AlphaFold 3 - Aided Design of DNA Motifs To Assemble into Triangles.

Self-assembly of biomolecules provides a powerful tool for a wide range of applications in nanomedicine, biosensing and imaging, vaccines, computation, nanophotonics, etc. The key is to rationally design building blocks and the intermolecule interactions. Along this line, structural DNA nanotechnology has rapidly developed by limiting DNA secondary structures to primarily well-established, B-form DNA duplexes, which can be readily and reliably predicted. As the field evolves, more sophisticated structural elements must be introduced. While increasing the structural complexity, they bring challenges to predicting DNA nanostructures. In the past, a brutal and tedious error-and-trial approach has often been used to solve this problem. Here, we report a case study of applying AlphaFold 3 to model the structural elements to facilitate DNA nanostructure design. This protocol is expected to be generally applicable and greatly facilitates the further development of structural DNA nanotechnology.

Antidote-controlled DNA aptamer modulates human factor IXa activity.

Thrombosis leads to elevated mortality rates and substantial medical expenses worldwide. Human factor IXa (HFIXa) protease is pivotal in tissue factor (TF)-mediated thrombin generation, and represents a promising target for anticoagulant therapy. We herein isolated novel DNA aptamers that specifically bind to HFIXa through systematic evolution of ligands by exponential enrichment (SELEX) method. We identified two distinct aptamers, seq 5 and seq 11, which demonstrated high binding affinity to HFIXa (Kd = 74.07 ± 2.53 nM, and 4.93 ± 0.15 nM, respectively). Computer software was used for conformational simulation and kinetic analysis of DNA aptamers and HFIXa binding. These aptamers dose-dependently prolonged activated partial thromboplastin time (aPTT) in plasma. We further rationally optimized the aptamers by truncation and site-directed mutation, and generated the truncated forms (Seq 5-1t, Seq 11-1t) and truncated-mutated forms (Seq 5-2tm, Seq 11-2tm). They also showed good anticoagulant effects. The rationally and structurally designed antidotes (seq 5-2b and seq 11-2b) were competitively bound to the DNA aptamers and effectively reversed the anticoagulant effect. This strategy provides DNA aptamer drug-antidote pair with effective anticoagulation and rapid reversal, developing advanced therapies by safe, regulatable aptamer drug-antidote pair.

AMP Aptamer Programs DNA Tile Cohesion without Canonical Base Pairing.

Tile-based DNA self-assembly provides a versatile approach for the construction of a wide range of nanostructures for various applications such as nanomedicine and advanced materials. The inter-tile interactions are primarily programmed by base pairing, particularly Watson-Crick base pairing. To further expand the tool box for DNA nanotechnology, herein, we have designed DNA tiles that contain both ligands and aptamers. Upon ligand-aptamer binding, tiles associate into geometrically well-defined nanostructures. This strategy has been demonstrated by the assembly of a series of DNA nanostructures, which have been thoroughly characterized by gel electrophoresis and atomic force microscopy. This new inter-tile cohesion could bring new potentials to DNA self-assembly in the future. For example, the addition of free ligand could modulate the nanostructure formation. In the case of biological ligands, DNA self-assembly could be related to the presence of certain ligands.

Rational Design of Abasic Site-Containing DNA Triplexes To Bind Small Molecules with Low Nanomolar Dissociation Constants.

De novo design of functional biomacromolecules is of great interest to a wide range of fundamental science and technological applications, including understanding life evolution and biomacromolecular structures, developing novel catalysts, inventing medicines, and exploring high-performance materials. However, it is an extremely challenging task and its success is very limited. It requires a deep understanding of the relationships among the primary sequences, the 3D structures, and the functions of biomacromolecules. Herein, we report a rational, de novo design of a DNA aptamer that can bind melamine with high specificity and high affinity (dissociation constant Kd = 4.4 nM). The aptamer is essentially a DNA triplex, but contains an abasic site, to which the melamine binds. The aptamer-ligand recognition involves hydrogen-bonding, π-π stacking, and electrostatic interactions. This strategy has been further tested by designing aptamers to bind to guanosine. It is conceivable that such a rational strategy, with further development, would provide a general framework for designing functional DNA molecules.

Solution-Phase Synthesis of DNA Amphiphiles for DNA Micellar Assembly.

Hydrophobic moieties of amphiphilic DNAs can help DNAs penetrate cell membranes, but the conjugation of hydrophobic moieties to DNAs in solution phase remains challenging. Herein we report a solution-phase synthesis method to conjugate hydrophobic molecules to DNAs. This method is simple and efficient. The resulted amphiphilic DNAs can spontaneously assemble into micelles, which may serve as nanocarriers for cellular delivery of nucleic acids and water-insoluble drugs.

Enriching adenosine by thymine-rich DNA oligomers.

Adenosine levels are important in various physiological and pathological activities, but detecting them is difficult because of interference from a complex matrix. This study designed a series of DNA oligomers rich in thymine to enrich adenosine. Their binding affinity (Kd range: 1.25-5.0 mM) to adenosine varied based on the DNA secondary structures, with a clamped hairpin structure showing the highest binding affinity. Compared to other designs, this clamped DNA hairpin underwent the least conformational change during adenosine binding. These DNAs also suppressed the precipitation of supersaturated adenine. Taken together, these results suggest that thymine-rich DNAs could be used to enrich and separate adenosine.

MethHC 2.0: information repository of DNA methylation and gene expression in human cancer.

DNA methylation is an important epigenetic regulator in gene expression and has several roles in cancer and disease progression. MethHC version 2.0 (MethHC 2.0) is an integrated and web-based resource focusing on the aberrant methylomes of human diseases, specifically cancer. This paper presents an updated implementation of MethHC 2.0 by incorporating additional DNA methylomes and transcriptomes from several public repositories, including 33 human cancers, over 50 118 microarray and RNA sequencing data from TCGA and GEO, and accumulating up to 3586 manually curated data from >7000 collected published literature with experimental evidence. MethHC 2.0 has also been equipped with enhanced data annotation functionality and a user-friendly web interface for data presentation, search, and visualization. Provided features include clinical-pathological data, mutation and copy number variation, multiplicity of information (gene regions, enhancer regions, and CGI regions), and circulating tumor DNA methylation profiles, available for research such as biomarker panel design, cancer comparison, diagnosis, prognosis, therapy study and identifying potential epigenetic biomarkers. MethHC 2.0 is now available at http://awi.cuhk.edu.cn/∼MethHC.

Characteristics of distal radius fractures in east China-an observational cohort study of 1954 individual fractures.

OBJECTIVE: To investigate the characteristics and seasonal patterns of distal radius fractures (DRFs) over the preceding five years, with the aim of establishing a clinical foundation for the prevention and management of such fractures within this region. METHODS: Utilizing the Picture Archiving and Communication Systems (PACS), the clinical records of 1954 patients diagnosed with DRFs and admitted to the Affiliated Hospital of Jiangsu University between January 2017 and December 2021 were compiled. The analysis encompassed factors such as age, gender, visitation timing, fracture side, and presence of osteoporosis. RESULTS: Out of the total 1954 distal radius fractures, 731 were males (37.4%) and the male to female ratio was 0.59:1. The median age of patients with DRFs was 56 years, with the 25th percentile being 38 years and the 75th percentile being 67 years. The average age was 50 years (standard deviation 23.3) and 1033 cases (52.7%) occurred on the left side, 885 cases (45.1%) on the right side, and 36 cases (1.8%) were bilateral, with the left side being the most frequently affected. The age group of 61-70 years (23.9%, 467/1954) exhibited the highest proportion, and the most prominent age group for males was 11-20 years (23.8%, 174/731), whereas for females it was 61-70 years (30.83%, 377/1223). In the 50 years and older group, there were 276 males and 991 females (ratio 1:3.59), with osteoporosis in 536 cases, accounting for 42.03% of the group. In terms of seasonal distribution, the highest incidence occurred during the summer and autumn months (55.1%, 1076/1954) and there were gender differences in different seasons. CONCLUSION: In east China, DRFs were predominantly female and left-sided, with the highest proportion in the age group of 61-70 years and in summer and autumn. Furthermore, gender differences were observed between the warm and cold seasons.

Effects of Natural Products on Enzymes Involved in Ferroptosis: Regulation and Implications.

Ferroptosis is a form of regulated cell death that is characterized by the accumulation of iron-dependent lipid peroxides. The regulation of ferroptosis involves both non-enzymatic reactions and enzymatic mechanisms. Natural products have demonstrated potential effects on various enzymes, including GPX4, HO-1, NQO1, NOX4, GCLC, and GCLM, which are mainly involved in glutathione metabolic pathway or oxidative stress regulation, and ACSL3 and ACSL4, which mainly participate in lipid metabolism, thereby influencing the regulation of ferroptosis. In this review, we have provided a comprehensive overview of the existing literature pertaining to the effects of natural products on enzymes involved in ferroptosis and discussed their potential implications for the prevention and treatment of ferroptosis-related diseases. We also highlight the potential challenge that the majority of research has concentrated on investigating the impact of natural products on the expression of enzymes involving ferroptosis while limited attention is given to the regulation of enzyme activity. This observation underscores the considerable potential and scope for exploring the influence of natural products on enzyme activity.

Structure-Guided Designing Pre-Organization in Bivalent Aptamers.

Multivalent interaction is often used in molecular design and leads to engineered multivalent ligands with increased binding avidities toward target molecules. The resulting binding avidity relies critically on the rigid scaffold that joins multiple ligands as the scaffold controls the relative spatial positions and orientations toward target molecules. Currently, no general design rules exist to construct a simple and rigid DNA scaffold for properly joining multiple ligands. Herein, we report a crystal structure-guided strategy for the rational design of a rigid bivalent aptamer with precise control over spatial separation and orientation. Such a pre-organization allows the two aptamer moieties simultaneously to bind to the target protein at their native conformations. The bivalent aptamer binding has been extensively characterized, and an enhanced binding has been clearly observed. This strategy, we believe, could potentially be generally applicable to design multivalent aptamers.

LncRNA MHENCR Predicts Poor Outcomes in Patients with Colorectal Carcinoma and Modulates Tumorigenesis by Impairing MiR-532-3p.

The long noncoding RNAs (lncRNAs) are widely involved in the progression of various malignant tumors. The current study investigated the role and mechanism of lncRNA melanoma highly expressed noncoding RNA (MHENCR) in colorectal carcinoma. The expression of MHENCR was measured by real-time quantitative reverse transcription PCR (RT-qPCR). The chi-square analysis was used to analyze the correlation between MHECNR and miR-532-3p. Kaplan-Meier curve and multivariate Cox regression analysis were conducted to assess the significance of MHENCR in clinic. The interaction of MHENCR and miR-532-3p was probed using Pearson analysis and dual-luciferase reporter assay. Cellular experiments were implemented to explore the effects of MHENCR/miR-532-3p on colorectal carcinoma cells. Compared with para-cancerous tissues, MHENCR expression was increased and miR-532-3p expression was decreased in tumor tissues. High expression of MHENCR exhibited shorter overall survival. Interfering of MHENCR suppressed cellular activities while the silence of miR-532-3p diminished the decreased cellular behaviors in colorectal carcinoma cells. Interfering with MHENCR expression represses colorectal carcinoma cell proliferation, migration, and invasion by regulating miR-532-3p. MHENCR may act as a novel prognostic marker in colorectal carcinoma and MHENCR/miR-532-3p may serve as a potential target for treating colorectal carcinoma.

Enzyme Activity of Natural Products on Cytochrome P450.

Drug-metabolizing enzymes, particularly the cytochrome P450 (CYP450) monooxygenases, play a pivotal role in pharmacokinetics. CYP450 enzymes can be affected by various xenobiotic substrates, which will eventually be responsible for most metabolism-based herb-herb or herb-drug interactions, usually involving competition with another drug for the same enzyme binding site. Compounds from herbal or natural products are involved in many scenarios in the context of such interactions. These interactions are decisive both in drug discovery regarding the synergistic effects, and drug application regarding unwanted side effects. Herein, this review was conducted as a comprehensive compilation of the effects of herbal ingredients on CYP450 enzymes. Nearly 500 publications reporting botanicals' effects on CYP450s were collected and analyzed. The countries focusing on this topic were summarized, the identified herbal ingredients affecting enzyme activity of CYP450s, as well as methods identifying the inhibitory/inducing effects were reviewed. Inhibitory effects of botanicals on CYP450 enzymes may contribute to synergistic effects, such as herbal formulae/prescriptions, or lead to therapeutic failure, or even increase concentrations of conventional medicines causing serious adverse events. Conducting this review may help in metabolism-based drug combination discovery, and in the evaluation of the safety profile of natural products used therapeutically.

[Clinical Effect of Unilateral Biportal Endoscopic Lumbar Interbody Fusion and Minimally Invasive Transforaminal Lumbar Interbody Fusion on Single-segment Lumbar Stenosis with Instability].

Objective To compare the early clinical effects of unilateral biportal endoscopic lumbar interbody fusion (ULIF) and minimally invasive transforaminal lumbar interbody fusion (MIS-TLIF)on single-segment lumbar stenosis with instability. Methods The patients who had single-segment lumbar spinal stenosis with instability and were treated in our hospital from August 2020 to May 2021 were selected.According to the operation methods,they were classified into ULIF group and MIS-TLIF group.The operation duration,hospital stay after operation,perioperative blood loss (drainage volume 48 h after operation,total blood loss),creatine kinase,inflammatory cytokines (C-reactive protein,interleukin-6),D-dimer,and the incidence of lower-extremity venous thrombosis were compared between the two groups.The visual analogue scale and Oswestry disability index were used to evaluate the functional recovery of the two groups in 1 week,1 month,and 3 months after operation. Results The ULIF group had longer operation duration (P<0.001) and shorter hospital stay after operation (P=0.022)than the MIS-TLIF group.The drainage volume 48 h after operation and total blood loss in ULIF group were lower than those in MIS-TLIF group (all P<0.001).The levels of creatine kinase (all P<0.001),C-reactive protein (P<0.001,P=0.002),and interleukin-6 (P=0.003,P<0.001) in ULIF group were lower than those in MIS-TLIF group on the 1st and 3rd day after operation.However,the D-dimer in ULIF group was insignificantly different from that in MIS-TLIF group on the 1st and 3rd day after operation (P=0.117,P=0.683).Lower-extremity venous thrombosis occurred in neither group.The score of visual analogue scale showed no significant difference between the two groups 1 week,1 month,and 3 months after operation (P=0.447,P=0.578,P=0.538),so did the Oswestry disability index (P=0.832,P=0.797,P=0.619). Conclusion ULIF shows similar clinical effect on single-segment lumbar stenosis with instability to MIS-TLIF,which features less bleeding,mild inflammation,mild muscle injury,but long operation duration.

DNA Ring-Opening Polymerization Driven by Base Stacking.

Supramolecular polymers, relying on reversible intermolecular interactions, promise a wide range of applications, including optoelectronic materials, self-healing materials, and biomedical delivery materials. Among potential molecular candidates, DNA strands act as an excellent platform. DNA has a well-established secondary structure (double helix), and its intermolecular interactions can be readily thermodynamically engineered and kinetically controlled. Extensive studies have demonstrated that various DNA motifs can polymerize/assemble into large polymers with different topology, geometry, and dimensionalities. Most of the reported polymerization is driven by hybridization of DNA strands. Herein, we report a novel system of DNA supramolecular polymerization that is driven by DNA base stacking. The polymerization has been confirmed by native polyacrylamide gel electrophoresis (PAGE) and atomic force microscopy (AFM). We believe that this work will expand the toolbox for DNA supramolecular polymerization and would, with further development, increase further control of DNA supramolecular polymerization.

Molecular evidence of herbal formula: a network-based analysis of Si-Wu decoction.

INTRODUCTION: Emerging network pharmacology (NP) combines phytochemical information with bioinformatics tools allowing herbal formulae to be illustrated holistically in the context of phytochemical basis and therapeutic mechanisms. OBJECTIVE: This study attempted to explore the holistic molecular evidence of herbal formula Si-Wu decoction (SWD) by using the method of NP. MATERIAL AND METHOD: Databases of traditional medicines combined with PubChem, SciFinder, SEA, STRING, and KEGG were employed to gather information for establishing the "compound similarity" (CS) network and the "target-(pathway)-target" (TPT) network. Gephi software was applied to visualise the networks, with further module-based and node-based network topological analysis. Moreover, the approved drugs and shortest path analysis were used to validate the TPT network. RESULTS: The CS network presented the phytochemical profile of SWD, including the major compound groups of iridoid glycosides, glycosides, phthalide lactones, phenylpropanoids, and monoterpenoids. Furthermore, the topological analysis of TPT network depicted the holistic property of SWD in interpretable neuroendocrine immunomodulation (NIM) perspective, and the node degree analysis indicated a closer connection of SWD with endocrine or metabolism system. Moreover, by combing the analysis of the CS network and TPT network, potential active ingredients could be primarily identified. CONCLUSION: The phytochemical profile and molecular target profile, which might pave the way for an understanding of SWD in modern science and provide a reference for relevant quality research and evaluation, were demonstrated by network analysis. Moreover, the methods could be further applied to discover the phytochemical or biomolecular evidence with distinct advantages in dealing with the tremendous separated information.

Distance-Dependence Study of Plasmon Resonance Energy Transfer with DNA Spacers.

Plasmon resonance energy transfer (PRET) in hybrid plasmonic-molecular systems has a broad range of applications from catalysis to analytical/biochemical/biophysical imaging and sensing. Herein, we experimentally and theoretically probed the influence of the distance (d) between the plasmonic nanoparticle and the conjugated molecules on the PRET efficiency (ηPRET) using two PRET systems, which involved tetramethylrhodamine (TAMRA) or Cy3 molecules as acceptors and single spherical gold nanoparticles (AuNPs) as donors. The double-stranded DNA (dsDNA) sequences precisely adjusted within 12.0 nm were utilized as a donor-acceptor spacer. Then, the ηPRET of the two systems under varied d-values was available from the reduction of the scattering intensity of AuNPs. Both experimental and quasi-static approximation data show that ηPRET displays a d-value-dependent decay function. This study would provide new insights into optimal PRET-based chemical/biochemical sensors.

Self-Therapeutic Nanoparticle That Alters Tau Protein and Ameliorates Tauopathy Toward a Functional Nanomedicine to Tackle Alzheimer's.

Tauopathy is a complex disorder associated at the junction of several other pathologies. Intrinsically disordered tau protein remains therapeutically challenging due to its undruggable nature and is a possible reason for monumental failure of several tau-based therapies. Herein, nanogold remodeled tau is reported as a pseudo-nanochaperon and shows therapeutic benefit by passive targeting in transgenic tau P301L mutant mice. Treatment with nanogold polyethylene glycol (Au-PEG) conjugate moderately improves the learning ability of the tau P301L mice that corroborates with diminished phosphorylated tau burden. Circulating total tau level that acts in a prion fashion is significantly reduced upon Au-PEG treatment. Similarly, a high level of tau is found in macaque monkey serum and Au-PEG inhibits amyloidosis of Alzheimer's patients and primate's serum samples ex vivo. Addtionally, brain MRI of an old aged macaque monkey shows the decrease of grey matter, which correlates with mutual loss of grey matter upon progressive dementia as reported. Au-PEG tunes tau and other circulating pro-dementia factors that are present in human AD serum, by remodeling the protein and repairing aberrant proteostasis. Alteration of proteotoxic tau function by nanogold as a kinetic stablizer holds translational potential to combat socially challenging dementia.

Interactions of antithrombotic herbal medicines with Western cardiovascular drugs.

Thrombotic events act as a critical factor that interferes with Cardiovascular Diseases (CVDs), and antithrombotic herbal medicine is a long-standing controversial issue. Although a dispute is involved in their clinical application, all parties unanimously agree that herbal products have been widely used in folk medicine, and their interactions with conventional drugs are of high concern. This study aims to investigate how antithrombotic herbal medicines interact with Western cardiovascular drugs on the molecular level by taking an example of the most frequently used herbal pair, Danshen-Chuanxiong (DS-CX), and to discover more scientific evidence on their potential herb-drug interactions. Network pharmacology (NP), as an analytical approach of a complex system, is used to visualize and compare target profiles of DS-CX and Western cardiovascular drugs, which can be applied to predict common herb-drug targets and to construct a solid context for discussing herb-drug interactions. These interactions are further validated by in vitro assays, while in vivo zebrafish model employed for evaluating an overall pharmacological efficacy of herbal pairs in specific combination ratios. The study finds that DS could react directly to the Western cardiovascular drug targets relevant to antithrombotic pathways (i.e., thrombin, coagulation factor Xa and cyclooxygenase-1), whereas CX could not react directly and can synergistically affect antithrombotic effects with DS in specific combination ratios. Moreover, it is indicated that DS-CX may generate wide biological functions by a complicated mechanism of "neuro-immune-metabolism/endocrine" (NIM), which can further cause multiple direct and indirect interactions with Western cardiovascular drugs. From the clinical perspective, herb-drug interactions should be given high attention, especially when multiple herbs are used simultaneously.

Preparation of tilmicosin-resin complex microsphere and its Pharmacokinetics study in rat.

The objective of this study is to mask the extremely bitter taste of tilmicosin, and the tilmicosin-resin complex (DRC) microsphere were prepared by entrapping tilmicosin into resins (Tulsion® 339 and Eudragit® RS/ RL 100) for further pharmacokinetics study in rat. The DRC was characterized by FTIR and X-ray diffraction, and the microsphere containing DRC and Eudragit® RS/RL 100 were characterized by scanning electron microscopy (SEM). The rats were orally administrated with tilmicosin phosphate (10 mg/kg) and the microsphere containing the same dose of tilmicosin, respectively. These microspheres do not taste bitter and the kinetics study suggests that the drug released from microsphere meet the first order kinetics (r = 0.9911). The experimental results showed that T½ and Tmax of microsphere were much longer than tilmicosin phosphate, which indicates that the oral microsphere can be a promising long-active formulation for taste masking of tilmicosin.

Paeonol reverses promoting effect of the HOTAIR/miR-124/Notch1 axis on renal interstitial fibrosis in a rat model.

Renal interstitial fibrosis (RIF) is a common manifestation of inflammatory and noninflammatory renal diseases, which correlates to renal excretory dysfunction. Recently, the long noncoding RNAs (lncRNAs) have been demonstrated to be involved in the development of various renal diseases. Here, we aim to determine whether paeonol (PAE) affects RIF with involvement of the lncRNA HOX transcript antisense intergenic RNA (HOTAIR)/microRNA-124 (miR-124)/Notch1 axis. RIF rat models were established by performing unilateral ureteral occlusion (UUO), in which interactions between HOTAIR, Notch1, and miR-124 were determined. To identify the roles of PAE and HOTAIR in RIF, rats were injected with HOTAIR or PAE. Subsequently, to further investigate the underlying mechanism of PAE in RIF, epithelial to mesenchymal transition (EMT)- and migration-related genes in NRK-49F cells were measured. Next, rats were further treated with IMR-1 (inhibitor of the Notch1/Jagged1 signaling pathway) to determine how PAE influences the Notch1/Jagged1 signaling pathway. HOTAIR interacted with miR-124, and miR-124 directly targeted Notch1, and HOTAIR was observed to be upregulated in RIF rats. PAE was found to decrease HOTAIR and Notch1 expression but to increase the miR-124 expression in RIF rats. PAE inhibited EMT and migration of NRK-49F cells facilitated by HOTAIR. HOTAIR activated the Notch1/Jagged1 signaling pathway by downregulating miR-124, while PAE reversed these effects of HOTAIR on the Notch1/Jagged1 signaling pathway. Overall, our study demonstrates the contributory effect of lncRNA HOTAIR on RIF by activating the Notch1/Jagged1 signaling pathway via inhibition of miR-124, whereas administration of PAE can alleviate the effects of HOTAIR on RIF.