Journal: Nucleic Acids Research

Article Title: RNA G-quadruplexes promote codon repeat-associated ribosomal frameshifting in human genes

doi: 10.1093/nar/gkaf1481

Figure Lengend Snippet: RBM4 binds to the RNA G-quadruplex structure in HDAC1 mRNA. ( A ) A putative RNA G-quadruplex (rG4) was found downstream of the (UAC)3 codon repeat site in the HDAC1 gene using QGRS Mapper. Bases predicted to form G4 structures are highlighted in purple. Sequence alignment analysis shows that the (UAC)3 codon repeats (red box) and downstream rG4 motifs (black box) in HDAC1 are conserved across mammalian species. ( B ) A putative rG4 structure was predicted by AlphaFold 3. ( C ) CD analyses of G4 structures in HDAC1 . The positive G4 sequences were sourced from a previous publication. ( D and E ) The CD spectrum shows HDAC1 RNA oligonucleotides in the presence of different concentrations of either K + (D) or the rG4 destabilizer TMPyP4 (E). ( F and G ) RNA-IP demonstrates that RBM4 potentially interacts with the rG4 sequence of HDAC1 : FLAG-RBM4 enrichment confirmed by western blot (F), and RT–qPCR shows specific HDAC1 RNA enrichment compared with negative controls ( KCTD11, VAV3 , and APCDD1 ) and the positive control ( RBM4 ) (G). Error bars represent the SD of triplicates (** P < 0.01; n.s ., not significant; Student’s t- test for pairwise comparisons). All experimental procedures included three biological replicates. ( H ) Putative working model of RBM4 regulating HDAC1 frameshifting.

Article Snippet: Immediately after dropwise addition of the DNA–PEI mixture, cells were treated with 2 μM PhenDC3 (MedChemExpress, HY-15594A) or 2 μM TMPyP4 (MedChemExpress, HY-108477), with dimethylsulfoxide (DMSO) serving as the vehicle control.

Techniques: Sequencing, Western Blot, Quantitative RT-PCR, Positive Control

Journal: Nucleic Acids Research

Article Title: RNA G-quadruplexes promote codon repeat-associated ribosomal frameshifting in human genes

doi: 10.1093/nar/gkaf1481

Figure Lengend Snippet: Stabilizers and destabilizers of rG4 structures affect ribosomal frameshifting of HDAC1 . The effect of a G4-stabilizing ligand (PhenDC3, A ) or a G4 destabilizer (TMPyP4, B ) on the HDAC1 frameshifting ratio. The red arrows and numbers indicate the decreased percentage. Data in this figure represent the mean ± SD ( n ≥ 3 biological replicates; * P < 0.05, ** P < 0.01, Student’s t- test). n.s . indicates not significant.

Article Snippet: Immediately after dropwise addition of the DNA–PEI mixture, cells were treated with 2 μM PhenDC3 (MedChemExpress, HY-15594A) or 2 μM TMPyP4 (MedChemExpress, HY-108477), with dimethylsulfoxide (DMSO) serving as the vehicle control.

Techniques:

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