EXO1 protects BRCA1-deficient cells against toxic DNA lesions.

Inactivating mutations in the BRCA1 and BRCA2 genes impair DNA double-strand break (DSB) repair by homologous recombination (HR), leading to chromosomal instability and cancer. Importantly, BRCA1/2 deficiency also causes therapeutically targetable vulnerabilities. Here, we identify the dependency on the end resection factor EXO1 as a key vulnerability of BRCA1-deficient cells. EXO1 deficiency generates poly(ADP-ribose)-decorated DNA lesions during S phase that associate with unresolved DSBs and genomic instability in BRCA1-deficient but not in wild-type or BRCA2-deficient cells. Our data indicate that BRCA1/EXO1 double-deficient cells accumulate DSBs due to impaired repair by single-strand annealing (SSA) on top of their HR defect. In contrast, BRCA2-deficient cells retain SSA activity in the absence of EXO1 and hence tolerate EXO1 loss. Consistent with a dependency on EXO1-mediated SSA, we find that BRCA1-mutated tumors show elevated EXO1 expression and increased SSA-associated genomic scars compared with BRCA1-proficient tumors. Overall, our findings uncover EXO1 as a promising therapeutic target for BRCA1-deficient tumors.

Nuclear mRNPs are compact particles packaged with a network of proteins promoting RNA-RNA interactions.

Messenger RNAs (mRNAs) are at the center of the central dogma of molecular biology. In eukaryotic cells, these long ribonucleic acid polymers do not exist as naked transcripts; rather, they associate with mRNA-binding proteins to form messenger ribonucleoprotein (mRNP) complexes. Recently, global proteomic and transcriptomic studies have provided comprehensive inventories of mRNP components. However, knowledge of the molecular features of distinct mRNP populations has remained elusive. We purified endogenous nuclear mRNPs from Saccharomyces cerevisiae by harnessing the mRNP biogenesis factors THO and Sub2 in biochemical procedures optimized to preserve the integrity of these transient ribonucleoprotein assemblies. We found that these mRNPs are compact particles that contain multiple copies of Yra1, an essential protein with RNA-annealing properties. To investigate their molecular and architectural organization, we used a combination of proteomics, RNA sequencing, cryo-electron microscopy, cross-linking mass spectrometry, structural models, and biochemical assays. Our findings indicate that yeast nuclear mRNPs are packaged around an intricate network of interconnected proteins capable of promoting RNA-RNA interactions via their positively charged intrinsically disordered regions. The evolutionary conservation of the major mRNA-packaging factor (yeast Yra1 and Aly/REF in metazoans) points toward a general paradigm governing nuclear mRNP packaging.

Resilience of DNA chains to molecular fracture after PCR heating cycles and implications on PCR reliability.

Soon after its introduction in 1987, polymerase chain reaction (PCR) has become a technique widely employed in diagnostic medical devices and forensic science with the intention of amplifying genetic information. PCR prescribes that each of its cycles must include a heating subprocess at 95 °C or more (denominated DNA denaturation and provided for allowing a claimed orderly separation of the two complementary nucleotides strands), which can produce significant damage to DNA, caused by high-speed collisions with surrounding molecules. Since such disruption should be prevented in order to reliably employ PCR, a study of the mechanics of such loss of structural integrity is herein presented, preceded by a review of the fundamental literature which has elucidated the effects of molecular agitation on DNA fragmentation. The main conclusion of this retrospective survey is that the body of examined theoretical and experimental evidence consistently and redundantly confirms scarce resilience and significant loss of structural integrity when DNA is heated at temperatures above 90 °C, even for 1 minute. Such conclusion contradicts the claimed paradigm of PCR fidelity and raises the concern that, at least for long sequences, if PCR can amplify some information, such amplified information may be unreliable for diagnostic or forensic applications, since it originates from sequences of nucleotides subjected to random fragmentation and reaggregation. Such a low-reliability scenario should be preventively considered in the various fields where DNA amplification methodologies are employed which provide for high-temperature heating under conditions equal to or similar to those prescribed by the PCR protocols reviewed in this study.

FANCA Promotes DNA Double-Strand Break Repair by Catalyzing Single-Strand Annealing and Strand Exchange.

FANCA is a component of the Fanconi anemia (FA) core complex that activates DNA interstrand crosslink repair by monoubiquitination of FANCD2. Here, we report that purified FANCA protein catalyzes bidirectional single-strand annealing (SA) and strand exchange (SE) at a level comparable to RAD52, while a disease-causing FANCA mutant, F1263Δ, is defective in both activities. FANCG, which directly interacts with FANCA, dramatically stimulates its SA and SE activities. Alternatively, FANCB, which does not directly interact with FANCA, does not stimulate this activity. Importantly, five other patient-derived FANCA mutants also exhibit deficient SA and SE, suggesting that the biochemical activities of FANCA are relevant to the etiology of FA. A cell-based DNA double-strand break (DSB) repair assay demonstrates that FANCA plays a direct role in the single-strand annealing sub-pathway (SSA) of DSB repair by catalyzing SA, and this role is independent of the canonical FA pathway and RAD52.

Quantum advantage in variational Bayes inference.

Variational Bayes (VB) inference algorithm is used widely to estimate both the parameters and the unobserved hidden variables in generative statistical models. The algorithm-inspired by variational methods used in computational physics-is iterative and can get easily stuck in local minima, even when classical techniques, such as deterministic annealing (DA), are used. We study a VB inference algorithm based on a nontraditional quantum annealing approach-referred to as quantum annealing variational Bayes (QAVB) inference-and show that there is indeed a quantum advantage to QAVB over its classical counterparts. In particular, we show that such better performance is rooted in key quantum mechanics concepts: i) The ground state of the Hamiltonian of a quantum system-defined from the given data-corresponds to an optimal solution for the minimization problem of the variational free energy at very low temperatures; ii) such a ground state can be achieved by a technique paralleling the quantum annealing process; and iii) starting from this ground state, the optimal solution to the VB problem can be achieved by increasing the heat bath temperature to unity, and thereby avoiding local minima introduced by spontaneous symmetry breaking observed in classical physics based VB algorithms. We also show that the update equations of QAVB can be potentially implemented using ⌈logK⌉ qubits and 𝒪(K) operations per step, where K is the number of values hidden categorical variables can take. Thus, QAVB can match the time complexity of existing VB algorithms, while delivering higher performance.

Mechanisms restraining break-induced replication at two-ended DNA double-strand breaks.

DNA synthesis during homologous recombination is highly mutagenic and prone to template switches. Two-ended DNA double-strand breaks (DSBs) are usually repaired by gene conversion with a short patch of DNA synthesis, thus limiting the mutation load to the vicinity of the DSB. Single-ended DSBs are repaired by break-induced replication (BIR), which involves extensive and mutagenic DNA synthesis spanning up to hundreds of kilobases. It remains unknown how mutagenic BIR is suppressed at two-ended DSBs. Here, we demonstrate that BIR is suppressed at two-ended DSBs by proteins coordinating the usage of two ends of a DSB: (i) ssDNA annealing proteins Rad52 and Rad59 that promote second end capture, (ii) D-loop unwinding helicase Mph1, and (iii) Mre11-Rad50-Xrs2 complex that promotes synchronous resection of two ends of a DSB. Finally, BIR is also suppressed when Sir2 silences a normally heterochromatic repair template. All of these proteins are particularly important for limiting BIR when recombination occurs between short repetitive sequences, emphasizing the significance of these mechanisms for species carrying many repetitive elements such as humans.

Quantum annealing-based clustering of single cell RNA-seq data.

Cluster analysis is a crucial stage in the analysis and interpretation of single-cell gene expression (scRNA-seq) data. It is an inherently ill-posed problem whose solutions depend heavily on hyper-parameter and algorithmic choice. The popular approach of K-means clustering, for example, depends heavily on the choice of K and the convergence of the expectation-maximization algorithm to local minima of the objective. Exhaustive search of the space for multiple good quality solutions is known to be a complex problem. Here, we show that quantum computing offers a solution to exploring the cost function of clustering by quantum annealing, implemented on a quantum computing facility offered by D-Wave [1]. Out formulation extracts minimum vertex cover of an affinity graph to sub-sample the cell population and quantum annealing to optimise the cost function. A distribution of low-energy solutions can thus be extracted, offering alternate hypotheses about how genes group together in their space of expressions.

LoopSage: An energy-based Monte Carlo approach for the loop extrusion modeling of chromatin.

The connection between the patterns observed in 3C-type experiments and the modeling of polymers remains unresolved. This paper presents a simulation pipeline that generates thermodynamic ensembles of 3D structures for topologically associated domain (TAD) regions by loop extrusion model (LEM). The simulations consist of two main components: a stochastic simulation phase, employing a Monte Carlo approach to simulate the binding positions of cohesins, and a dynamical simulation phase, utilizing these cohesins' positions to create 3D structures. In this approach, the system's total energy is the combined result of the Monte Carlo energy and the molecular simulation energy, which are iteratively updated. The structural maintenance of chromosomes (SMC) protein complexes are represented as loop extruders, while the CCCTC-binding factor (CTCF) locations on DNA sequence are modeled as energy minima on the Monte Carlo energy landscape. Finally, the spatial distances between DNA segments from ChIA-PET experiments are compared with the computer simulations, and we observe significant Pearson correlations between predictions and the real data. LoopSage model offers a fresh perspective on chromatin loop dynamics, allowing us to observe phase transition between sparse and condensed states in chromatin.

Annealing synchronizes the 70S ribosome into a minimum-energy conformation.

Researchers commonly anneal metals, alloys, and semiconductors to repair defects and improve microstructures via recrystallization. Theoretical studies indicate that simulated annealing on biological macromolecules helps predict the final structures with minimum free energy. Experimental validation of this homogenizing effect and further exploration of its applications are fascinating scientific questions that remain elusive. Here, we chose the apo-state 70S ribosome from Escherichia coli as a model, wherein the 30S subunit undergoes a thermally driven intersubunit rotation and exhibits substantial structural flexibility as well as distinct free energy. We experimentally demonstrate that annealing at a fast cooling rate enhances the 70S ribosome homogeneity and improves local resolution on the 30S subunit. After annealing, the 70S ribosome is in a nonrotated state with respect to corresponding intermediate structures in unannealed or heated ribosomes. Manifold-based analysis further indicates that the annealed 70S ribosome takes a narrow conformational distribution and exhibits a minimum-energy state in the free-energy landscape. Our experimental results offer a facile yet robust approach to enhance protein stability, which is ideal for high-resolution cryogenic electron microscopy. Beyond structure determination, annealing shows great potential for synchronizing proteins on a single-molecule level and can be extended to study protein folding and explore conformational and energy landscapes.

Moderate activity of RNA chaperone maximizes the yield of self-spliced pre-RNA in vivo.

CYT-19 is a DEAD-box protein whose adenosine-triphosphate (ATP)-dependent helicase activity facilitates the folding of group I introns in precursor RNA (pre-RNA) of Neurospora crassa (N. crassa). In the process, they consume a substantial amount of ATP. While much of the mechanistic insight into CYT-19 activity has been gained through the studies on the folding of Tetrahymena group I intron ribozyme, the more biologically relevant issue, namely the effect of CYT-19 on the self-splicing of pre-RNA, remains largely unexplored. Here, we employ a kinetic network model, based on the generalized iterative annealing mechanism (IAM), to investigate the relation between CYT-19 activity, rate of ribozyme folding, and the kinetics of the self-splicing reaction. The network rate parameters are extracted by analyzing the recent biochemical data for CYT-19-facilitated folding of Tetrahymena ribozyme. We then build extended models to explore the metabolism of pre-RNA. We show that the timescales of chaperone-mediated folding of group I ribozyme and self-splicing reaction compete with each other. As a consequence, in order to maximize the self-splicing yield of group I introns in pre-RNA, the chaperone activity must be sufficiently large to unfold the misfolded structures, but not too large to unfold the native structures prior to the self-splicing event. We discover that despite the promiscuous action on structured RNAs, the helicase activity of CYT-19 on group I ribozyme gives rise to self-splicing yields that are close to the maximum.

Atomic Reconstruction of Au Thin Films through Interfacial Strains.

Interfaces play a critical thermodynamic role in the existence of multilayer systems. Due to their utility in bridging energetic and compositional differences between distinct species, the formation of interfaces inherently creates internal strain in the bulk due to the reorganization needed to accommodate such a change. We report the effect of scaling interfacial stress by deposition of different adlayers on a host thin metal film. Intrinsic property differences between host and deposited metal atoms result in varying degree of composition and energy gradient within the interface. Interfacial stress can increase defects in the host leading to (i) energy dissipation and reorganization to minimize surface energy, and (ii) increased material strength. We infer that dissipation of interfacial stress induces defect migration, hence bulk and surface atomic reconstruction as captured by the surface roughness and grain size reduction coupled with a concomitant increase in material strength.

Texture Transfer in Dielectric Layers via Nanocrystalline Networks: Insights from in Situ 4D-STEM.

Transition metal oxide dielectric layers have emerged as promising candidates for various relevant applications, such as supercapacitors or memory applications. However, the performance and reliability of these devices can critically depend on their microstructure, which can be strongly influenced by thermal processing and substrate-induced strain. To gain a more in-depth understanding of the microstructural changes, we conducted in situ transmission electron microscopy (TEM) studies of amorphous HfO2 dielectric layers grown on highly textured (111) substrates. Our results indicate that the minimum required phase transition temperature is 180 °C and that the developed crystallinity is affected by texture transfer. Using in situ TEM and 4D-STEM can provide valuable insights into the fundamental mechanisms underlying the microstructural evolution of dielectric layers and could pave the way for the development of more reliable and efficient devices for future applications.

A glimpse into the hidden world of the flexible C-terminal protein binding domains of human RAD52.

Human RAD52 protein binds DNA and is involved in genomic stability maintenance and several forms of DNA repair, including homologous recombination and single-strand annealing. Despite its importance, there are very few structural details about the variability of the RAD52 ring size and the RAD52 C-terminal protein-protein interaction domains. Even recent attempts to employ cryogenic electron microscopy (cryoEM) methods on full-length yeast and human RAD52 do not reveal interpretable structures for the C-terminal half that contains the replication protein A (RPA) and RAD51 binding domains. In this study, we employed the monodisperse purification of two RAD52 deletion constructs and small angle X-ray scattering (SAXS) to construct a structural model that includes RAD52's RPA binding domain. This model is of interest to DNA repair specialists as well as for drug development against HR-deficient cancers.

Primer extension refractory PCR: an efficient and reliable genome walking method.

Genome walking, a molecular technique for obtaining unknown flanking genomic sequences from a known genomic sequence, has been broadly applied to determine transgenic sites, mine new genetic resources, and fill in chromosomal gaps. This technique has advanced genomics, genetics, and related disciplines. Here, an efficient and reliable genome walking technique, called primer extension refractory PCR (PER-PCR), is presented. PER-PCR uses a set of primary, secondary, and tertiary walking primers. The middle 15 nt of the primary walking primer overlaps with the 3' parts of the secondary and tertiary primers. The 5' parts of the three primers are heterologous to each other. The short overlap allows the walking primer to anneal to its predecessor only in a relaxed-stringency PCR cycle, resulting in a series of single-stranded DNAs; however, the heterologous 5' part prevents the creation of a perfect binding site for the walking primer. In the next stringent cycle, the target single strand can be extended into a double-stranded DNA molecule by the sequence-specific primer and thus can be exponentially amplified by the remaining stringent cycles. The nontarget single strand fails to be enriched due to the lack of a perfect binding site for any primer. PER-PCR was validated by extension into unknown flanking regions of the hyg gene in rice and the gadR gene in Levilactobacillus brevis CD0817. In summary, in this study, a new practical PER-PCR method was constructed as a potential alternative to existing genome walking methods.

CO2 Laser Crystallization in Ambient for Highly Efficient FAPbI3 Perovskite Solar Cells.

Metal halide perovskite solar cells have achieved tremendous progress and have attracted enormous research and development efforts since the first report of demonstration in 2009. Due to fabrication versatility, many heat treatment methods can be utilized to achieve perovskite film crystallization. Herein, 10.6 µm carbon dioxide laser process is successfully developed for the first time for perovskite film crystallization. In addition, this is the first time formamidinium lead triiodide solar cells by laser annealing under ambient are demonstrated. The champion cell produces a power conversion efficiency of 21.8%, the highest for laser-annealed perovskite cells. And this is achieved without any additive, passivation, or post-treatment.

Unzipping Carbon Nanotubes to Sub-5-nm Graphene Nanoribbons on Cu(111) by Surface Catalysis.

Graphene nanoribbons (GNRs) are promising in nanoelectronics for their quasi-1D structures with tunable bandgaps. The methods for controllable fabrication of high-quality GNRs are still limited. Here a way to generate sub-5-nm GNRs by annealing single-walled carbon nanotubes (SWCNTs) on Cu(111) is demonstrated. The structural evolution process is characterized by low-temperature scanning tunneling microscopy. Substrate-dependent measurements on Au(111) and Ru(0001) reveal that the intermediate strong SWCNT-surface interaction plays a pivotal role in the formation of GNRs.

Monolayer Borophene Formation on Cu(111) Surface Triggered by ⟨ 1 1 ¯ 0 ⟩ $\langle {1\bar{1}0} \rangle $ Step Edge.

Borophene, a promising material with potential applications in electronics, energy storage, and sensors, is successfully grown as a monolayer on Ag(111), Cu(111), and Au(111) surfaces using molecular beam epitaxy. The growth of two-dimensional borophene on Ag(111) and Au(111) is proposed to occur via surface adsorption and boron segregation, respectively. However, the growth mode of borophene on Cu(111) remains unclear. To elucidate this, scanning tunneling microscopy in conjunction with theoretical calculations is used to study the phase transformation of boron nanostructures under post-annealing treatments. Results show that by elevating the substrate temperature, boron nanostructures undergo an evolution from amorphous boron to striped-phase borophene (η = 1/6) adhering to the Cu ⟨ 1 1 ¯ 0 ⟩ $\langle {1\bar{1}0} \rangle $ step edge, and finally to irregularly shaped ß-type borophene (η = 5/36) either on the substrate surface or embedded in the topmost Cu layer. dI/dV spectra recorded near the borophene/Cu lateral interfaces indicate that the striped-phase borophene is a metastable phase, requiring more buckling and electron transfer to stabilize the crystal structure. These findings offer not only an in-depth comprehension of the ß-type borophene formation on Cu(111), but also hold potential for enabling borophene synthesis on weakly-binding semiconducting or insulating substrates with 1D active defects.

Tuning the Inter-Nanoplatelet Distance and Coupling Strength by Thermally Induced Ligand Decomposition.

CdSe nanoplatelets (NPLs) are promising 2D semiconductors for optoelectronic applications, in which efficient charge transport properties are desirable. It is reported that thermal annealing constitutes an effective strategy to control the optical absorption and electrical properties of CdSe NPLs by tuning the inter-NPL distance. Combining optical absorption, transmission electron microscopy, and thermogravimetric analysis, it is revealed that the thermal decomposition of ligands (e.g., cadmium myristate) governs the inter-NPL distance and thus the inter-NPL electronic coupling strength. Employing ultrafast terahertz spectroscopy, it is shown that this enhanced electronic coupling increases both the free carrier generation efficiency and the short-range mobility in NPL solids. The results show a straightforward method of controlling the interfacial electronic coupling strength for developing functional optoelectronic devices through thermal treatments.

Suppression of Thermally Induced Surface Traps in Colloidal Quantum Dot Solids via Ultrafast Pulsed Light.

Thermal annealing (TA) of colloidal quantum dot (CQD) films is considered an important process for recent high-performing CQD solar cells (SCs) due to its beneficial effects on CQD solids, including enhanced electrical conductivity, denser packing of CQD films, and the removal of organic residues and solvents. However, the conventional TA for CQDs, which requires several  minutes, leads to hydroxylation and oxidation on the CQD surface, resulting in the formation of trap states and a subsequent decline in SC performance. To address these challenges, this study introduces a flashlight annealing (FLA) technique that significantly reduces the annealing time to the millisecond scale. Through the FLA approach, it successfully suppressed hydroxylation and oxidation, resulting in decreased trap states within the CQD solids while simultaneously preserving their charge transport properties. As a result, CQD SCs treated with FLA exhibited a notable improvement, achieving an open-circuit voltage of 0.66 V compared to 0.63 V in TA-treated devices, leading to an increase in power conversion efficiency from 12.71% to 13.50%.

Controlled Epitaxial Growth of (hk1)-Sb2Se3 Film on Cu9S5 Single Crystal via Post-Annealing Treatment for Photodetection Application.

Antimony selenide (Sb2Se3) is a promising semiconductor for photodetector applications due to its unique photovoltaic properties. Achieving optimal carrier transport in (001)-Sb2Se3 by the material of contacting substrate requires in-depth study. In this paper, the induced growth of Sb2Se3 films from (hk0) to (hk1) planes is achieved on digenite (Cu9S5) films by post-annealing treatment. The flake-like and flower-like morphologies on the surface of Sb2Se3 films are caused by different thicknesses of the Cu9S5 films, which are related to the (hk0) and (hk1) planes of Sb2Se3 surface. The epitaxial growth of Sb2Se3 films on (105)-Cu9S5 surfaces exhibits thickness dependence. The results inform research into the controlled induced growth of low-dimensional materials. The device of Sb2Se3/Cu9S5/Si has good broadband response (visible to near-infrared), self-powered characteristics, and stability. As the crystalline quality of the Sb2Se3 film increases along the (hk1) plane, the carrier transport is enhanced correspondingly. Under the 980 nm light irradiation, the device has an excellent switching ratio of 2 × 104 at 0 bias, with responsivity, detectivity, and response time up to 17 µA W-1, 1.48 × 107 Jones, and 355/490 µs, respectively. This suggests that Sb2Se3 is suitable for self-powered photodetectors and related optical and optoelectronic devices.