Journal: Nucleic Acids Research

Article Title: A 96-well DNase I footprinting screen for drug–DNA interactions

doi: 10.1093/nar/gkm467

Figure Lengend Snippet: Infrared gel electrophoresis images of DNase I footprinting products following incubation of compounds 1–6 with TOPOIIα promoter DNA. Compounds were incubated for 17 h with TOPOIIα promoter DNA IR-labelled on the sense (A) or antisense (B) strand. Each gel consists of 50 lanes: two GA marker lanes (GA) and six sets of eight lanes for compound (l–r; 0, 0.0016, 0.008, 0.04, 0.2, 1, 5 and 25 μM). The sequence positions relating to Supplementary Figure 1 are given vertically.

Article Snippet: The proximal 705 bp of the human Topoisomerase II alpha (TOPOIIα) promoter was amplified by PCR from human genomic DNA (Promega) using primers TIIA-F (CACCGCACACAGCCTAC) and TIIA-R (TGGTGACGGTCGTGAAG) (Supplementary Figure 1).

Techniques: Nucleic Acid Electrophoresis, Footprinting, Incubation, Marker, Sequencing

Journal: Nucleic Acids Research

Article Title: A 96-well DNase I footprinting screen for drug–DNA interactions

doi: 10.1093/nar/gkm467

Figure Lengend Snippet: A comparison of footprint profiles of compounds 1–6 on the proximal region of the TOPOIIα promoter. Single footprint profiles were program-generated starting with the IR footprint gel image shown in A. Where no footprinting is seen, the sequence has been given an arbitrary score of −3.9 (log 125 μM). The DNA sequence is given in Supplementary Figure 1.

Article Snippet: The proximal 705 bp of the human Topoisomerase II alpha (TOPOIIα) promoter was amplified by PCR from human genomic DNA (Promega) using primers TIIA-F (CACCGCACACAGCCTAC) and TIIA-R (TGGTGACGGTCGTGAAG) (Supplementary Figure 1).

Techniques: Generated, Footprinting, Sequencing

Journal: medRxiv

Article Title: Polymorphism in IFNAR contributes to glucocorticoid response and outcome in ARDS and COVID-19

doi: 10.1101/2022.03.10.22272123

Figure Lengend Snippet: (A ) STAT1 expression in the lung after 4-day culture in the presence of IFN beta with or without hydrocortisone (HC). ( B) pSTAT1 expression in the same specimens as in A. ( C) Example photomicrographs showing higher STAT2 expression in a TT patient than in a CT patient and the effect of HC on its nuclear translocation. Most STAT2 remains in the cytoplasm of the CT patients, whereas nuclear expression is prominent in the TT patient. Indicated insets are shown in the bottom row. Arrows. ( D ) Combined results of all patients noting that two CT samples are excluded in the data as the patients were already under glucocorticoid treatment at the time of sample acquisition. Ns, not significant; *P<0.05; **P<0.01; and ***P<0.001

Article Snippet: The first stage antibodies were anti-alpha chain of the IFN alpha/beta receptor (St John’s Laboratory STJ112765) that was used 1:2000 and 1:5000 and anti-Stat1 (1:400, 9175S), anti-pStat1(1:100, 9167S) and anti-Stat2 (1:200, 72604S) all from Cell Signalling.

Techniques: Expressing, Translocation Assay