Search Results (669)

DNA damage requires repair via the endonuclease IV-mediated base excision repair (BER) pathway, which corrects apurinic/apyrimidinic (AP) sites. Chlamydophila pneumoniae AP endonuclease IV (CpEndoIV), the sole AP endonuclease in this pathogen, is crucial for genomic integrity. As humans lack a homologous protein, it represents a potential therapeutic target. In this study, we report the first crystal structure of CpEndoIV at 1.97 Å resolution. The structure reveals two Zn²⁺, one Mg²⁺, and a malonate molecule bound in the active site, marking the first observation of Mg²⁺ coordination in the EndoIV family. Compared to the three-Zn²⁺ model with a narrow, deep pocket for precise AP-site cleavage, the Zn²⁺/Mg²⁺-bound state has a wider, shallower pocket that might promote diverse catalytic activities. Combined with enzymatic assays, we suggest that the mixed Zn²⁺/Mg²⁺ model is better adapted for CpEndoIV to operate under host oxidative stress. Malonate binds to the metal ions, occupying the positions normally coordinated by water molecules. This binding mode may mimic the coordination of the substrate to the metal ions, and the protein conformation resembles that of the enzyme upon substrate binding at the active site. This study provides a structural basis for the functional characterization of CpEndoIV and offers a reference for the development of targeted inhibitors against diseases caused by Chlamydophila pneumoniae. Full article

Background: Curcumin, a dietary polyphenol with anticancer potential, has been reported to enhance the efficacy of chemotherapeutic agents. Methods: The effects of combined curcumin and doxorubicin treatment on apoptosis and associated signaling pathways were investigated in human osteosarcoma HOS cells. Results: Combined treatment significantly reduced cell viability and induced apoptotic morphological changes, which were confirmed by increased sub-G1 population, enhanced DNA fragmentation, and elevated cleaved poly(ADP-ribose) polymerase (PARP) levels. Mechanistically, combined treatment markedly increased c-Jun N-terminal kinase (JNK) phosphorylation, whereas extracellular signal-regulated kinase (ERK) phosphorylation showed no appreciable change. Pharmacological inhibition revealed that JNK suppression attenuated PARP cleavage, while ERK inhibition also reduced apoptotic responses, suggesting a permissive role of basal ERK activity. In addition, combined treatment was associated with increased expression of the endoplasmic reticulum stress marker GRP78 and modulation of autophagy-associated markers. Although thioredoxin domain-containing protein 5 (TXNDC5) expression was reduced, TXNDC5 overexpression failed to attenuate apoptosis, indicating that apoptosis induction occurs independently of TXNDC5. Conclusions: These findings indicate that combined curcumin and doxorubicin induce apoptosis primarily through JNK-dependent MAPK signaling, accompanied by stress-associated cellular responses. Full article

Wheat, soybean, and peanut are recognized as major food allergens, with their prevalence rising globally, necessitating rapid and reliable detection methods. A new detection approach was developed in this research, which integrates Ladder-shape Melting Temperature Isothermal Amplification (LMTIA) with Proofreading Enzyme-Mediated Probe Cleavage (Proofman) technology to enable the concurrent identification of wheat, soybean, and peanut allergens. Compared with the loop-mediated isothermal amplification (LAMP) method under the experimental conditions set in this study, this approach can reduce the false-positive results associated with LAMP, and it does not rely on sophisticated instrumentation required by technologies like mass spectrometry. The GAG56D (wheat), Ara h 2.01 (peanut), and Lectin (soybean) genes were selected as target genes for the three allergens. Specific primers and probes were designed according to these target genes, and the reaction system was optimized. A systematic evaluation of the triplex Proofman-LMTIA method was then conducted regarding its specificity, sensitivity, limit of detection, and repeatability. Finally, the method’s practical applicability was validated using commercial products. The optimized system achieved simultaneous detection within 40 min at 61 °C, showing no cross-reactivity with common foods. The method demonstrated good sensitivity, with a sensitivity of 5 pg/μL for genomic DNA and a detection limit of 5% (w/w) in a powder matrix, along with excellent repeatability. In practical sample testing, the results were fully consistent with product label declarations, accurately identifying single and multiple allergen contaminations. The Proofman-LMTIA detection method, with its rapid, simple, sensitive, and specific characteristics, demonstrates significant potential for applications in food safety supervision. Full article

Antibody–drug conjugates (ADCs) have become an important class of targeted anticancer therapeutics by integrating the tumor selectivity of monoclonal antibodies with the potent cytotoxicity of small-molecule payloads through rational linker design. This review summarizes the structural fundamentals of ADCs, including antibodies, linkers, and payloads, and describes their coordinated mechanism of action. We trace the evolutionary trajectory of ADCs across three generations, highlighting key breakthroughs, limitations, and representative agents for each era. Furthermore, we elaborate on cleavage mechanisms of linkers (cleavable and non-cleavable). We also categorize and discuss cytotoxic payloads, covering traditional microtubule-disrupting agents, DNA-damaging agents, and novel mechanism-based payloads, along with their modification strategies and preclinical/clinical performance. Finally, we discuss representative and clinically influential ADC designs, with emphasis on the relationships among antibody, linker, and payload. Full article

Mitogen-activated protein kinase kinase kinase 1 (MAP3K1) possesses dual enzymatic functions, i.e., kinase and E3 ubiquitin ligase activities, orchestrating proliferation, survival, apoptosis, DNA damage response, and immune modulation. Recent genomic and mechanistic studies have revealed MAP3K1’s paradoxical, context-dependent roles as both an oncogene and a tumor suppressor. We discuss MAP3K1’s multidomain architecture, featuring an N-terminal RING and PHD domain (E3 ligase activity), a TOG domain (microtubule dynamics), and a C-terminal kinase domain, enabling the integration of c-jun N-terminal kinase (JNK), p38 mitogen-activated protein kinase (p38 MAPK), extracellular signal-regulated kinase (ERK), and nuclear factor kappa B (NF-κB) signaling pathways. MAP3K1 functions as a molecular switch balancing survival and apoptosis, with caspase-3 cleavage at Asp878 activating pro-apoptotic JNK/p38 signaling. Genomic analyses across >35 cancer types reveal MAP3K1 alterations at frequencies of <1–14%, highest in breast and endometrial cancers. These alterations show tissue specificity: loss-of-function mutations predominate in hormone receptor-positive breast cancer with a favorable prognosis, whereas gain-of-function mutations in melanoma activate oncogenic ERK signaling. MAP3K1 mutations predict response to mitogen-activated protein kinase kinase (MEK) and phosphoinositide 3-kinase (PI3K) inhibitors, with mutant cancers showing higher MEK inhibitor response than wild-type tumors. Despite substantial progress, critical gaps remain regarding MAP3K1’s E3 ligase substrates, context-dependent activity determinants, and therapeutic strategies. Addressing these through inhibitor development, biomarker validation, and mechanistic studies will accelerate potential clinical translation of MAP3K1 biology. Full article

Background/Objectives: Early embryonic arrest during the cleavage stage (days 2–4) accounts for a substantial proportion of developmental failure in in vitro fertilization. This phenomenon remains poorly understood at the molecular level, even in chromosomally normal embryos identified by preimplantation genetic testing. This review aims to redefine cleavage-stage arrest from a passive energy deficit to a checkpoint-regulated endpoint caused by inadequate coordination among metabolism, transcriptome integrity, and stress-response pathways. Methods: We integrate evidence from long-read transcriptomics, metabolomics, epigenetics, and immunobiology relevant to pre-blastocyst development. These data are assembled into a unifying mechanistic framework and a clinically oriented stratification model, together with candidate multimodal readouts for early classification. Results: We propose a three-axis model linking: (i) metabolic–epigenetic insufficiency, including defective histone lactylation and impaired alpha-ketoglutarate-dependent DNA demethylation; (ii) isoform-level abnormalities, including intron retention and retrotransposon activation within a hidden transcriptomic landscape better resolved by long-read sequencing; and (iii) stress-related immune signaling, in which NLRP7 links alternative splicing and DNA-damage-response dysfunction with mitochondrial stress and p53-associated arrest. Within this framework, we distinguish three molecular arrest states: an early transition failure marked by defective maternal-to-embryonic reprogramming and severe splicing disruption; a metabolically quiescent state that may retain a limited rescue window; and a later stress-associated state characterized by senescence-like features, oxidative stress, and broad transcriptomic and genomic instability. Conclusions: Early embryo arrest should no longer be viewed as a nonspecific developmental failure, but as a mechanistically stratifiable condition with distinct metabolic, transcriptomic, and stress-associated trajectories. A diagnostic platform combining fluorescence lifetime imaging microscopy, long-read sequencing, and digital polymerase chain reaction may improve early mechanistic classification, help identify embryos with possible reversibility, and reduce uncertainty in embryo selection during in vitro fertilization. Full article

Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9, a genome-editing technology pioneered in 2012, enables the precise correction of deleterious mutations or disruption of disease-causing genes through targeted double-strand breaks (DSBs), offering potential for treating genetic diseases. However, CRISPR/Cas9 can cause off-target cleavage at non-specific DNA sites, leading to unintended insertions or deletions (indels), which limit its safety and applicability despite ongoing improvements in specificity. Recently, prime editing (PE), an advanced CRISPR-derived technology, has been employed with a Cas9 nickase (Cas9n) fused with a reverse transcriptase and a prime editing guide RNA (pegRNA) to enable precise insertions, deletions, and transversions without inducing DSBs, thus reducing risks of indels and chromosomal aberrations. Furthermore, ongoing optimizations, such as improved pegRNA design and enhanced editing efficiency, have expanded the applications of PE in medical therapeutics, agriculture, and fundamental research. This review summarizes recent advancements in the PE system, including optimized pegRNA designs and enzyme engineering for enhanced efficiency and specificity, alongside novel delivery methods. It also evaluates cutting-edge delivery strategies, such as adeno-associated virus (AAV) vectors, lipid nanoparticles (LNPs) and novel extracellular vesicle (EV)-based systems, and explores PE applications in vitro and in vivo, including disease modeling and therapeutic gene correction. Full article

CRISPR-Cas12a enables rapid and specific detection of PCR/LAMP (loop-mediated isothermal amplification) reaction products; however, this approach often requires open-tube manipulation, rendering it prone to cross-contamination. Here, we developed a novel one-pot reaction system that eliminated carryover contamination and facilitated endpoint detection using a CRISPR/Cas12a-based system. We leveraged the dependence of the CRISPR-Cas12a cleavage system on the protospacer-adjacent motif (PAM) to design PCR/LAMP primers that incorporated the PAM site (TTT) into amplified DNA. Pre-incubation of Cas12a with crRNA1 and crRNA2 using PCR/LAMP resulted in efficient cleavage of cross-contaminating DNA, while the target gene remained intact due to the lack of PAM sites. Furthermore, a Cas12a-detection complex (comprising Cas12a, crRNA3, trehalose, and the ssDNA probe) pre-stored on the lid was introduced to mix with the PCR/LAMP amplicons, which triggered the non-specific cleavage of fluorescent probes for direct visual detection under a blue LED instrument. This method effectively degraded up to 10⁶ copies of carryover contaminants within one hour, demonstrating the potential of one-pot detection methods in complex samples. Full article

The objective of this study is to develop a label-free fluorescent sensor for the quantitative detection of hypochlorite ions (ClO⁻) and validate its applicability in biological samples, particularly exploring the potential of ClO⁻ as a biomarker for stress-induced hypertension (SIH). Male Sprague-Dawley rats (8 weeks old, 250–300 g) were used to establish the SIH model. A guanine-rich (G-rich) signal DNA sequence (S-DNA) was rationally designed, with a ClO⁻-responsive phosphorothioate (PS) moiety integrated into the probe architecture. In the absence of ClO⁻, the S-DNA folds into a stable G-quadruplex structure, which specifically binds to ThT and triggers a significant enhancement of the dye’s fluorescence intensity. Upon introduction of ClO⁻, the specific hydrolysis reaction between the PS moiety and ClO⁻ induces cleavage of the S-DNA into two discrete fragments, thereby abrogating G-quadruplex formation and resulting in a remarkable quenching of ThT fluorescence. This proposed method exhibits excellent anti-interference capability against other reactive oxygen species (ROS) and achieves a low detection limit of 41.2 nM for ClO⁻. Furthermore, this strategy was successfully applied to the quantitative determination of endogenous ClO⁻ in human cells and the plasma of stress-induced hypertensive (SIH) rats, highlighting its substantial potential for clinical and physiological research. Full article

We synthesized seven carbocyclic nucleoside analogs featuring a cyclopentane ring in place of the (deoxy)ribose sugar, which serves as a linker in DNA/RNA nucleosides. We assessed the stability of cyclopentane nucleosides in 98% w/w sulfuric acid at room temperature via ¹H and ¹³C NMR spectroscopy. We observe that adenine (A1, A4), guanine (G1) and thymine (T1) cyclopentane nucleoside analogs remain stable for at least two weeks at room temperature, with only minor (~4%) degradation in A1. In contrast, the cytosine analog (C1) rapidly degrades to release a soluble cytosine. Methyl-substituted adenine analogs mimicking polymer backbone attachments at positions prone to tertiary carbocation formation (A2, A3) prove unstable and release soluble adenine. Only the 3,3-dimethylcyclopentyl adenine analog (A4) exhibits sufficient stability. Our findings reveal that cyclopentane serves as a viable stable linker in concentrated sulfuric acid for select nucleic acid bases, provided that the backbone connections avoid tertiary carbons susceptible to carbocation-mediated cleavage. We thus identify one potential key structural feature for engineering examples of genetic-like polymers that could potentially persist in Venus’s concentrated sulfuric acid cloud environment. Full article

Over the past two decades, numerous studies have examined the etiological significance of DNA fragmentation in human sperm using methods such as the comet assay (CA), the sperm chromatin structure assay, the sperm chromatin dispersion assay, and the TUNEL assay. We developed single-cell pulsed-field gel electrophoresis techniques, including one-dimensional (1D-SCPFGE) and angle-modulated two-dimensional (2D-SCPFGE), to detect early signs of naturally occurring DNA fragmentation. Comparative studies using purified human sperm with and without DNA fragmentation revealed some technical limitations in the conventional methods. This technical review outlines the procedures to ensure the quantitative performance of SCPFGE: (1) The mass of naked DNA was prepared through simultaneous in-gel swelling and proteolysis, which are highly sensitive to chemical and physical factors. Notably, these processes are vulnerable to reactive oxygen species (ROS). We developed the anti-ROS SCPFGE system to prevent artifactual cleavages. (2) 1D-SCPFGE discharges long-chain fibers from the origin, separating fibrous and granular segments beyond the tips of the fibers. (3) During continuous electrophoresis after 150° rotation (2D-SCPFGE-0-150), long-chain fibers unexpectedly extended diagonally backward from the origin, with long fibrous segments pulled out from a bundle that extended during the first electrophoresis, indicating some fibrous segments were embedded within the long-chain fibers. Even when SCPFGE was employed, one-directional current led to false negatives. (4) 2D-SCPFGE with angle rotation is currently the most sensitive imaging method for single-nuclear DNA fibers. However, without knowing the size of DNA fragments, it remains a semi-quantitative analysis. (5) To prevent artifactual DNA cleavage caused by ice crystals, low-temperature liquid storage is recommended. (6) The in-gel proteolyzed naked DNA is suitable as a substrate for chemical and enzymatic DNA cleavage analyses. Full article

Female reproductive aging is associated with a progressive decline in oocyte competence and reduced success in assisted reproductive technologies. While chromosomal abnormalities, mitochondrial dysfunction, and DNA damage have been extensively studied, these mechanisms do not fully explain developmental arrest in chromosomally euploid embryos or the variability in embryo competence. Human oocytes enter a transcriptionally quiescent state during meiotic maturation and rely almost entirely on the regulated translation of stored maternal messenger RNAs to support fertilization and early embryonic development until zygotic genome activation. In this context, translational fidelity becomes a critical determinant of proteome integrity and cellular function. Age-related alterations affecting ribosomal RNA integrity, transfer RNA modification, aminoacylation accuracy, and translational regulatory networks may impair the precision, timing, and coordination of protein synthesis. These defects can disrupt essential processes such as spindle assembly, cytoskeletal organization, and early cleavage dynamics, ultimately compromising embryo viability despite chromosomal normality. In addition, the follicular microenvironment, including redox balance, metabolic support, and signaling pathways, plays a crucial upstream role in maintaining translational integrity. This review integrates mechanistic evidence from molecular, cellular, and developmental studies to propose that progressive decline in translational fidelity represents a fundamental and previously underrecognized driver of reproductive aging. Understanding translational control as a central regulator of oocyte competence may provide new insights into unexplained IVF failure and support the development of novel biomarkers and therapeutic strategies aimed at preserving reproductive potential. Full article

Background/Objectives: TP53 mutation or deletion status is important for determining cellular responses to DNA-damaging drugs. Oxaliplatin (OXA) is combined with the fluoropyrimidine (FP) drug 5-fluorouracil (5-FU) in the FOLFOX regimen used to treat advanced colorectal cancer (CRC). However, the effects of TP53 deletion on 5-FU + OXA synergy are not well known. We investigated potential synergy between OXA and 5-FU and compared it with OXA synergy with a novel polymeric FP, CF10, in four cell lines harboring either wild-type (WT) or TP53-null status. Methods: Using CompuSyn and the highest single agent (HSA) models, we compared synergy between CF10 and OXA (COXA) and between 5-FU and OXA (FOXA). Cell cycle analysis was performed, as was Western blot quantification of canonical DNA damage pathway proteins. Likewise, immunofluorescent and confocal analysis allowed us to compare topoisomerase 1 cleavage complex and double-strand DNA break formation. Results: COXA synergy displayed minimal TP53 dependence with greatly improved potency compared to FOXA. COXA synergy resulted from OXA increasing: (i) Topoisomerase 1 (Top1) cleavage complex formation; (ii) DNA double-strand breaks (DSBs), and (iii) Checkpoint Kinase 1 and 2 (p-Chk1/2) phosphorylation, consistent with increased replication stress. Additionally, increased S-phase entry in TP53-null cells enhanced synergy between CF10, 5-FU, and OXA as S-phase drugs. Conclusions: Our results demonstrate that OXA synergizes with CF10 more effectively than with 5-FU through enhanced replication stress in both WT and TP53-null cells by causing greater Top1-mediated DNA double-strand breaks. Our studies provide a foundation for further testing of this combination in an orthotopic liver metastatic setting and eventual clinical development. Full article

Radiotherapy is the central component in non-small cell lung cancer (NSCLC) treatment. Nonetheless, its therapeutic effectiveness is frequently compromised by adaptive engagement of prosurvival signaling pathways that foster radioresistance. STAT3 functions as the central signaling node that orchestrates cellular survival responses following radiation exposure. This study investigated whether nitroxoline, a clinically approved antimicrobial agent with STAT3-inhibitory activity, enhances radiosensitivity of NSCLC cells and how these effects are mechanistically regulated. We examined the combined effects of nitroxoline and radiation on cell viability and associated signaling pathways in NSCLC cells. Nitroxoline significantly enhanced radiation-induced cytotoxicity and suppressed clonogenic survival compared with radiation alone. Irradiation increased STAT3, AKT, and mTOR phosphorylation, whereas nitroxoline effectively suppressed the basal and radiation-induced activation of these pathways. The combination treatment markedly augmented radiation-induced apoptosis, as demonstrated by increased p53 expression and enhanced PARP and caspase-3 cleavage. Additionally, nitroxoline amplified radiation-induced DNA damage signaling, resulting in pronounced γ-H2AX and DNA-PKcs accumulation. Nitroxoline enhanced NSCLC cell radiosensitivity by suppressing STAT3–AKT–mTOR survival signaling, promoting apoptosis, and amplifying radiation-induced DNA damage, indicating the potential of repurposing nitroxoline as a radiosensitizer to improve radiotherapy outcomes in patients with NSCLC. Full article

Copper is an essential element for living organisms, being a cofactor for numerous enzymes or proteins involved in oxidation-reduction reactions, intervening in numerous metabolic processes. In recent decades, complex copper combinations have consolidated their position in medicinal chemistry, which is manifested by the increasing number of compounds that have demonstrated their efficacy following in vitro or in vivo testing. While attempting to mimic the DNA-metal complex interactions typical of cisplatin, most studies of the mechanisms of action of copper complexes continue to consider DNA as the main biological target. Starting from this, studies are focused on understanding in detail how copper complexes manage to destroy tumor cells, and this has led to the discovery of a wide range of such mechanisms of antitumor action. In this review we present the main mechanisms of action of copper complexes discovered in recent decades, from the most well-known (production of ROS following the reaction with DNA) to the newest (cuproptosis). Research into understanding the mechanisms of action of copper complexes continues to be a topic of great interest in developing new potential antitumor agents. Full article