Search Results (205)

We designed a label-free fluorescent aptasensor assisted by exonuclease III (Exo III) for sensitive insulin (Ins) detection. The method has high sensitivity, anti-interference properties and repeatability. Additionally, the label-free fluorescent aptasensor assisted by Exo III used to detect Ins has not been reported on yet. In this study, we connected a modified DNA sequence to the 5′ end of an aptamer, modifying it into a hairpin structure and exposing 11 nucleotides at the 3′ end containing the base adenine (A). The A was substituted with base 2-aminopurine (2AP) to provide a label-free stable hairpin fluorescent probe (2AP-hairpin probe). This strategy took advantage of the high binding affinity of the Ins aptamer and the susceptibility of 2AP to the local base stacking environment. When Ins is added to the detection system, the 2AP-hairpin probe binds to Ins, adopts a folded state, and blocks Exo III’s access to the binding site for cutting DNA. 2AP cannot be released, and the fluorescence of the 2AP-hairpin probe/cDNA/Ins/Exo III system cannot be restored. Ins detection is achieved by comparing changes in the fluorescent intensity before and after adding Ins to the detection system. The detection limit of the aptasensor is as low as 1.62 nM with a linear range of 3–130 nM. Furthermore, it is able to selectively and directly detect Ins in biological fluids, demonstrating significant clinical application value and research significance. Full article

African swine fever (ASF) is a highly lethal viral disease of pigs caused by the African swine fever virus (ASFV). The mortality rate is nearly 100%. Currently, it is known that the ASFV has a complex structure, and its genome encodes various immune escape proteins. However, the pathogenic mechanism of ASFV remains to be studied. This study found that ASFV pD345L significantly inhibits the activation of the ISRE promoter triggered by interferon (IFN) β and the production of downstream IFN-stimulated genes (ISG). We further reveal that pD345L may degrade STAT1 via the autophagy pathway and impede its nuclear translocation; this inhibitory effect is closely associated with its exonuclease activity. Our research results have clarified the impact of ASFV pD345L on the JAK/STAT signaling pathway, expanding our understanding of the inhibitory effect of ASFV-encoded proteins on the host’s innate immunity, and to some extent, contributing to the development of an African swine fever vaccine. Full article

For more than 75 years, the Jacobson–Stockmayer J-factor has been regarded as the fundamental physical limit on DNA cyclization efficiency. Here, we show that this limit can be substantially exceeded by simultaneous restriction cutting and ligation with the Type IIS enzyme BsaI-HFv2 and T4 DNA ligase. We achieved 75% circularization efficiency at a practically relevant concentration of 120 ng/$\mathrm{\mu }$L for 452 bp minicircles. Using DNA with pre-cut and purified overhangs, we calibrated the J-factor to establish the theoretical values expected under classical theory, and showed that cut-ligation with BsaI-HFv2 exceeds these expectations by 3.4-fold. Experimental results with additional enzymes (Esp3I and BbsI) provided insight into possible mechanisms underlying this outstanding performance. These findings demonstrate the existence of biological mechanisms that can dramatically increase effective local concentration beyond free-diffusion expectations, thereby exceeding long-standing theoretical limitations by over threefold and opening the way for systematic discovery of additional high-efficiency enzyme systems for DNA circularization. Full article

Background: Endometrial carcinoma (EC) is now classified primarily by molecular subtype—POLE-ultramutated, mismatch repair–deficient (dMMR), TP53-mutant/copy-number-high (CNH), and “no specific molecular profile” (NSMP)—a framework that has reshaped prognostic counseling and adjuvant therapy decisions. Yet several practically important questions remain insufficiently addressed in real-world cohorts: whether all four mismatch repair genes confer an equivalent favorable prognosis, whether all POLE alterations carry the same survival benefit or only specific pathogenic variants, and whether molecular subtypes retain prognostic value after adjustment for histology and tumor burden. Methods: We addressed these questions in 2901 patients pooled from the MSK-IMPACT 50K Clinical Sequencing Cohort (n = 2372; discovery) and the TCGA UCEC PanCancer Atlas (n = 529; validation)—the largest dual-cohort genomic analysis of EC reported to date. We performed individual MMR gene and combined dMMR survival stratification, multivariable Cox regression adjusted for age, histology, and sample type, and a pathogenicity-aware sensitivity analysis for POLE variants, with tumor mutational burden (TMB) compared across subgroups. Results: Across both cohorts, all four MMR gene–mutant subgroups (MLH1, MSH2, MSH6, PMS2) conferred equivalently favorable overall survival (OS) (six-group log-rank p = 7.66 × 10⁻¹² in discovery; p = 6.78 × 10⁻³ in validation), confirming dMMR as a class-level prognostic designation independent of which MMR gene is altered. Multivariable Cox regression demonstrated that POLE-ultramutated status retained an independent favorable effect (HR = 0.62, p = 0.038 in MSK; HR = 0.35, p = 0.028 in TCGA) after adjustment for age, histology, and sample type, while the favorable dMMR effect was largely accounted for by histologic context. Critically, a pathogenicity-aware sensitivity analysis revealed that the exceptional survival of the POLE subgroup is confined to canonical exonuclease-domain hotspot mutations (event rate 0.9% in MSK), whereas POLE variants of uncertain significance behave indistinguishably from NSMP-like tumors. Consistent with this finding, TMB was markedly elevated in canonical pathogenic POLE cases (median 138.7 mut/Mb in MSK; 247.4 in TCGA) but not in POLE-VUS-only cases (median 29.0 and 15.0, respectively; p < 0.001 between groups in both cohorts), confirming that the ultramutator phenotype is confined to canonical pathogenic POLE variants. We additionally characterize Uterine Clear Cell Carcinoma as a distinct histologic entity (n = 73; 3.0%) and report the POLE + TP53 co-mutant group (n = 90; 3.8%). Conclusions: These findings refine the molecular classification of EC in clinically meaningful ways: they support class-level immunotherapy eligibility based on dMMR status regardless of the specific MMR gene altered, demonstrate that POLE-ultramutated classification requires variant-level pathogenicity assessment, and identify TP53-mutant/CNH patients as the population with the most urgent unmet therapeutic need. Full article

The safety of genetically modified crops, particularly the commercial cultivation of glyphosate-resistant genetically modified soybeans, has given rise to significant public concern. Consequently, there is an urgent need to develop efficient and precise methods for detecting genetically modified components. The present study constructed a novel electrochemical biosensor based on nucleic acid exonuclease III (Exo III)-assisted cyclic signal amplification and hairpin probe recognition for the highly sensitive and specific detection of the CP4-EPSPS gene in genetically modified soybeans. The sensor achieves exponential signal amplification by triggering Exo III to cyclically cleave the hairpin probe (H1) upon target DNA binding. Subsequent to this, the released DNA fragments hybridize with the methylene blue-labeled signal probe (HS-MB) that has been immobilized on the electrode surface. This process induces conformational changes and a decrease in the current signal, thereby enabling quantitative analysis of the target gene. The experimental phase of the study successfully validated the sensor’s mechanism and systematically optimized key parameters such as Exo III concentration and reaction time. In optimal conditions, the sensor demonstrated excellent linearity with target DNA concentrations ranging from 100 fM to 10 nM, achieving a detection limit as low as 0.1072 pM. Furthermore, it exhibited remarkable repeatability and stability. This study provides an analytical tool with broad application prospects for the rapid and precise detection of genetically modified crops. Full article

Background/Objectives: Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with limited treatment options. Patients are treated with DNA damaging chemotherapies which act by inducing DNA damage in rapidly dividing tumor cells. Unfortunately, these tumors frequently develop treatment resistance, underscoring the need to understand resistance mechanisms in order to develop better treatment strategies. DNA damage response (DDR) detects and repairs DNA damage, and the DDR pathway has been shown to contribute to chemoresistance. Another factor known to drive chemoresistance in PDAC is the dense stroma, composed of extracellular matrix proteins secreted by cancer-associated fibroblasts (CAFs). Our recent work identified a CAF-induced resistance mechanism involving N-myc downstream regulated gene 1 (NDRG1). CAF-induced signaling resulted in the phosphorylation of NDRG1 and NDRG1-dependent DNA repair and protection from chemotherapies. Loss of NDRG1 resulted in increased chemotherapy-induced DNA damage and decreased replication fork speed and recovery. Methods: To gain insight into the molecular mechanism of NDRG1-mediated DNA repair and replication, we performed a BioID screen to identify binding partners of NDRG1. We further assessed the mechanistic roles of the identified interaction partners on DNA repair using DNA replication and repair assays such as the Comet assay and DNA fiber assays. Results: Our BioID screen identified meiotic recombination 11 (MRE11) protein, a nuclease involved in DDR, as a putative NDRG1 interacting protein. Interaction between MRE11 and NDRG1 was enriched during the late S/early G2 cell cycle phases and under replication stress. However, this interaction is likely indirect as the interaction only occurred in a cellular context and not with in vitro purified proteins. Blocking NDRG1 phosphorylation or blocking MRE11 exonuclease activity both resulted in protection of newly synthesized DNA at stalled replication forks. In NDRG1 knockout cells, blocking MRE11 led to decreased protection of nascent DNA, suggesting that NDRG1 and MRE11 may be acting in the same pathway and that NDRG1 is required for MRE11’s activity at stalled forks. Conclusions: In summary, our work has uncovered a protein complex between NDRG1 and MRE11 that may play a key role in chemoresistance due to its role in the processing of stalled replication forks. Full article

Obesity-associated carcinogenesis offers a model to explore the transition from metabolic dysregulation to genomic instability and carcinogenesis. Adenosine 5′-monophosphate-activated protein kinase (AMPK), the principal cellular energy sensor, coordinates adenosine triphosphate (ATP) production with metabolic demand; however, in obesity, AMPK activity is impaired, resulting in reduced ATP, elevated Adenosine Monophosphate (AMP), and cellular energy stress. Deoxyribonucleic Acid (DNA) polymerases ε (Pol ε) and δ (Pol δ) maintain replication fidelity via a 3′→5′ exonuclease proofreading activity that removes misincorporated nucleotides. Elevated AMP directly binds and selectively inhibits the exonucleases, conserving energy at the expense of genomic accuracy. As a result, replication errors escape correction and accumulate, some conferring a selective advantage and driving carcinogenic evolution. Therapeutic and lifestyle interventions that activate AMPK—including weight loss, exercise, metformin, and aspirin—restore ATP production, lower AMP, and relieve inhibition of exonuclease proofreading, thereby preserving genomic integrity and slowing mutation-driven carcinogenesis. This framework reveals two core biological principles: 1. Energy metabolism and DNAreplication fidelity are mechanistically coupled at the DNA polymerase active site. 2. The mutation rate is an adaptive metabolic phenotype, modulated by AMP levels. These concepts redefine the metabolic–genetic interface in carcinogenesis and highlight AMPK activation as a rational target for obesity-associated cancer prevention. Full article

Ribosome biogenesis is a fundamental process underlying plant growth, development, and environmental adaptation, and processing of precursor rRNA (pre-rRNA) represents one of its most critical regulatory steps. This review provides a systematic overview of the multi-layered regulatory mechanisms controlling pre-rRNA processing in plants, with Arabidopsis thaliana as the primary model system. We focus on the genomic organization of ribosomal DNA (rDNA) and its epigenetic regulation, illustrating how highly repetitive and sequence-diverse rDNA arrays maintain genomic stability while enabling tissue-specific expression of distinct rDNA variants. We further summarize the dynamic pathways of pre-rRNA processing and their plastic regulation under environmental conditions such as elevated temperature. In addition, we review the quality control systems that monitor pre-rRNA maturation, including non-templated tailing and exonuclease-dependent degradation pathways, which play essential roles in removing aberrant processing intermediates. We further examine how perturbations in pre-rRNA processing give rise to plant ribosomopathies and discuss complementary models of ribosome homeostasis and ribosome heterogeneity as frameworks for interpreting shared developmental phenotypes. Finally, by synthesizing genetic and molecular evidence, we highlight the pivotal role of pre-rRNA processing in orchestrating plant development and propose directions for future research. Full article

DNA cloning traditionally relies on two approaches: restriction endonuclease digestion-ligation, and homologous recombination involving exonucleases, polymerases, and other enzymes. Here, we present a novel cloning method that requires only restriction endonucleases, eliminating the need for exonucleases or polymerases. The linearized cloning vector and the foreign DNA fragment (FDF) containing overlapping sequences were mixed and incubated at the melting temperature of the overlapping DNA sequences for 5 min, then cooled slowly to 0 °C. The mixture was transformed into E. coli and positive transformants were obtained. This cloning method was named DNA ‘breathing’ recombination (DBR) cloning. The overlapping sequence between the linearized vector and the FDF is preferably from 12 to 16 base pairs. Even when the ends of the linearized vector contain mismatches of up to 20 base pairs with the ends of the FDF, the DBR cloning method can still proceed efficiently, enabling truly seamless assembly. Meanwhile, the DBR method supports one-step assembly of multiple fragments. Therefore, the DBR cloning method simplifies experimental operations and reduces experimental costs while maintaining high cloning efficiency. Full article

Background/Objectives: DNA polymerase ε (Pol ε), encoded by POLE1, plays a pivotal role in high-fidelity DNA replication and in coordinating DNA repair. While pathogenic exonuclease-domain variants are well established in cancer, biallelic POLE1 variants remain largely unexplored in non-malignant human cells. Methods: Here, we analyzed primary fibroblasts derived from a skin biopsy of a compound-heterozygous patient carrying two POLE1 variants. Western blot analysis confirmed detectable Pol ε protein levels, indicating preserved protein expression despite the underlying variants. Results: Nevertheless, functional alterations were observed across multiple independent assays. Compared with healthy control fibroblasts, this patient-derived Pol ε fibroblast line exhibited reduced clonogenic survival following ionizing radiation. Surviving fractions were consistently lower across radiation doses from 2 to 4 Gy, with an approximately twofold reduction at 2 Gy and progressively greater differences at higher doses. The isoeffect dose corresponding to 10% survival was reduced relative to pooled control fibroblasts. In addition, chromosomal breakage was increased, supporting altered processing of radiation-induced DNA damage in this cellular model. Live-cell imaging and senescence assays revealed delayed proliferation and an increased proportion of senescent or senescence-like cells under baseline and genotoxic stress conditions, including enhanced senescence-associated β-galactosidase activity. Flow-cytometric analysis demonstrated S phase accumulation and G2/M arrest, consistent with replication stress and cell-cycle perturbation. Immunofluorescence staining revealed increased γH2AX foci, consistent with persistent DNA double strand breaks. RAD51 foci formation was not reduced; instead, increased RAD51 recruitment was observed under combined cisplatin and irradiation treatment, arguing against a primary defect in RAD51-mediated homologous recombination. POLE1-variant fibroblasts also showed impaired proliferative recovery, reduced wound closure, increased γH2AX accumulation following cisplatin exposure, suggesting heightened susceptibility to DNA crosslinking stress. Conclusions: Collectively, these findings provide the first functional characterization of a patient-derived POLE1-variant fibroblast cell line and indicate that altered Pol ε function may influence cellular responses to genotoxic stress. While based on primary fibroblasts from a single compound-heterozygous patient, validation in additional patient-derived or isogenic models will be required to determine the broader relevance of these findings. Full article

This study developed and validated a Self-competitive Fishing (SCF) primer qPCR system as a rapid, cost-effective alternative to next-generation sequencing (NGS) for detecting POLE exonuclease domain mutations (EDMs) in endometrial cancer. The system detects 11 pathogenic POLE EDMs using SuperSelective primers combined with wild-type-blocking oligonucleotides that prevent amplification of wild-type DNA, thereby enhancing mutant DNA detection. The validation process involved comparing specificity using genomic DNA from tumors with known POLE mutations identified by NGS. Sensitivity testing used POLE-mutated DNA diluted in wild-type DNA, while precision was confirmed by analyzing 86 endometrial cancer samples against NGS results. The SCF qPCR system demonstrated superior specificity compared to the original SuperSelective primer-based qPCR, achieving 1% mutation-detection sensitivity across various mutation points. Importantly, results from all endometrial cancer cases showed complete concordance with NGS analysis for the 11 pathogenic POLE-EDM points tested. This cost-effective and efficient SCF primer qPCR system provides an accessible method for routine molecular classification of endometrial cancer in clinical settings, offering a practical alternative to NGS for detecting pathogenic POLE mutations and supporting clinical decision-making. Full article

Background/Objectives: Traditional histopathological classification of endometrial cancer (EC) exhibits limited prognostic precision due to interobserver variability and incomplete reflection of tumor biology. The Cancer Genome Atlas (TCGA) introduced molecular subtypes, with POLE-ultramutated tumors showing superior outcomes. This systematic review and meta-analysis assesses the prognostic impact of pathogenic/likely pathogenic POLE exonuclease-domain mutations (EDM) on survival in EC. Methods: PRISMA 2020-compliant search of PubMed, Embase, and Web of Science (2015–2025) identified 20 studies (n = 7708 EC patients; 159 POLE-mutant, 2.1%). Eligibility: Adult EC patients with POLE EDM vs. non-POLE, reporting OS/PFS/DFS/RFS/CSS hazard ratios (HR). ROBINS-I assessed bias; random-effects meta-analysis pooled multivariable HR. Results: The meta-analysis revealed a significantly reduced risk of death in POLE-mutant endometrial cancer patients, with an OS pooled hazard ratio (HR) of 0.35 (95% CI 0.21–0.58; I² = 17.9%) across eight studies. Disease control endpoints (DFS/PFS/RFS) from 10 studies showed an even more substantial benefit, with a pooled HR of 0.22 (95% CI 0.12–0.41; I² = 0%). Cancer-specific survival HRs ranged from 0.00 to 0.32 across four studies, often with zero events in POLE cohorts. ROBINS-I bias was low to moderate; heterogeneity stemmed from the comparators and stages. Conclusions: POLE-EDM confers a robust, favorable prognosis across EC stages, supporting molecular risk stratification and treatment de-escalation. Full article

Tissue decellularization aims to obtain bioscaffolds for regenerative applications by removing all cellular components while preserving the extracellular matrix (ECM) architecture. Although decellularization removes the majority of linear nuclear DNA (nDNA), residual amounts remain detectable. However, the fate of circular mitochondrial DNA (mtDNA) after decellularization has not yet been reported. Cell death or injury can cause the release of mtDNA, which is resistant to breakdown by exonucleases. Extracellular mtDNA acts as a damage-associated molecular pattern (DAMP) that can trigger immune responses. The aim of this study is to assess the presence of residual mtDNA in the liver, bile duct, and vascular scaffolds after decellularization and whether this causes inflammatory responses in macrophages. Decellularized tissues showed a marked reduction in total DNA content well below the threshold of 50 ng/mg tissue. However, in liver and vascular scaffolds, a relative increase in the mtDNA:nDNA ratio was detected in the remnant DNA fraction. Residual mtDNA in bioscaffolds acted as DAMPs causing macrophage activation, as shown by increased cell proliferation and cytokine production. Strategies to further reduce remnant mtDNA were tested. We found that treatment with the endonuclease enzyme HpaII was effective in degrading residual mtDNA. Importantly, mtDNA removal resulted in a significantly reduced macrophage activation. In conclusion, our study shows that mtDNA is relatively resistant to the decellularization procedure and can act as a DAMP in bioscaffolds. This underscores the importance of removing mtDNA from decellularized bioscaffolds to improve the immunocompatibility for biomedical applications. Full article

This study addresses the need for detecting human papillomavirus type 16 DNA (HPV-16), a high-risk factor for cervical cancer, by developing a highly sensitive fluorescence sensing method based on tungsten disulfide (WS₂) nanosheets and exonuclease III (EXO III)-assisted cyclic amplification. The method is constructed by combining the highly efficient fluorescence quenching capability of tungsten disulfide (WS₂) nanosheets with a fluorescein (FAM)-labeled complementary DNA (cDNA) probe. When the target HPV-16 is present, it specifically hybridizes with the cDNA to form a double-stranded structure. This double-stranded structure can be cleaved by EXO III. The cleaved cDNA is not adsorbed by WS₂ nanosheets, generating a significant fluorescence signal. The released HPV-16 can then participate in the reaction again, achieving multiple rounds of fluorescence signal amplification. Under optimal conditions, the detection limit of the method is 0.35 pM. The method was successfully applied to the detection of HPV-16 in spiked serum samples, demonstrating the advantages of operational simplicity, high sensitivity, and good specificity. It provides a promising rapid detection method for clinical application research related to human papillomavirus. Full article

The modified DNA base 2,6 aminopurine (2-aminoadenine, (d)Z base) was originally found in phages to counteract host-encoded restriction systems. However, only a limited number of restriction endonucleases (REases) have been tested on dZ-modified DNA. Here, we report the activity results of 147 REases on dZ-modified PCR DNA. Among the enzymes tested, 53% are resistant or partially resistant, and 47% are sensitive when their restriction sites contain one to six modified bases. Sites with four to six dZ substitutions are most likely to resist Type II restriction. Our results support the notion that dZ-modified phage genomes evolved to combat host-encoded restriction systems. dZ-modified DNA can also reduce phage T5 exonuclease degradation, but has no effect on RecBCD digestion. When two genes for dZ biosynthesis and one gene for dATP hydrolysis from Salmonella phage PMBT28 (purZ (adenylosuccinate synthetase), datZ (dATP triphosphohydrolase), and mazZ ((d)GTP-specific diphosphohydrolase) were cloned into an E. coli plasmid, the level of dZ incorporation reached 19–20% of adenosine positions. dZ levels further increased to 29–44% with co-expression of a DNA polymerase gene from the same phage. High levels of dZ incorporation in recombinant plasmid are possible by co-expression of purZ, mazZ, datZ and phage DNA helicase, dpoZ (DNA polymerase) and ssb (single-stranded DNA binding protein SSB). This work expands our understanding of the dZ modification of DNA and opens new avenues for engineering restriction systems and therapeutic applications. Full article