalyzing the DNA melting and nicking reactions during the hairpin rolling replication process to complete the second-strand synthesis of the AAV genome. We report the cryo-electron microscopy structures of Rep68 bound to the adeno-associated virus integration site 1 in different nucleotide-bound states. In the nucleotide-free state, Rep68 forms a heptameric complex around DNA, with three origin-binding domains (OBDs) bound to the Rep-binding element sequence, while three remaining OBDs form transient dimers with them. The AAA+ domains form an open ring without interactions between subunits and DNA. We hypothesize that the heptameric structure is crucial for loading Rep68 onto double-stranded DNA. The ATPγS complex shows that only three subunits associate with the nucleotide, leading to a conformational change that promotes the formation of both intersubunit and DNA interactions. Moreover, three phenylalanine residues in the AAA+ domain induce a steric distortion in the DNA. Our study provides insights into how an SF3 helicase assembles on DNA and provides insights into the DNA melting process.

Jaiswal, Rahul↗
DOE OSTI2019

Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 Å

HhaI, a Type II restriction endonuclease, recognizes the symmetric sequence 5'-GCG↓C-3' in duplex DNA and cleaves (‘↓’) to produce fragments with 2-base, 3'-overhangs. We determined the structure of HhaI in complex with cognate DNA at an ultra-high atomic resolution of 1.0 Å. Most restriction enzymes act as dimers with two catalytic sites, and cleave the two strands of duplex DNA simultaneously, in a single binding event. HhaI, in contrast, acts as a monomer with only one catalytic site, and cleaves the DNA strands sequentially, one after the other. HhaI comprises three domains, each consisting of a mixed five-stranded β sheet with a defined function. The first domain contains the catalytic-site; the second contains residues for sequence recognition; and the third contributes to non-specific DNA binding. The active-site belongs to the ‘PD-D/EXK’ superfamily of nucleases and contains the motif SD-X11-EAK. The first two domains are similar in structure to two other monomeric restriction enzymes, HinP1I (G↓CGC) and MspI (C↓CGG), which produce fragments with 5'-overhangs. The third domain, present only in HhaI, shifts the positions of the recognition residues relative to the catalytic site enabling this enzyme to cleave the recognition sequence at a different position. The structure of M.HhaI, the biological methyltransferase partner of HhaI, was determined earlier. Together, these two structures represent the first natural pair of restriction-modification enzymes to be characterized in atomic detail.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

GTP binding by Arabidopsis extra-large G protein 2 is not essential for its functions

The extra-large guanosine-5'-triphosphate (GTP)-binding protein 2, XLG2, is an unconventional Gα subunit of the Arabidopsis (Arabidopsis thaliana) heterotrimeric GTP-binding protein complex with a major role in plant defense. In vitro biochemical analyses and molecular dynamic simulations show that affinity of XLG2 for GTP is two orders of magnitude lower than that of the conventional Gα, AtGPA1. Here we tested the physiological relevance of GTP binding by XLG2. We generated an XLG2(T476N) variant with abolished GTP binding, as confirmed by in vitro GTPγS binding assay. Yeast three-hybrid, bimolecular fluorescence complementation, and split firefly-luciferase complementation assays revealed that the nucleotide-depleted XLG2(T476N) retained wild-type XLG2-like interactions with the Gβγ dimer and defense-related receptor-like kinases. Both wild-type and nucleotide-depleted XLG2(T476N) restored the defense responses against Fusarium oxysporum and Pseudomonas syringae compromised in the xlg2 xlg3 double mutant. Additionally, XLG2(T476N) was fully functional restoring stomatal density, root growth, and sensitivity to NaCl, but failed to complement impaired germination and vernalization-induced flowering. We conclude that XLG2 is able to function in a GTP-independent manner and discuss its possible mechanisms of action.

Plant Sciences↗
DOE OSTI2024

Putative rhamnogalacturonan-II glycosyltransferase identified through callus gene editing bypasses embryo lethality

Rhamnogalacturonan II (RG-II) is a structurally complex and conserved domain of the pectin present in the primary cell walls of vascular plants. Borate crosslinking of RG-II is required for plants to grow and develop normally. Mutations that alter RG-II structure also affect crosslinking and are lethal or severely impair growth. Thus, few genes involved in RG-II synthesis have been identified. Here we developed a method to generate viable loss-of-function Arabidopsis (Arabidopsis thaliana) mutants in callus tissue via CRISPR/Cas9-mediated gene editing. We combined this with a candidate gene approach to characterize the male gametophyte defective 2 (MPG2) gene that encodes a putative family GT29 glycosyltransferase. Plants homozygous for this mutation do not survive. We showed that in the callus mutant cell walls, RG-II does not crosslink normally because it lacks 3-deoxy-D-manno-octulosonic acid (Kdo) and thus cannot form the α-L-Rhap-(1→5)-α-D-kdop-(1→ sidechain. We suggest that MGP2 encodes an inverting RG-II CMP-β-Kdo transferase (RCKT1). Our discovery provides further insight into the role of sidechains in RG-II dimerization. Our method also provides a viable strategy for further identifying proteins involved in the biosynthesis of RG-II.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

N-Terminal domain homologs of the orange carotenoid protein increase quenching of cyanobacterial phycobilisomes

Stress exerted by excess captured light energy in cyanobacteria is prevented by the photoprotective activity of the orange carotenoid protein (OCP). Under high light, the OCP converts from an orange, inactive form (OCP O ) into the red form (OCP R ) that binds to and quenches the phycobilisome (PBS). Structurally, the OCP consists of 2 domains: the N-terminal effector domain and a C-terminal regulatory domain. Structural analysis of the OCP-PBS complex showed that the N-terminal domains of an OCP dimer interact with the PBS core. These N-terminal OCP domains have single-domain protein paralogs known as helical carotenoid proteins (HCPs). Using PBS quenching assays, we show that the HCP4 and HCP5 homologs efficiently quench PBS fluorescence in vitro, surpassing the quenching ability of the OCP. This is consistent with computational quantum mechanics/molecular mechanics results. Interestingly, when using a maximum quenching concentration of OCP with PBSs, HCP5 addition further increases PBS quenching. Our results provide mechanistic insight into the quenching capacity and roles of HCP4 and HCP5 in cyanobacteria, suggesting that they are more than simply functionally redundant to the OCP.

Sheppard, Damien I.↗
DOE OSTI2020

Uncovering dark multichromophoric states in Peridinin–Chlorophyll–Protein

It has long been recognized that visible light harvesting in Peridinin–Chlorophyll–Protein is driven by the interplay between the bright (S 2 ) and dark (S 1 ) states of peridinin (carotenoid), along with the lowest-lying bright (Q y ) and dark (Q x ) states of chlorophyll-a. Here, we analyse a chromophore cluster in the crystal structure of Peridinin–Chlorophyll–Protein, in particular, a peridinin–peridinin and a peridinin–chlorophyll-a dimer, and present quantum chemical evidence for excited states that exist beyond the confines of single peridinin and chlorophyll chromophores. These dark multichromophoric states, emanating from the intermolecular packing native to Peridinin–Chlorophyll–Protein, include a correlated triplet pair comprising neighbouring peridinin excitations and a charge-transfer interaction between peridinin and the adjacent chlorophyll-a. Lastly, we surmise that such dark multichromophoric states may explain two spectral mysteries in light-harvesting pigments: the sub-200-fs singlet fission observed in carotenoid aggregates, and the sub-200-fs chlorophyll-a hole generation in Peridinin–Chlorophyll–Protein.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

ssDNA is an allosteric regulator of the C. crescentus SOS-independent DNA damage response transcription activator, DriD

DNA damage repair systems are critical for genomic integrity. However, they must be coordinated with DNA replication and cell division to ensure accurate genomic transmission. In most bacteria, this coordination is mediated by the SOS response through LexA, which triggers a halt in cell division until repair is completed. Recently, an SOS-independent damage response system was revealed in Caulobacter crescentus. This pathway is controlled by the transcription activator, DriD, but how DriD senses and signals DNA damage is unknown. To address this question, we performed biochemical, cellular, and structural studies. We show that DriD binds a specific promoter DNA site via its N-terminal HTH domain to activate transcription of genes, including the cell division inhibitor didA. A structure of the C-terminal portion of DriD revealed a WYL motif domain linked to a WCX dimerization domain. Strikingly, we found that DriD binds ssDNA between the WYL and WCX domains. Comparison of apo and ssDNA-bound DriD structures reveals that ssDNA binding orders and orients the DriD domains, indicating a mechanism for ssDNA-mediated operator DNA binding activation. Biochemical and in vivo studies support the structural model. Our data thus reveal the molecular mechanism underpinning an SOS-independent DNA damage repair pathway.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural and biochemical analyses of the nuclear IκBζ protein in complex with the NF-κB p50 homodimer

As part of the efforts to understand nuclear IκB function in NF-κB-dependent gene expression, we report an X-ray crystal structure of the IκBζ ankyrin repeat domain in complex with the dimerization domain of the NF-κB p50 homodimer. IκBζ possesses an N-terminal α helix that conveys domain folding stability. Affinity and specificity of the complex depend on a small portion of p50 at the nuclear localization signal. The model suggests that only one p50 subunit supports binding with IκBζ, and biochemical experiments confirm that IκBζ associates with DNA-bound NF-κB p50:RelA heterodimers. Comparisons of IκBζ:p50 and p50:κB DNA complex crystallographic models indicate that structural rearrangement is necessary for ternary complex formation of IκBζ and p50 with DNA.

Cell Biology↗
DOE OSTI2025

Delocalized Excitation Transfer in Open Quantum Systems with Long-Range Interactions

The interplay between coherence and system-environment interactions is at the basis of a wide range of phenomena, from quantum information processing to charge and energy transfer in molecular systems, biomolecules, and photochemical materials. In this work, we use a Frenkel exciton model with long-range interacting qubits coupled to a damped collective bosonic mode to investigate vibrationally assisted transfer processes in donor-acceptor systems featuring internal substructures analogous to light-harvesting complexes. We find that certain delocalized excitonic states maximize the transfer rate and that the entanglement is preserved during the dissipative transfer over a wide range of parameters. We investigate the reduction in transfer caused by static disorder, white noise, and finite temperature and study how transfer efficiency scales as a function of the number of dimerized monomers and the component number of each monomer, finding which excitonic states lead to optimal transfer. Finally, we provide a realistic experimental setting to realize this model in analog trapped-ion quantum simulators. Analog quantum simulation of systems comprising many and increasingly complex monomers could offer valuable insights into the design of light-harvesting materials, particularly in the nonperturbative intermediate parameter regime examined in this study, where classical simulation methods are resource intensive.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Dynamical phase transition in a strongly hybridized phonon-triplon chain

In this article, we study a dimerized spin-1/2 chain, such as CuGeO 3 , hosting triplon excitations coupled to optical phonons under weak terahertz laser driving. Both phonons and triplons weakly lose energy into the surrounding baths, forming a non-equilibrium steady state. In the strong phonon-triplon coupling regime, phonons near the two-triplon continuum hybridize strongly with triplons. Using mean-field Lindblad dynamics, we show that strong hybridization induces sharp first-order phase transitions—either single or simultaneous double—in the emission spectrum, mainly due to nonlinearities in the chain and the instantaneous breaking of spatial inversion symmetry, as captured by the phonon displacement. Using mean-field Floquet analysis of harmonic modes in both sectors, we analytically confirm the existence of these phase transitions. Furthermore, we map the complete steady-state phase diagram by varying key control parameters and provide experimentally relevant parameters for observing these transitions in laser-driven CuGeO 3 .

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

Structural transition and possible pressure-induced superconductivity in a suboxide La 5 Pb 3 O

Here, in this study, we report a structural phase transition and its interplay with superconductivity in the suboxide La 5⁢ Pb 3 ⁢O. Upon cooling through 𝑇 𝑡 = 225K, La 5⁢ Pb 3⁢ O transforms from a high-temperature 𝐼⁢4/mcm to a low-temperature 𝑃⁢4/ncc structure in which La-Pb dimerization along the 𝑐 axis occurs. This transition is accompanied by anomalies in the temperature dependence of electrical resistivity and specific heat. High-pressure electrical transport measurements reveal that hydrostatic pressure suppresses the structural transition and possibly induces superconductivity with a maximum superconducting temperature of 10 K. Density functional theory calculations show minimal changes in the electronic density of states and no gap opening at 𝐸 𝐹 across 𝑇 𝑡 , suggesting that the transition is driven by bonding effects rather than Fermi surface instability. These findings establish La 5⁢ Pb 3 ⁢O as a promising platform for exploring the interplay between weak structural transitions and superconductivity.

Yan, Jiaqiang [Oak Ridge National Laboratory (ORNL↗
DOE OSTI2026

Ultrafast One-Dimensional Peierls-Distortion Dynamics in 1⁢T′−Re⁢S 2 Revealed by 4D Electron Microscopy

Rhenium disulfide (ReS 2 ), a prototypical 2D semiconductor with an anisotropic 1⁢T′ structure due to the pronounced Peierls distortion, has demonstrated great potential for polarization-dependent optoelectronics and photonics. Here, we report an ultrafast phase transition occurring within 1 ps, accompanied by a one-dimensional Peierls-distortion relaxation in 1⁢T′−ReS 2 revealed with combined 4D electron microscopy and time-dependent density functional theory calculations. Upon femtosecond laser pulse excitation, the Re-Re dimerization morphology rapidly transforms from a diamond cluster to zigzag chains and persists for several nanoseconds. Here, this ultrafast Peierls-distortion relaxation is further verified by transient changes in optical anisotropy via polarization-dependent transient absorption spectroscopy. Time-dependent density functional theory calculations attribute this novel phase transition to strong correlation between Peierls distortion and impulsive photoexcited carrier doping, predicting a transient band-gap collapse. This Letter opens up an exciting avenue for ultrafast control of Peierls-distortion-induced anisotropy and the metal-insulator transition in 1⁢T′−ReS 2 .

1T’-ReS2↗
DOE OSTI2021

Topological protection of coherence in disordered open quantum systems

Here, we consider topological protection mechanisms in dissipative quantum systems in the presence of quenched disorder, with the intent to prolong the coherence time of a fiducial qubit. The qubit is part of a network of other qubits and dissipative cavities whose coupling parameters are tunable, such that topological edge states can be stabilized. The evolution of the fiducial qubit is entirely determined by a non-Hermitian Hamiltonian which thus emerges from a bona fide physical process. Even in the presence of disorder, a winding number W can be defined and evaluated in real space, as long as certain symmetries are preserved. Hence we can construct the topological phase diagrams of noisy open quantum models, such as the non-Hermitian disordered Su-Schrieffer-Heeger dimer model and a trimer model that includes longer-range couplings. For finite-size systems we find that there are precisely W modes localized at one end of the chain. In such topological phases the qubit's coherence lifetime is exponentially large in the system size. In the presence of competing disorder parameters, interesting reentrance phenomena of topologically nontrivial sectors are observed. This means that in certain parameter regions, increasing disorder drastically increases the coherence time of the fiducial qubit.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Toward witnessing molecular exciton entanglement from spectroscopy

Entanglement is a defining feature of quantum mechanics that can be a resource in engineered and natural systems, but measuring entanglement in experiment remains elusive especially for large chemical systems. Most practical approaches require determining and measuring a suitable entanglement witness which provides some level of information about the entanglement structure of the probed state. A fundamental quantity of quantum metrology is the quantum Fisher information (QFI), which is a rigorous witness of multipartite entanglement that can be evaluated from linear response functions for certain states. Here, in this paper, we explore measuring the QFI of molecular exciton states of the first-excitation subspace from spectroscopy. In particular, we utilize the fact that the linear response of a pure state subject to a weak electric field over all possible driving frequencies encodes the variance of the collective dipole moment in the probed state, which is a valid measure for QFI. The systems that are investigated include the molecular dimer, N-site linear aggregate with nearest-neighbor coupling, and N-site circular aggregate, all modeled as a collection of interacting qubits. Our theoretical analysis shows that the variance of the collective dipole moment in the brightest dipole-allowed eigenstate is the maximum QFI. The optical response of a thermally equilibrated state in the first-excitation subspace is also a valid QFI. Theoretical predictions of the measured QFI for realistic linear dye aggregates as a function of temperature and energetic disorder due to static variations of the host matrix show that two- to three-partite entanglement is realizable. This paper lays some groundwork and inspires measurement of multipartite entanglement of molecular excitons with ultrafast pump-probe experiments.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Bayesian inference for plasmonic nanometrology

Here, we introduce a Bayesian method for the characterization of plasmonic nanoparticles, which is applicable to both near- and far-field problems. Designed to combine data generated from any photon-plasmon interaction experiment with physically motivated theoretical models, our approach leverages state-of-the-art Markov chain Monte Carlo sampling techniques and returns parameter estimates on nanometric scales. Simulated spectral data sets, describing resonant scattering of photons from ellipsoidal and toroidal nanoparticles, are explored as concrete examples of our approach, with the resulting Bayesian estimates showing excellent agreement with the ground truth, even under conditions of high statistical noise. By incorporating Bayes factors into the method as well, we reveal how model selection can determine which one of competing geometric shapes better explains the observed data. Our comprehensive nanometrology procedure can be tailored to a variety of light-particle interaction models, and its reliance on Bayesian inference furnishes automatic uncertainty quantification. In addition to applicability to a host of plasmonic configurations such as nanoparticle dimers, trimers, and array studies, it is proposed that the presented analysis can be extended to the quantum regime, where nonclassical photon statistics may provide additional insight for inference of scatterer properties.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Charge Ordering and Low-Temperature Lattice Distortion in the {beta}'-(BDT-TTF){sub 2}CF{sub 3}CF{sub 2}SO{sub 3} Dime Mott Insulator.

We present single-crystal x-ray diffraction measurements, optical investigations, and electronic structure calculations for the organic charge-transfer salt beta'-(BEDT-TTF)(2)CF3CF2SO3 synthesized by electrocrystallization. Electronic structure calculations confirm the quasi-one-dimensional behavior of the compound and optical conductivity measurements reveal the dimer-Mott insulating nature of the system. The splitting of the charge-sensitive nu(2) mode in Raman spectra demonstrates the onset of an interlayer charge-ordered phase below 25 K, also suggested by the crystal structure considerations. This transition is accompanied by clear signatures of a lattice distortion in the BEDT-TTF donor layer, as shown by a splitting of the vibrational nu(3) mode in infrared spectra. At the same time, the sharp redshift of the nu(1) mode involving the BEDT-TTF ethylene groups strongly suggests a significant modification of the hydrogen-type bonding present between the BEDT-TTF donor layer and the CF3CF2SO3- anion layer. These observations point to a subtle interplay of charge and lattice degrees of freedom at the phase transition.

Olejniczak, I.↗
DOE OSTI2020

Stable Higgs mode in anisotropic quantum magnets

Low-energy excitations associated with the amplitude fluctuation of an order parameter in condensed-matter systems can mimic the Higgs boson, an elementary particle in the standard model, and are dubbed as Higgs modes. Identifying the condensed-matter Higgs mode is challenging because it is known in many cases to decay rapidly into other low-energy bosonic modes, which renders the Higgs mode invisible. Therefore, it is desirable to find a way to stabilize the Higgs mode, which can offer an insight into the stabilization mechanism of the Higgs mode in condensed-matter physics. In quantum magnets, magnetic order caused by spontaneous symmetry breaking supports transverse (magnons) and longitudinal (Higgs modes) fluctuations. Additionally, when a continuous symmetry is broken, the Goldstone magnon mode generally has an excitation energy lower than that of the Higgs mode, causing a rapid decay of the latter. In this work, we show that a stable Higgs mode exists in anisotropic quantum magnets near the quantum critical point between the dimerized and magnetically ordered phases. We find that an easy axis anisotropy increases the magnon gap such that the magnon mode is above the Higgs mode near the quantum critical point, and the decay of the Higgs mode into the magnon mode is forbidden kinematically. Our results suggest that the anisotropic quantum magnets provide ideal platforms to explore the Higgs physics in condensed-matter systems.

36 MATERIALS SCIENCE↗