Journal: bioRxiv

Article Title: RNA secondary structures modulate hnRNPH1-mediated alternative splicing of cold-shock protein RBM3

doi: 10.64898/2025.12.18.694734

Figure Lengend Snippet: RBM3 PE skipping increases on destabilization of rG4 structures. See also Figure S1 (A) Schematic of the experimental design in i3-neurons to evaluate the effect of TMPyP4 in RBM3 PE inclusion (B) RT-PCR of RBM3 mRNA (Exon 2–4) in i3-neurons at 37°C or 32°C (72h) in the presence of increasing concentration of TMPyP4 (5-200 µM) showing the PE-included (red arrows) and PE-skipped (green arrow) isoforms. (C) Graph showing the PSI values of RBM3 PE which are calculated based on the intensity of PE-included (red arrows) and PE-skipped (green arrow) isoforms from (B). (D) qRT-PCR quantifying the PSI values of RBM3 PE relative to RBM3 mRNA in i3-neurons at 37°C or 32°C (72h) in the presence of increasing concentration of TMPyP4 (5-200 µM). (E) Schematic of the experimental design in HeLa to evaluate the effect of TMPyP4 in RBM3 PE inclusion (top). RT-PCR of RBM3 mRNA (Exon 2–4) in HeLa at 37°C or 32°C (72h) in the presence of increasing concentration of TMPyP4 (5-200 µM) showing the PE-included (red arrows) and PE-skipped (green arrow) isoforms (bottom). (F) Graph showing the PSI values of RBM3 PE which are calculated based on the intensity of PE-included (red arrows) and PE-skipped (green arrow) isoforms from (E). Data information: N = 3 biological replicates. Mean ± SEM; ns (not significant), *(P<0.05), **(P<0.01); ***(P<0.001); one-way ANOVA with multiple comparisons.

Article Snippet: After 24h, the medium was replaced with fresh medium containing TMPyP4 (Merck-Sigma) at different concentrations (0, 5, 10, 25, 50, 100, or 200 nM).

Techniques: Reverse Transcription Polymerase Chain Reaction, Concentration Assay, Quantitative RT-PCR

Journal: Nucleic Acids Research

Article Title: G-quadruplex structures in 16S rRNA regions correlate with thermal adaptation in prokaryotes

doi: 10.1093/nar/gkaf042

Figure Lengend Snippet: Effects of TMPyP4 and TMPyP2 treatments on Thermotoga and Pseudothermotoga growth, protein content, and ribosomal gene expression. ( A ) Schematic representation of the experimental setup, showing treatment with TMPyP4 or TMPyP2 and incubation for 6 and 24 h. ( B ) Bacterial growth measured as OD 600 after 6 and 24 h. ( C ) Total protein content after 6 and 24 h of treatment. Relative expression levels of ribosomal genes 5S ( D ), 16S ( E ), and 23S ( F ) determined by qPCR at 6 and 24 h post-treatment. Data are shown as mean ± standard error (SE). Statistical significance is indicated as * P < 0.05, ** P < 0.01, *** P < 0.001 (Student's t test). Abbreviations: mar: T. maritima , elf: T. elfii .

Article Snippet: To incubate with TMPyP4 (Frontier Scientific, USA), the compound was added to the annealed mixture at a final concentration of 20 μM and incubated overnight at 4°C, after which CD melting tests were conducted.

Techniques: Expressing, Incubation

Journal: Journal of Biomedical Science

Article Title: Targeting the G-quadruplex as a novel strategy for developing antibiotics against hypervirulent drug-resistant Staphylococcus aureus

doi: 10.1186/s12929-024-01109-3

Figure Lengend Snippet: Confirmation of antibacterial activity. A The antibacterial activities of NMM, TMPyP2, BRACO19, TMPyP4, and Thioflavin T against SAUSA300 were examined by measuring cell growth in terms of OD at 600 nm. B, C SAUSA300 cell growth assessed as CFU/mL ( B ); representative sheep-blood agar plates showing the appearance of colonies during CFU enumeration ( C ). D , E Comparative killing kinetics of vancomycin (Van), Tetracycline (Tet), and NMM against SAUSA300 based on CFU/mL at 1.0 × ( D ); and 10 × ( E ) MIC of Van, Tet, NMM, and 0.05% Triton X-100 at different time points (0 to 12 h). F Comparative live/dead assay of SAUSA300 with 1 × MIC of NMM (5 µM) and Van (0.6 µM) using confocal microscopy, showing the proportion of live/dead SAUSA300 cells. SYTO9 and PI were used to stain the number of total and dead cells as green-fluorescent and red-fluorescent cells, respectively. All experiments were performed in triplicate and the average data was plotted with standard deviation. Significance of the data was analyzed using Student’s t -test. p -values less than 0.05 were considered significant (ns = non-significant p > 0.05, * p < 0.05, ** p < 0.01, *** p < 0.005, and **** p < 0.0001)

Article Snippet: The G4 compounds were procured as BRACO19 trihydrochloride (GC50140, GLPBIO); Quarfloxin or CX-3543 (A12380, AdooQ), TMPyP2 or meso-Tetra (3-pyridyl) porphine (T40846, Frontier Scientific), TMPyP4 tosylate (GC12092, GLPBIO), PDS or Pyridostatin trifluoroacetate salt (18013, Cayman Chemical), PhenDC3 trifluoromethanesulfonate (CS-7711, Chemscene), Thioflavin T (2390-54-7, MedChemExpress), Quinacrine dihydrochloride (69-05-6, MedChemExpress), N-methyl mesoporphyrin IX or NMM (GC44416, GLPBIO), and Quercetin (117-39-5, MedChemExpress) (Fig. S1).

Techniques: Activity Assay, Live Dead Assay, Confocal Microscopy, Staining, Standard Deviation