G-quadruplexes on chromosomal DNA negatively regulates topoisomerase 1 activity.

Human DNA topoisomerase 1 (Top1) is a crucial enzyme responsible for alleviating torsional stress on DNA during transcription and replication, thereby maintaining genome stability. Previous researches had found that non-working Top1 interacted extensively with chromosomal DNA in human cells. However, the reason for its retention on chromosomal DNA remained unclear. In this study, we discovered a close association between Top1 and chromosomal DNA, specifically linked to the presence of G-quadruplex (G4) structures. G4 structures, formed during transcription, trap Top1 and hinder its ability to relax neighboring DNAs. Disruption of the Top1-G4 interaction using G4 ligand relieved the inhibitory effect of G4 on Top1 activity, resulting in a further reduction of R-loop levels in cells. Additionally, the activation of Top1 through the use of a G4 ligand enhanced the toxicity of Top1 inhibitors towards cancer cells. Our study uncovers a negative regulation mechanism of human Top1 and highlights a novel pathway for activating Top1.

Thionation toward High-Contrast ACQ-DIE Probes by Reprogramming the Aqueous Segregation Behavior: Enlightenment from a Sulfur-Substituted G-Quadruplex Ligand.

Small-molecule-based fluorescent chemosensors provide powerful tools for analytical chemistry. However, their organic essence often "cursed" them for aggregation-caused quenching (ACQ) in an aqueous context. Albeit the praxis of the disaggregation-induced emission (DIE) strategy as a potential solution, it still awaited improvement due to the uncontrollability of the aggregation/segregation process. To address this issue, herein, we supposed that sulfur substitution on a molecule could serve as a promising strategy to achieve an evolved ACQ-DIE probe. To prove this concept, a precursor G-quadruplex (G4) ligand CQ was modified to get its thionation version CTQ. Strikingly, CTQ exhibited more arranged aqueous segregation behavior, as compared with CQ, and therefore enhanced fluorescence performance. Our research, in the meantime, manifested that CTQ remained to possess favorable G4 selectivity, whereby it could function as an evolved probe for more accurate in vitro G4-related assays, specifically, a classification assay for distinguishing virus variants.

Advances in the joint profiling technologies of 5mC and 5hmC.

DNA cytosine methylation, a crucial epigenetic modification, involves the dynamic interplay of 5-methylcytosine (5mC) and its oxidized form, 5-hydroxymethylcytosine (5hmC), generated by ten-eleven translocation (TET) DNA dioxygenases. This process is central to regulating gene expression, influencing critical biological processes such as development, disease progression, and aging. Recognizing the distinct functions of 5mC and 5hmC, researchers often employ restriction enzyme-based or chemical treatment methods for their simultaneous measurement from the same genomic sample. This enables a detailed understanding of the relationship between these modifications and their collective impact on cellular function. This review focuses on summarizing the technologies for detecting 5mC and 5hmC together but also discusses the limitations and potential future directions in this evolving field.

Endoplasmic Reticulum-Targeting Quinazolinone-Based Lipophilic Probe for Specific Photoinduced Ferroptosis and Its Induced Lipid Dynamic Regulation.

Lethal lipid peroxidation caused by reactive oxygen species occurs in different types of programmed cell death, especially in ferroptosis. Ferroptosis inducers, which serve as small-molecule probes, can provide insight into the mechanism of ferroptosis and facilitate drug discovery. The classical ferroptosis inducers indirectly lead to lipid peroxidation; thus, it is difficult to explore lipid regulation during the ferroptotic process. In this study, we designed two quinazolinone-based lipophilic probes BODIQPy-TPA and QPy-TPA, which proved to directly induce lipid peroxidation by light irradiation in vitro. The probe BODIQPy-TPA, which was mainly distributed in the endoplasmic reticulum (ER), specifically triggered ferroptosis in B16 and HepG2 cells upon light irradiation. As a comparison, the probe QPy-TPA, which was mainly distributed in lipid droplets (LDs), induced cell death by a nonferroptotic pathway. Further lipidomic analysis revealed that these two probes caused different patterns of lipid regulation and lipid peroxidation, suggesting that ferroptosis might activate distinct lipid regulation.