puc19 plasmid vector dna  (TaKaRa)

Journal: Nucleic Acids Research

Article Title: Design and in vitr o anticancer assessment of a click chemistry-derived dinuclear copper artificial metallo-nuclease

doi: 10.1093/nar/gkae1250

Figure Lengend Snippet: ( A ) Cleavage profile for supercoiled pUC19 DNA in the presence of Cu 2 -BPL-C6. ( B ) DNA cleavage profile of Cu 2 -BPL-C6 in the presence of scavengers DMTU, NaN 3 , tiron and D -mannitol, L -methionine and L -histidine. At the highest tested complex concentration in the presence of tiron, all three forms of pUC19 are present (lane 30) and DNA condensation is observed. In comparison, the control lane at the same concentration (lane 8) has no observable SC DNA. ( C ) Topoisomerase I inhibition by Cu 2 -BPL-C6, displaying negatively supercoiled DNA (lanes 37–43) and positively supercoiled DNA (lanes 45–49) together with evidence of DNA nicking.

Article Snippet: Procedures were adapted from previously published protocols ( , ), where reactions were carried out in 80 mM HEPES (pH 7.2) unless otherwise stated and followed the general procedure: Assays were performed in 20 μL of 80 mM HEPES buffer (pH 7.2) with 25 mM of NaCl, 1 mM of Na- L -ascorbate, 400 ng of superhelical pUC19 plasmid DNA (NEB, N3041) and increasing concentrations of each tested complex.

Techniques: Concentration Assay, Comparison, Control, Inhibition

Journal: Nucleic Acids Research

Article Title: Design and in vitr o anticancer assessment of a click chemistry-derived dinuclear copper artificial metallo-nuclease

doi: 10.1093/nar/gkae1250

Figure Lengend Snippet: ( A ) Composite image of the self-activation profile of Cu 2 -BPL-C6 with supercoiled pUC19 DNA in the absence of reductant at 30, 60 and 180 min time points. ( B ) Self-activation ROS scavenger profile of Cu 2 -BPL-C6 in the absence of reductant with NaN 3 and D -Mannitol, tiron, DMTU, L -methionine and L -histidine after a 60 min incubation.

Article Snippet: Procedures were adapted from previously published protocols ( , ), where reactions were carried out in 80 mM HEPES (pH 7.2) unless otherwise stated and followed the general procedure: Assays were performed in 20 μL of 80 mM HEPES buffer (pH 7.2) with 25 mM of NaCl, 1 mM of Na- L -ascorbate, 400 ng of superhelical pUC19 plasmid DNA (NEB, N3041) and increasing concentrations of each tested complex.

Techniques: Activation Assay, Incubation

Journal: Nucleic Acids Research

Article Title: Design and in vitr o anticancer assessment of a click chemistry-derived dinuclear copper artificial metallo-nuclease

doi: 10.1093/nar/gkae1250

Figure Lengend Snippet: In-liquid AFM showing the self-activation activity of 20 μM Cu 2 -BPL-C6 on pUC19. ( A ) Representative AFM images of untreated pUC19, Cu 2 -BPL-C6 treated pUC19 after 0, 30, 60 and 180 min and the 180 min time point after the addition of 200 μM EDTA. Scale bars = 200 nm, height scales = −3 to 4 nm. ( B ) Quantification of the proportion of circular and linear molecules present in the images. ( C ) Quantitative analysis of the smallest bounding area of individual circular molecules. ( D ) The total volume of the masked grains. N-values are as follows: pUC19 only: 213; 0 min: 110, 30 min: 140, 60 min: 127, 180 min: 69, 180 min + EDTA: 79.

Article Snippet: Procedures were adapted from previously published protocols ( , ), where reactions were carried out in 80 mM HEPES (pH 7.2) unless otherwise stated and followed the general procedure: Assays were performed in 20 μL of 80 mM HEPES buffer (pH 7.2) with 25 mM of NaCl, 1 mM of Na- L -ascorbate, 400 ng of superhelical pUC19 plasmid DNA (NEB, N3041) and increasing concentrations of each tested complex.

Techniques: Activation Assay, Activity Assay

Journal: bioRxiv

Article Title: Translation as a Biosignature

doi: 10.1101/2023.08.10.552839

Figure Lengend Snippet: Buffer and biomolecule samples were run in the following order: buf1, pUC19, buf2, DNA1kb, buf3, DNAHR, buf4 ( Table S1 ). Buffer (negative control) event counts demonstrate low carry-over between different samples as evidenced by low (<10) event abundance for run times of approximately 3 minutes for each buffer, and 6-10 minutes for each biomolecule sample.

Article Snippet: Aliquots of thawed biomolecule samples (single-stranded RNA [ssRNA] ladder [NEB #N0362], 1 kilobase [kb] double-stranded RNA [dsRNA] ladder [NEB #N0363], 1 kilobase double-stranded DNA [dsDNA] ladder [Thermo Scientific #SM0311], high range dsDNA ladder [Thermo Scientific # SM1351], DNA plasmid pUC19 [NEB #N3041], E. coli ribosome [NEB P0763S]) were added to Ontera Start-Up Buffer (2M LiCl, conductivity 11.96 S/m).

Techniques: Negative Control

Journal: bioRxiv

Article Title: Translation as a Biosignature

doi: 10.1101/2023.08.10.552839

Figure Lengend Snippet: Left panels (A, D, G, J) show selected event examples. Middle panels (B, E, H, K) show heat maps of change in conductance vs. dwell time (time molecule spends disrupting nanopore’s ionic current). Heat map color scale correspond to probability of an event being in that region of the heat map. Red boxes indicate regions of interest for right panels. Right panels (C, F, I) show all overlaid events within red boxes with a signal-to-noise ratio greater than 5, with time scaled to 1. Panel L shows schematic representations of the three measured types of DNA. In Panel K, each probability distribution (pUC19, 1kb ladder, high range ladder) is evenly weighted to facilitate comparison between the different classes.

Article Snippet: Aliquots of thawed biomolecule samples (single-stranded RNA [ssRNA] ladder [NEB #N0362], 1 kilobase [kb] double-stranded RNA [dsRNA] ladder [NEB #N0363], 1 kilobase double-stranded DNA [dsDNA] ladder [Thermo Scientific #SM0311], high range dsDNA ladder [Thermo Scientific # SM1351], DNA plasmid pUC19 [NEB #N3041], E. coli ribosome [NEB P0763S]) were added to Ontera Start-Up Buffer (2M LiCl, conductivity 11.96 S/m).

Techniques: