Journal: STAR Protocols

Article Title: Protocol to investigate human mitochondrial transcription initiation by integrating biochemical and cryo-EM approaches

doi: 10.1016/j.xpro.2025.104347

Figure Lengend Snippet: DNA annealing evaluation by 4-20% TBE gel Lane 1: LSP (−43 to +20) single strand (ss) template (T) DNA, Lane 2: LSP (−43 to +20) ss non-template (NT) DNA, Lane 3: LSP (−43 to +20) duplex DNA.

Article Snippet: Maintain the duplex DNA concentration above 10 μM. c. Verify the annealing of the DNA strands by running a sample on a 4-20% TBE gel (Invitrogen) at 100 V for 4 h at 4°C, using TBE as the running buffer ( ).

Techniques:

Journal: Redox Biology

Article Title: Context-specific Angiogenin-mediated tRNA fragments (tDRs) biogenesis shapes the mitochondrial stress response

doi: 10.1016/j.redox.2026.104038

Figure Lengend Snippet: Analysis of tDR production in response to mitochondrial stress. A: MTT cytotoxicity assay after exposure to different stressors for 4 h. Asterisk indicates statistical significance compared to control (i.e. untreated) cells. B: Puromycin incorporation assay 4 h after stress induction. C: Western blot analysis of P38 and p-P38 4 h after stress induction. D: Western blot analysis of eIF2α and p -eIF2α 4 h after stress induction. E: Western blot analysis of P70S6 K and p-P70S6 K 4 h after stress induction. F: SYBR gold staining of TBE-Urea gels (long exposure) showing the production of tDRs after different stresses . 5s rRNA band shown is cropped from the same membrane at shorter exposure time. G: Sequencing strategy for the detection of tDRs production after mitochondrial stress. Cells were exposed to Rotenone (10 μM), Antimycin A (10 μg/mL) or Arsenite (100 μM) for 8 h then small RNAs extracted and sequenced. Three biological replicates were sequenced per group, except control where 2 biological replicates were sequenced. H-J: Volcano plots showing the differentially expressed tDRs in each condition versus the control group. K: PLS-DA clustering analysis revealing the differential clustering patterns observed in each stress condition. Abbreviations: CO: control; RO: Rotenone; TTFA; Thenoyltrifluoroacetone; AM: Antimycin A; KCN: Potassium Cyanide; OLI: Oligomycin; AS: Arsenite.

Article Snippet: In brief, 3 μg of total RNA were mixed with Novex TBE-Urea Sample Buffer (Thermo Fisher Scientific, Cat# LC6876), heated at 70 °C for 3 min, and loaded onto Novex 10 % TBE-Urea gels (Invitrogen, Cat# EC68755BOX) in 0.5 × TBE buffer (Bio-Rad, Cat# 1610733).

Techniques: Cytotoxicity Assay, Control, Western Blot, Staining, Membrane, Sequencing

Journal: Redox Biology

Article Title: Context-specific Angiogenin-mediated tRNA fragments (tDRs) biogenesis shapes the mitochondrial stress response

doi: 10.1016/j.redox.2026.104038

Figure Lengend Snippet: Analysis of tDR production in response to mitochondrial stress. A: MTT cytotoxicity assay after exposure to different stressors for 4 h. Asterisk indicates statistical significance compared to control (i.e. untreated) cells. B: Puromycin incorporation assay 4 h after stress induction. C: Western blot analysis of P38 and p-P38 4 h after stress induction. D: Western blot analysis of eIF2α and p -eIF2α 4 h after stress induction. E: Western blot analysis of P70S6 K and p-P70S6 K 4 h after stress induction. F: SYBR gold staining of TBE-Urea gels (long exposure) showing the production of tDRs after different stresses . 5s rRNA band shown is cropped from the same membrane at shorter exposure time. G: Sequencing strategy for the detection of tDRs production after mitochondrial stress. Cells were exposed to Rotenone (10 μM), Antimycin A (10 μg/mL) or Arsenite (100 μM) for 8 h then small RNAs extracted and sequenced. Three biological replicates were sequenced per group, except control where 2 biological replicates were sequenced. H-J: Volcano plots showing the differentially expressed tDRs in each condition versus the control group. K: PLS-DA clustering analysis revealing the differential clustering patterns observed in each stress condition. Abbreviations: CO: control; RO: Rotenone; TTFA; Thenoyltrifluoroacetone; AM: Antimycin A; KCN: Potassium Cyanide; OLI: Oligomycin; AS: Arsenite.

Article Snippet: Briefly, 3 μg of total RNA were mixed with Novex TBE-Urea sample buffer (Thermo Fisher Scientific, Cat# LC6876) and heated at 70 °C for 3 min.

Techniques: Cytotoxicity Assay, Control, Western Blot, Staining, Membrane, Sequencing