Structural insights into the N-terminal APHB domain of HrpA: mediating canonical and i-motif recognition.

RNA helicases function as versatile enzymes primarily responsible for remodeling RNA secondary structures and organizing ribonucleoprotein complexes. In our study, we conducted a systematic analysis of the helicase-related activities of Escherichia coli HrpA and presented the structures of both its apo form and its complex bound with both conventional and non-canonical DNAs. Our findings reveal that HrpA exhibits NTP hydrolysis activity and binds to ssDNA and ssRNA in distinct sequence-dependent manners. While the helicase core plays an essential role in unwinding RNA/RNA and RNA/DNA duplexes, the N-terminal extension in HrpA, consisting of three helices referred to as the APHB domain, is crucial for ssDNA binding and RNA/DNA duplex unwinding. Importantly, the APHB domain is implicated in binding to non-canonical DNA structures such as G-quadruplex and i-motif, and this report presents the first solved i-motif-helicase complex. This research not only provides comprehensive insights into the multifaceted roles of HrpA as an RNA helicase but also establishes a foundation for further investigations into the recognition and functional implications of i-motif DNA structures in various biological processes.

The convergence of head-on DNA unwinding forks induces helicase oligomerization and activity transition.

Helicases are multifunctional motor proteins with the primary task of separating nucleic acid duplexes. These enzymes often exist in distinct oligomeric forms and play essential roles during nucleic acid metabolism. Whether there is a correlation between their oligomeric state and cellular function, and how helicases effectively perform functional switching remains enigmatic. Here, we address these questions using a combined single-molecule approach and Bloom syndrome helicase (BLM). By examining the head-on collision of two BLM-mediated DNA unwinding forks, we find that two groups of BLM, upon fork convergence, promptly oligomerize across the fork junctions and tightly bridge two independent single-stranded (ss) DNA molecules that were newly generated by the unwinding BLMs. This protein oligomerization is mediated by the helicase and RNase D C-terminal (HRDC) domain of BLM and can sustain a disruptive force of up to 300 pN. Strikingly, onsite BLM oligomerization gives rise to an immediate transition of their helicase activities, from unwinding dsDNA to translocating along ssDNA at exceedingly fast rates, thus allowing for the efficient displacement of ssDNA-binding proteins, such as RPA and RAD51. These findings uncover an activity transition pathway for helicases and help to explain how BLM plays both pro- and anti-recombination roles in the maintenance of genome stability.

Nonstructural N- and C-tails of Dbp2 confer the protein full helicase activities.

Human DDX5 and its yeast ortholog Dbp2 are ATP-dependent RNA helicases that play a key role in normal cell processes, cancer development, and viral infection. The crystal structure of the RecA1-like domain of DDX5 is available but the global structure of DDX5/Dbp2 subfamily proteins remains to be elucidated. Here, we report the first X-ray crystal structures of the Dbp2 helicase core alone and in complex with ADP at 3.22 Å and 3.05 Å resolutions, respectively. The structures of the ADP-bound post-hydrolysis state and apo-state demonstrate the conformational changes that occur when the nucleotides are released. Our results showed that the helicase core of Dbp2 shifted between open and closed conformation in solution but the unwinding activity was hindered when the helicase core was restricted to a single conformation. A small-angle X-ray scattering experiment showed that the disordered amino (N) tail and carboxy (C) tails are flexible in solution. Truncation mutations confirmed that the terminal tails were critical for the nucleic acid binding, ATPase, and unwinding activities, with the C-tail being exclusively responsible for the annealing activity. Furthermore, we labeled the terminal tails to observe the conformational changes between the disordered tails and the helicase core upon binding nucleic acid substrates. Specifically, we found that the nonstructural terminal tails bind to RNA substrates and tether them to the helicase core domain, thereby conferring full helicase activities to the Dbp2 protein. This distinct structural characteristic provides new insight into the mechanism of DEAD-box RNA helicases.

Dual mode of DDX3X as an ATP-dependent RNA helicase and ATP-independent nucleic acid chaperone.

Human DDX3X, an important member of the DEAD-box family RNA helicases, plays a crucial role in RNA metabolism and is involved in cancer development, viral infection, and neurodegenerative disease. Although there have been many studies on the physiological functions of human DDX3X, issues regarding its exact targets and mechanisms of action remain unclear. In this study, we systematically characterized the biochemical activities and substrate specificity of DDX3X. The results demonstrate that DDX3X is a bidirectional RNA helicase to unwind RNA duplex and RNA-DNA hybrid driven by ATP. DDX3X also has nucleic acid annealing activity, especially for DNA. More importantly, it can function as a typical nucleic acid chaperone which destabilizes highly structured DNA and RNA in an ATP-independent manner and promotes their annealing to form a more stable structure. Further truncation mutations confirmed that the highly disordered N-tail and C-tail are critical for the biochemical activities of DDX3X. They are functionally complementary, with the N-tail being crucial. These results will shed new light on our understanding of the molecular mechanism of DDX3X in RNA metabolism and DNA repair, and have potential significance for the development of antiviral/anticancer drugs targeting DDX3X.

Hybrid diffractive-refractive lens for chromatic confocal measurement system.

A novel chromatic confocal measurement (CCM) method using a hybrid diffractive- refractive lens is presented. This hybrid diffractive- refractive lens is designed to optimize the linearity of chromatic dispersion and minimize the size of the optical system. The hybrid diffractive- refractive lens is fabricated by etching a diffractive surface onto a quartz aspheric lens through lithography, which combines the high numerical aperture (NA) of a refractive lens with the unique dispersion properties of the diffractive optical elements (DOE). The lens is incorporated as a dispersive objective lens in a CCM experimental system. The system has a measurement range of 514.8 µm, calibrated using a laser displacement interferometer. The experimental results show that the wavelength-to-axial position coding of the CCM system achieves high linearity (R2= 0.9999) in the working wavelength range (500-700 nm). The system has an axial resolution of 0.08 µm and a displacement measurement nonlinear error of less than 2.05 µm.

Substrate calibration method of a computer-generated hologram based on ray propagation in a three-dimensional model.

In interferometry with a computer-generated hologram (CGH), the substrate error of the CGH limits its high-precision aspheric measurement application. The propagation form of the substrate error is still ambiguous although 0th-order calibration can partly correct it. We established the ray propagation in a three-dimensional model in order to solve the ambiguity of substrate error propagation. This method shows the modulation process of the CGH substrate error on the transmitted wavefront for the first time, until now, to the best of our knowledge. The experiments show that the propagation of the substrate error can be accurately analyzed, and the CGH design efficiency also is significantly improved after applying this method.

Structural mechanism underpinning Thermus oshimai Pif1-mediated G-quadruplex unfolding.

G-quadruplexes (G4s) are unusual stable DNA structures that cause genomic instability. To overcome the potential barriers formed by G4s, cells have evolved different families of proteins that unfold G4s. Pif1 is a DNA helicase from superfamily 1 (SF1) conserved from bacteria to humans with high G4-unwinding activity. Here, we present the first X-ray crystal structure of the Thermus oshimai Pif1 (ToPif1) complexed with a G4. Our structure reveals that ToPif1 recognizes the entire native G4 via a cluster of amino acids at domains 1B/2B which constitute a G4-Recognizing Surface (GRS). The overall structure of the G4 maintains its three-layered propeller-type G4 topology, without significant reorganization of G-tetrads upon protein binding. The three G-tetrads in G4 are recognized by GRS residues mainly through electrostatic, ionic interactions, and hydrogen bonds formed between the GRS residues and the ribose-phosphate backbone. Compared with previously solved structures of SF2 helicases in complex with G4, our structure reveals how helicases from distinct superfamilies adopt different strategies for recognizing and unfolding G4s.

Synthesis of Benzofuran Derivatives via a DMAP-Mediated Tandem Cyclization Reaction Involving ortho-Hydroxy α-Aminosulfones.

An efficient cascade cyclization strategy was developed to synthesize aminobenzofuran spiroindanone and spirobarbituric acid derivatives utilizing 2-bromo-1,3-indandione, 5-bromo-1,3-dimethylbarbituric acid, and ortho-hydroxy α-aminosulfones as substrates. Under the optimized reaction conditions, the corresponding products were obtained with high efficiency, exceeding 95% and 85% yields for the respective derivatives. This protocol demonstrates exceptional substrate versatility and robust scalability up to the Gram scale, establishing a stable platform for the synthesis of 3-aminobenzofuran derivative. The successful synthesis paves the way for further biological evaluations with potential implications in scientific research.

A novel method for improving optical component smoothing quality in robotic smoothing systems by compensating path errors.

Path deviations caused by geometrical errors in machining equipment significantly affect the machining quality of optical components. To enhance the quality and efficiency of optical component processing, this paper presents a Chebyshev interpolated Levenberg-Marquardt algorithm (CILM) aimed at compensating for path deviations in a robotic smoothing system utilized for optical component processing. First, the positioning accuracy of the robotic smoothing system is measured using a laser tracker. Subsequently, an objective function is constructed based on robot kinematics and error models to optimize the geometric errors in the system. Then, the proposed method is adopted to identify the geometric parameters of the robotic smoothing system to compensate for the smoothing path deviations. The compensation results confirm the effectiveness of the proposed method in enhancing the absolute positioning accuracy of the robotic smoothing system. Additionally, experimental verification is conducted to validate the effectiveness of the proposed method in improving the surface quality of optical components through smoothing path compensation. The results of the three experiments indicate that the proposed CILM achieves optical components with peak-to-valley values 15.70%, 28.7%, and 4.01% lower than those obtained before compensation, along with root mean square of 33.67%, 21.57%, and 10.23% lower than before compensation values, respectively. Moreover, the power spectral density curves of CILM exhibit smoother characteristics in comparison to the curves before compensation.

Multidimensional stitching method with wavelength tuned interferometry and unconstrained support tooling for large-thin parallel plate.

Limited by measurement methods, measuring the surfaces and thickness of large thin parallel plates has been challenging. In this paper, we propose a multi-dimensional stitching method using thickness alignment (MSuTA), which use the sub-aperture stitching method based on the phenomenon of parallel plate self-interference with wavelength-tuned interferometer (WTI) for measuring the surfaces and thickness of large thin parallel plates. We establish the stitching correction model based on Legendre polynomial to separate the aberrations caused by the elastic deformation of the thin plate in the unconstrained support tooling by analyzing the influence of the stress state of the thin plate with unconstrained three-point support. The stitching experiment has carried out on 6.3 mm thick, 6-inch parallel plates that the stitching residual is better than 0.35 nm RMS. Compared with 12-inch vertical interferometer, the surfaces and thickness deviation are better than 0.8 nm RMS, and the 36 standard Legendre polynomial coefficient deviation are better than 2.5 nm. Moreover, MSuTA can improves the lateral resolution of the measurement by nearly four times, allowing for a display of more comprehensive surface information. The stitching method proposed in this paper will be widely applied in the manufacture and measurement of large thin parallel plates, and provide reference for the elastic deformation analysis of the thin optical elements in the unconstrained support tooling.

Discrimination of monozygotic twins using mtDNA heteroplasmy through probe capture enrichment and massively parallel sequencing.

Differentiating between monozygotic (MZ) twins remains difficult because they have the same genetic makeup. Applying the traditional STR genotyping approach cannot differentiate one from the other. Heteroplasmy refers to the presence of two or more different mtDNA copies within a single cell and this phenomenon is common in humans. The levels of heteroplasmy cannot change dramatically during transmission in the female germ line but increase or decrease during germ-line transmission and in somatic tissues during life. As massively parallel sequencing (MPS) technology has advanced, it has shown the extraordinary quantity of mtDNA heteroplasmy in humans. In this study, a probe hybridization technique was used to obtain mtDNA and then MPS was performed with an average sequencing depth of above 4000. The results showed us that all ten pairs of MZ twins were clearly differentiated with the minor heteroplasmy threshold at 1.0%, 0.5%, and 0.1%, respectively. Finally, we used a probe that targeted mtDNA to boost sequencing depth without interfering with nuclear DNA and this technique can be used in forensic genetics to differentiate the MZ twins.

Structural and functional studies of SF1B Pif1 from Thermus oshimai reveal dimerization-induced helicase inhibition.

Pif1 is an SF1B helicase that is evolutionarily conserved from bacteria to humans and plays multiple roles in maintaining genome stability in both nucleus and mitochondria. Though highly conserved, Pif1 family harbors a large mechanistic diversity. Here, we report crystal structures of Thermus oshimai Pif1 (ToPif1) alone and complexed with partial duplex or single-stranded DNA. In the apo state and in complex with a partial duplex DNA, ToPif1 is monomeric with its domain 2B/loop3 adopting a closed and an open conformation, respectively. When complexed with a single-stranded DNA, ToPif1 forms a stable dimer with domain 2B/loop3 shifting to a more open conformation. Single-molecule and biochemical assays show that domain 2B/loop3 switches repetitively between the closed and open conformations when a ToPif1 monomer unwinds DNA and, in contrast with other typical dimeric SF1A helicases, dimerization has an inhibitory effect on its helicase activity. This mechanism is not general for all Pif1 helicases but illustrates the diversity of regulation mechanisms among different helicases. It also raises the possibility that although dimerization results in activation for SF1A helicases, it may lead to inhibition for some of the other uncharacterized SF1B helicases, an interesting subject warranting further studies.

[Research progress in drugs targeting 5-lipoxygenase for age-related diseases].

With the acceleration of aging society, delaying aging or promoting healthy aging has become a major demand for human health. 5-Lipoxygenase (5-LOX) is a key enzyme catalyzing arachidonic acid into leukotrienes (LTs), which is a potent mediator of the inflammatory response. Previous studies showed that abnormal activation of 5-LOX and overproduction of LTs are closely related to the occurrence and development of aging-related inflammatory diseases. Therefore, inhibiting 5-LOX activation is a possibly potential strategy for treating age-related diseases. In this paper, the latest research progress in 5-LOX activation, 5-LOX in mediating aging-related diseases and its small molecule inhibitors is briefly reviewed to provide scientific theoretical basis and new ideas for the prevention and treatment of aging-related inflammatory diseases.

DEAD-box RNA helicase Dbp2 binds to G-quadruplex nucleic acids and regulates different conformation of G-quadruplex DNA.

G-quadruplexes (G4s) are important in regulating DNA replication, repair and RNA transcription through interactions with specialized proteins. Dbp2 has been identified as a G4 DNA binding protein from Saccharomyces cerevisiae cell lysates. The majority of G4 motifs in Saccharomyces cerevisiae display 5-50 nt loops, only a few have 1-2 nt loops. Human DDX5 could unfold MycG4 DNA, whether Dbp2 also participates in remodeling G4 motifs with short loops in Saccharomyces cerevisiae remains elusive. Here we find that Dbp2 prefers G-rich substrates and binds MycG4 with a high affinity. Dbp2 possesses a dual function for different conformations of MycG4, destabilizing the folded MycG4 and inducing further folding of the unfolded MycG4. Similarly, DDX5 can unfold MycG4, but it exhibits a weaker MycG4 folding-promoting activity relative to Dbp2. Furthermore, Dbp2 facilitates DNA annealing activity in the absence of ATP, suggesting that Dbp2 can work on DNA substrates and possibly participate in DNA metabolism. Our results demonstrate that Dbp2 plays an important role in regulating the folding and unfolding activities of MycG4.

Stitching method based on dual quaternion for cylindrical mirrors.

In this study, a stitching method based on dual quaternion is proposed. The application of a dual quaternion in sub-aperture stitching interferometry is analyzed in detail, and a calculation method for sub-aperture stitching based on a dual quaternion is deduced. The experimental results demonstrate the accuracy of the stitching method proposed in this study (residuals of overlapping area approximately 0.22 nm RMS). Finally, the residual differences of 0.79 nm RMS between the figure errors are acquired with a stitching by parts algorithm based on the dual quaternion and long trace profiler (FSP at HEPS). The high-accuracy and high-efficiency stitching method proposed in this study will expand its application in the metrology and manufacture of long cylindrical mirrors.

Dynamics of Staphylococcus aureus Cas9 in DNA target Association and Dissociation.

Staphylococcus aureus Cas9 (SaCas9) is an RNA-guided endonuclease that targets complementary DNA adjacent to a protospacer adjacent motif (PAM) for cleavage. Its small size facilitates in vivo delivery for genome editing in various organisms. Herein, using single-molecule and ensemble approaches, we systemically study the mechanism of SaCas9 underlying its interplay with DNA. We find that the DNA binding and cleavage of SaCas9 require complementarities of 6- and 18-bp of PAM-proximal DNA with guide RNA, respectively. These activities are mediated by two steady interactions among the ternary complex, one of which is located approximately 6 bp from the PAM and beyond the apparent footprint of SaCas9 on DNA. Notably, the other interaction within the protospacer is significantly strong and thus poses DNA-bound SaCas9 a persistent block to DNA-tracking motors. Intriguingly, after cleavage, SaCas9 autonomously releases the PAM-distal DNA while retaining binding to the PAM. This partial DNA release immediately abolishes its strong interaction with the protospacer DNA and consequently promotes its subsequent dissociation from the PAM. Overall, these data provide a dynamic understanding of SaCas9 and instruct its effective applications.

Bloom Syndrome Helicase Compresses Single-Stranded DNA into Phase-Separated Condensates.

Bloom syndrome protein (BLM) is a conserved RecQ family helicase involved in the maintenance of genome stability. BLM has been widely recognized as a genome "caretaker" that processes structured DNA. In contrast, our knowledge of how BLM behaves on single-stranded (ss) DNA is still limited. Here, we demonstrate that BLM possesses the intrinsic ability for phase separation and can co-phase separate with ssDNA to form dynamically arrested protein/ssDNA co-condensates. The introduction of ATP potentiates the capability of BLM to condense on ssDNA, which further promotes the compression of ssDNA against a resistive force of up to 60 piconewtons. Moreover, BLM is also capable of condensing replication protein A (RPA)- or RAD51-coated ssDNA, before which it generates naked ssDNA by dismantling these ssDNA-binding proteins. Overall, our findings identify an unexpected characteristic of a DNA helicase and provide a new angle of protein/ssDNA co-condensation for understanding the genomic instability caused by BLM overexpression under diseased conditions.

The HRDC domain oppositely modulates the unwinding activity of E. coli RecQ helicase on duplex DNA and G-quadruplex.

RecQ family helicases are highly conserved from bacteria to humans and have essential roles in maintaining genome stability. Mutations in three human RecQ helicases cause severe diseases with the main features of premature aging and cancer predisposition. Most RecQ helicases shared a conserved domain arrangement which comprises a helicase core, an RecQ C-terminal domain, and an auxiliary element helicase and RNaseD C-terminal (HRDC) domain, the functions of which are poorly understood. In this study, we systematically characterized the roles of the HRDC domain in E. coli RecQ in various DNA transactions by single-molecule FRET. We found that RecQ repetitively unwinds the 3'-partial duplex and fork DNA with a moderate processivity and periodically patrols on the ssDNA in the 5'-partial duplex by translocation. The HRDC domain significantly suppresses RecQ activities in the above transactions. In sharp contrast, the HRDC domain is essential for the deep and long-time unfolding of the G4 DNA structure by RecQ. Based on the observations that the HRDC domain dynamically switches between RecA core- and ssDNA-binding modes after RecQ association with DNA, we proposed a model to explain the modulation mechanism of the HRDC domain. Our findings not only provide new insights into the activities of RecQ on different substrates but also highlight the novel functions of the HRDC domain in DNA metabolisms.

Squaramide-catalysed asymmetric Michael addition/cyclization cascade reaction of 4-arylmethylidene-2,3-dioxopyrrolidines with 2-isothiocyanato-1-indanones.

A highly efficient cinchona alkaloid-derived squaramide catalysed asymmetric Michael/cyclization cascade reaction of 4-arylmethylidene-2,3-dioxopyrrolidines with 2-isothiocyanato-1-indanones was successfully developed. This protocol provides an efficient and mild access to indanone-derived spiropyrrolidone scaffolds containing three contiguous stereocenters with two spiroquaternary stereocenters in excellent yields (up to 99%) with high enantio- and diastereoselectivities (up to 99% ee and up to >20 : 1 dr). This method provides an economical and practical approach for the asymmetric synthesis of medicinally relevant molecules.

Absolute testing method of shift-rotation based on the influence function.

The absolute testing of an optical surface with the shift-rotation method is an effective way to obtain an optical surface with high accuracy. The traditional shift-rotation method based on Zernike polynomials has a large number of computations and poor fitting accuracy for high frequency. Additionally, the number of calculations of the pixel-level spatial frequency method in solving the test and reference error based on each pixel is too large, which leads to poor practicability in reality. An optimized absolute testing method of shift-rotation based on the influence function is presented in this paper. By introducing the concept of the influence function in adaptive optics instead of a Zernike polynomial, the calculation accuracy of the mid-and high-frequency surface is improved, and higher precision of the absolute surface can be obtained. Relevant theoretical simulation and experimental verification are carried out. The experimental results compared with the Zernike and pixel-level methods show that the reference and test surface can be well reconstructed by using the proposed shift-rotation method based on the influence function.