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: 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