Journal: PLOS ONE

Article Title: Influence of DNA characteristics on cell membrane damage stimulated by electrical short-circuiting via a low-conductive aqueous droplet in dielectric oil

doi: 10.1371/journal.pone.0285444

Figure Lengend Snippet: The population of calcein-leaked cells stimulated by short-circuiting (3.0 kV, 1 short) using a low-conductivity droplet containing different structural conformations of pUC19 DNA (A: circular, B: linear). Statistical significance was determined using a paired-samples t test; * p < 0.05. (C, D) Comparison of the population of calcein-leaked cells between circular and linear pUC19 DNA. The amount of DNA was 4.0 ng (C) and 40 ng (D). Data are expressed as the mean ± SD of three independent experiments. Statistical significance was determined using one-way ANOVA followed by Tukey’s multiple comparison tests; *** p < 0.001. The raw data are available in the .

Article Snippet: Circular pUC19 DNA was linearized by the restriction enzyme Bam HI (TOYOBO, Osaka, Japan) and then purified by gel filtration (Clontech CHROMA SPIN-1000, Takara Bio Inc., Shiga, Japan).

Techniques: Comparison

Journal: PLOS ONE

Article Title: Influence of DNA characteristics on cell membrane damage stimulated by electrical short-circuiting via a low-conductive aqueous droplet in dielectric oil

doi: 10.1371/journal.pone.0285444

Figure Lengend Snippet: The population of calcein-leaked cells stimulated by short-circuiting using a low-conductivity droplet containing different amounts of (A) linear pUC19 DNA and (B) λ DNA. Statistical significance was determined using a paired-samples t test; ** p < 0.01. (C, D) Comparison of the population of calcein-leaked cells between pUC19 DNA and λ DNA. The amount of DNA was 4.0 ng (C) and 40 ng (D). Data are expressed as the mean ± SD of three independent experiments. Statistical significance was determined using one-way ANOVA followed by Tukey’s multiple comparison tests. The raw data are available in the .

Article Snippet: Circular pUC19 DNA was linearized by the restriction enzyme Bam HI (TOYOBO, Osaka, Japan) and then purified by gel filtration (Clontech CHROMA SPIN-1000, Takara Bio Inc., Shiga, Japan).

Techniques: Comparison

Journal:

Article Title: H-NS mediated compaction of DNA visualised by atomic force microscopy

doi:

Figure Lengend Snippet: AFM images of circular nicked pUC19 molecules with and without H-NS. (A) DNA molecules after incubation with H-NS (1 dimer per 12 bp) on a 2.5 × 2.5 µm surface area and DNA molecules without H-NS on a 2 × 2 µm surface area (inset). (B) Close-up images of class I complexes. Complexes are laterally condensed and show a small reduction of DNA contour length (~3%). (C) Close-up images of class II complexes. Complexes show characteristic foci with a more dramatic level of condensation and a large reduction of DNA contour length (up to ~25%). All close-up images of condensed molecules show a 500 × 500 nm surface area. The colour scale ranges from 0.0 to 3.0 nm (from dark to bright).

Article Snippet: DNA substrate for atomic force microscopy Plasmid pUC19 was grown in E.coli strain XL10 and isolated by alkaline lysis and subsequent purification on Qiagen 100 columns according to the supplier’s instructions.

Techniques: Incubation

Journal:

Article Title: H-NS mediated compaction of DNA visualised by atomic force microscopy

doi:

Figure Lengend Snippet: Three-dimensional representation of circular nicked pUC19 molecules with and without H-NS. (A) DNA molecules without H-NS. (B) Class I complexes. (C) Higher order condensed class II complexes. Each series of images corresponds to characteristic structures found in that class. All images show a 400 × 400 nm surface area. The colour bar indicates sample height and corresponds to a 0.0–3.0 nm range (from dark to bright).

Article Snippet: DNA substrate for atomic force microscopy Plasmid pUC19 was grown in E.coli strain XL10 and isolated by alkaline lysis and subsequent purification on Qiagen 100 columns according to the supplier’s instructions.

Techniques:

Journal:

Article Title: H-NS mediated compaction of DNA visualised by atomic force microscopy

doi:

Figure Lengend Snippet: AFM images of circular nicked pUC19 molecules after incubation with H-NS (1 dimer per 6 bp). (A) Two-dimensional representation. Images show a 300 × 175 nm surface area. (B) Three-dimensional representation. Images show a 300 × 300 nm surface area. The colour bar indicates sample height and corresponds to a 0.0–3.0 nm range (from dark to bright).

Article Snippet: DNA substrate for atomic force microscopy Plasmid pUC19 was grown in E.coli strain XL10 and isolated by alkaline lysis and subsequent purification on Qiagen 100 columns according to the supplier’s instructions.

Techniques: Incubation

Journal: BMC Genomics

Article Title: GlaI digestion of mouse γ-satellite DNA: study of primary structure and ACGT sites methylation

doi: 10.1186/1471-2164-10-322

Figure Lengend Snippet: Mouse genomic DNA cleavage with enzymes GlaI, Sse9I, FatI, Bst2UI . 1,8% low melting point agarose, Tris-acetate buffer. M – DNA marker pUC19/MspI (the lengths of the fragments are shown at right).

Article Snippet: The following DNA preparations were used as DNA fragment length markers: 1 kbp DNA ladder and pUC19/MspI DNA ladder (SibEnzyme Ltd., Russia).

Techniques: Marker

Journal: BMC Genomics

Article Title: GlaI digestion of mouse γ-satellite DNA: study of primary structure and ACGT sites methylation

doi: 10.1186/1471-2164-10-322

Figure Lengend Snippet: A physical map of mouse γ-satellite DNA . A – gel photo of mouse genomic DNA cleavage with restriction enzymes (double digestions). Lanes: 4 – intact DNA; 1, 3, 5, 7, 9 – GlaI added; 1, 2 – AcsI added; 5, 6 – FatI added; 7, 8 – BstF5I added; 9, 10 – Bst2UI added; M – DNA marker pUC19/MspI. B-F – physical maps of mouse γ-satellite DNA with indication of experimentally obtained DNA fragments and theoretically predicted ones. B – GlaI; C – double digestion with GlaI and AcsI; D – double digestion with GlaI and FatI; E – double digestion with GlaI and BstF5I; F – double digestion with GlaI and Bst2UI. Experimental patterns of mouse DNA hydrolysis and DNA ladders are shown on a left side of each figure. Positions of cleavage sites are shown in brackets at the top. Intact GlaI fragments are shown in black, cleaved GlaI fragments are shown in grey, double digestion products are shown in brown. Horizontal dotted lines show a correspondence of predicted fragments (arrows) to those observed on gel photos.

Article Snippet: The following DNA preparations were used as DNA fragment length markers: 1 kbp DNA ladder and pUC19/MspI DNA ladder (SibEnzyme Ltd., Russia).

Techniques: Marker