Journal: Cell

Article Title: STK19 positions TFIIH for cell-free transcription-coupled DNA repair

doi: 10.1016/j.cell.2024.10.020

Figure Lengend Snippet: (A) Generic schematic of the plasmids used for in vitro transcription (IVT) and transcription-coupled DNA repair (including ones containing adenovirus major late and SCP2* promoters). The workflow for analyzing RNA transcripts and error-free DNA repair is outlined. UAS, upstream activation sequence; TSS, transcription start site; TS, template strand; NTS, non-template strand. (B) Plasmids without (pCtrl) or with cisplatin 1,3-GTG intrastrand crosslinks (pPt) positioned 122 bp or 322 bp downstream of the TSS were added to NPE containing GAL4-VP64, TBP, and [α- 32 P]UTP. At the indicated times, RNA was recovered, separated on a Urea-PAGE gel, and subjected to autoradiography. Open and closed circles indicate the absence or presence of a given condition (here the presence of a lesion), respectively. Arrows indicate transcripts of lesion-stalled Pol II. (C) pPt-322 was incubated with NPE that was optionally supplemented with IVT activation mix (GAL4-VP64 and TBP) and α-amanitin (2 μM), as indicated (but not [α- 32 P]UTP). DNA was recovered at indicated times, incubated with XhoI and PmlI , separated on an agarose gel, and visualized with SYBR Gold. Appearance of the 2.2 kb and 0.8 kb (bottom panel) restriction fragments indicates restoration of the PmlI site. A part of the gel without any bands has been removed. See for inhibitory effect of α-amanitin. (D) Same assay as in (C) but using pPt-122. GG-NER was inhibited via addition of an inhibitory XPC antibody, transcription was induced, and the TC-NER cocktail was added, as indicated. The smaller (0.6 kb) fragment is not shown. (E) Quantification of error-free repair of n = 3 experiments like the one shown in (D). To determine the percentage of repaired plasmids, the ratio of repaired to damaged DNA fragments in each lane was quantified (see ). Error bars represent the SD from the mean. (F) Bar graph quantifying the error-free repair relative to condition I (GG-NER) at the 120 minute time point from (E), our standard approach to present the data throughout the paper. See also .

Article Snippet: Protein A Mag Sepharose Xtra , Cytiva , Cat# 28967062.

Techniques: In Vitro, Activation Assay, Sequencing, Autoradiography, Incubation, Agarose Gel Electrophoresis

Journal: Cell

Article Title: STK19 positions TFIIH for cell-free transcription-coupled DNA repair

doi: 10.1016/j.cell.2024.10.020

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Protein A Mag Sepharose Xtra , Cytiva , Cat# 28967062.

Techniques: Virus, Recombinant, Gel Extraction, Staining, Protease Inhibitor, Ubiquitin Proteomics, Expressing, Conjugation Assay, Software

Journal: Cell reports

Article Title: Group A Streptococcal S Protein Utilizes Red Blood Cells as Immune Camouflage and Is a Critical Determinant for Immune Evasion

doi: 10.1016/j.celrep.2019.11.001

Figure Lengend Snippet:

Article Snippet: Protein A/G Agarose Max Flow, Highly Cross-linked Beads, 4% , Genesee Scientific Corporation , Cat#20–540.

Techniques: Virus, Recombinant, Modification, Saline, Staining, Protease Inhibitor, Mass Spectrometry, Sequencing, DNA Purification, Purification, Plasmid Preparation, Ligation, DC Protein Assay, Luciferase, Peptide Fractionation, Infection, Software, Expressing, Protein-Protein interactions