Journal: Nucleic Acids Research

Article Title: Topography of lacUV5 initiation complexes

doi:

Figure Lengend Snippet: DNase I and KMnO 4 footprinting of the RP i (14°C) and RP o (37°C) complexes formed on intact or partially depurinated (Depur.) lac UV5 promoter DNA. Either transcribed or non-transcribed DNA strands were end-labeled as indicated. Note that some depurinated sites (labeled with dots) are preferentially sensitive to DNase I (these bands are not detectable without DNase I digestion) and therefore are over-represented in the gel. Multiple bands present in the lanes containing KMnO 4 -treated depurinated DNA (beyond the –10 to +1 KMnO 4 -sensitive region) appear as a result of DNA cleavage at the depurinated sites during piperidine treatment (22). Some protection from DNase I close to DNA ends is likely to be explained by non-specific binding of the polymerase to DNA ends (28). D, DNA was treated with DNase I or KMnO 4 at 37°C; M1, Msp I digest of pBR322; M2, sequencing markers (G→A reaction; 22).

Article Snippet: After cross-linking, 10 mM CaCl2 was added to a final concentration of 1 mM and DNA was digested in 30 µl with 18 U micrococcal nuclease and 25 U DNase I (Worthington) at 37°C for 1 h (open complexes) or 14°C for 4 h (intermediate complex).

Techniques: Footprinting, Labeling, Binding Assay, Sequencing

Journal: Nucleic Acids Research

Article Title: Topography of lacUV5 initiation complexes

doi:

Figure Lengend Snippet: Analysis of protein composition of the cross-linked complexes. ( A ) 3.5–15% gradient SDS–PAGE of cross-linked products formed between RNAP and partially depurinated lac UV5 promoter DNA (end-labeled 122 bp fragment) at 37 (RP o ) and 14°C (RP i ). Brackets indicate positions of different β′/β- and σ-specific cross-linked products and protein-free DNA. Numbers 1–4 indicate the σ-specific products of different mobility. Different β′/β- and σ-specific cross-linked products have different mobilities due to cross-linking to different sites on the DNA (see text). ( B ) 8% SDS–PAGE of the cross-linked complexes formed at 37°C and digested with micrococcal nuclease and DNase I in solution. Two different exposures are shown. DNA was uniformly PCR-labeled. I and II, the final products of extensive digestion with nucleases. Intermediate products of digestion are indicated with a bracket. M, electrophoretic pattern of DNA-free RNAP in the same gel (Coomassie stain). ( C ) Two-dimensional SDS–PAGE of the cross-linked complexes formed at 37°C. The products resolved in the first dimension by 3.5–15% gradient SDS–PAGE (A) were digested with micrococcal nuclease and DNase I in the gel slice. Digestion products were separated in a second dimension 8% SDS–PAGE. Directions of separation and mobilities of the β′/β- and σ-specific cross-linked products in the first dimension are indicated. The electrophoretic pattern of free RNAP in the same gel (Coomassie stain) is shown on the left.

Article Snippet: After cross-linking, 10 mM CaCl2 was added to a final concentration of 1 mM and DNA was digested in 30 µl with 18 U micrococcal nuclease and 25 U DNase I (Worthington) at 37°C for 1 h (open complexes) or 14°C for 4 h (intermediate complex).

Techniques: SDS Page, Labeling, Polymerase Chain Reaction, Staining

Journal: PLoS Pathogens

Article Title: Neutrophil Extracellular Traps Contain Calprotectin, a Cytosolic Protein Complex Involved in Host Defense against Candida albicans

doi: 10.1371/journal.ppat.1000639

Figure Lengend Snippet: Identification of NET-associated proteins. (A) Silver stained SDS-PAGE and (B) immunoblots with samples from NET protein purification procedure. Human neutrophils were stimulated to form NETs. Supernatants from unstimulated (lane 1) and stimulated (lane 2) neutrophils; first wash (lane 3); second wash (lane 4); medium containing DNase-1 incubated with unstimulated neutrophils (lane 5); DNase-1-free medium incubated with washed NETs (lane 6); medium containing DNase-1 incubated with washed NETs (lane 7); medium containing DNase-1 incubated with washed NETs including protease inhibitor cocktail (lane 8).

Article Snippet: The concentration (F) of Dnase-1, as well as the time of digest (G), was confirmed in a silver-stained SDS-PAGE analysis to be optimal at 10 U/ml and 20 min for a maximal protein yield.

Techniques: Staining, SDS Page, Western Blot, Protein Purification, Incubation, Protease Inhibitor

Journal: PLoS Pathogens

Article Title: Neutrophil Extracellular Traps Contain Calprotectin, a Cytosolic Protein Complex Involved in Host Defense against Candida albicans

doi: 10.1371/journal.ppat.1000639

Figure Lengend Snippet: Histones are altered during NET formation. NETs from human neutrophils were washed and digested with DNase-1. (A) The NET-fraction (N) and the remaining pellet after DNase-1 digest (P) were analyzed by immunoblotting at the indicated time points. Unstimulated neutrophils served as controls. All core histones have a reduced molecular mass (2–5 kDa less) in NETs compared to the pellet fraction and the unstimulated control. A representative experiment out of three in total is shown. (B) High-resolution SEM analysis of NETs which consist of smooth fibers (white box) and globular domains (diameter 25–50 nm, arrows), scale bar = 100 nm. (C) High-resolution FESEM analysis of smooth stretch of a singular NET-fiber. Signal intensities were profiled vertically and horizontally showing similar diameters to nucleosomes (depicted as cartoon structure models taken from [41] , with approximate horizontal and vertical diameters of 5 nm and 10 nm, respectively). One experiment out of two is shown.

Article Snippet: The concentration (F) of Dnase-1, as well as the time of digest (G), was confirmed in a silver-stained SDS-PAGE analysis to be optimal at 10 U/ml and 20 min for a maximal protein yield.

Techniques:

Journal: Molecular and Cellular Biology

Article Title: NF-Y Associates with H3-H4 Tetramers and Octamers by Multiple Mechanisms

doi:

Figure Lengend Snippet: Recapitulation of the data obtained with DNase I, MNase, and Exo III assays. The X, Y, and Inr elements are boxed, and the major +1 start site of the Ea promoter is outlined. (A) DNase I. Arrows indicate the cuts in the nucleosomal region. (B) MNase. Thick arrows indicate the cuts with nucleosomes and dotted arrows with H3-H4 tetramers, thin arrows represent minor cutting sites, and brackets delimit the boundaries of the nucleosome. (C) Exo III. Thick and dotted lines indicate major stops with nucleosomes and H3-H4 tetramers, respectively. The small arrow indicates a major stop which is bypassed when NF-YB–NF-YC is reconstituted with nucleosomes. Asterisks refer to differences in the pattern observed when the NF-YB and NF-YC subunits are added to histones.

Article Snippet: In this procedure, 20,000 cpm of reconstituted tetramer or octamer particles was digested with 0.1 U of DNase I (grade I; Boehringer Mannheim) supplemented with 5 mM MgCl2 and 10 mM CaCl2 at 37°C for 3 min, while free DNA was digested with 0.001 U of DNase I.

Techniques:

Journal: Molecular and Cellular Biology

Article Title: NF-Y Associates with H3-H4 Tetramers and Octamers by Multiple Mechanisms

doi:

Figure Lengend Snippet: ]; labeled on the top strand [lanes 10 to 15] and bottom strand [lanes 16 to 23]). After reconstitutions with stoichiometric amounts of the indicated HFM protein combinations, aliquots were digested with DNase I and analyzed in sequencing gels. Asterisks denote bands that were diminished (lanes 8 and 9) or increased (lanes 20 and 21) when NF-YB–NF-YC was added to reconstitutions. To locate the position of the NF-Y footprinted area, samples in lanes 2, 11, 17, and 23 contained only the NF-Y trimer, without histones. Asterisks indicate protections (lane 9) and hypersensitivities (lanes 19 and 21) upon addition of NF-YB–NF-YC to histones. F, Free DNA; Nuc, nucleosomes. (B) The indicated complexes were DNase I digested, purified from gels (see Materials and Methods), eluted, and run on sequencing gels. Lane 1, free DNA; lane 2, DNA and NF-Y; lanes 3 to 6, H3-H4, H3–H4–NF-YB–NF-YC, nucleosome, and nucleosome–NF-YB–NF-YC, respectively. Asterisks indicate protections (lane 4) and hypersensitivity (lane 6).

Article Snippet: In this procedure, 20,000 cpm of reconstituted tetramer or octamer particles was digested with 0.1 U of DNase I (grade I; Boehringer Mannheim) supplemented with 5 mM MgCl2 and 10 mM CaCl2 at 37°C for 3 min, while free DNA was digested with 0.001 U of DNase I.

Techniques: Labeling, Sequencing, Purification

Journal: Molecular and Cellular Biology

Article Title: NF-Y Associates with H3-H4 Tetramers and Octamers by Multiple Mechanisms

doi:

Figure Lengend Snippet: MNase accessibility assay of histone–NF-YB–NF-YC combinations. Stoichiometric amounts of the indicated combinations of HFM proteins were reconstituted with fragment 2 (labeled on the top strand [lanes 4 to 9] and bottom strand [lanes 13 to 18]), cut with MNase, and analyzed on sequencing gels. In lane 17, the NF-Y trimer was used to show the NF-Y footprinted area. F refers to free, mock-reconstituted DNA (lanes 4 and 5; uncut and cut with MNase, respectively). Arrows correspond to the major and minor hypersensitive sites. Part of the H3-H4 and H3–H4–NF-YB–NF-YC reconstitutions were cut with DNase I and run in parallel (lanes 1, 2, 10, and 11). Bars correspond to the 10-bp cutting patterns of DNase I. Sequencing reactions (T; lanes 3 and 12) were run in parallel to precisely map the sites of MNase cuts.

Article Snippet: In this procedure, 20,000 cpm of reconstituted tetramer or octamer particles was digested with 0.1 U of DNase I (grade I; Boehringer Mannheim) supplemented with 5 mM MgCl2 and 10 mM CaCl2 at 37°C for 3 min, while free DNA was digested with 0.001 U of DNase I.

Techniques: Labeling, Sequencing

Journal: Nature Communications

Article Title: Atomic-resolution mapping of transcription factor-DNA interactions by femtosecond laser crosslinking and mass spectrometry

doi: 10.1038/s41467-020-16837-x

Figure Lengend Snippet: Schematic workflow of the fliX-MS pipeline. a A pulsed laser beam was generated using a femtosecond fiber laser with 515 nm wavelength, repetition rate of 0.5 MHz, and pulse duration of 500 fs. The wavelength was doubled to 258 nm by second harmonic generation (SHG) over a beta barium borate (BBO) crystal and the laser beam adjusted to fit the inner diameter of a regular 1.5 ml Eppendorf tube. b Protein–DNA complexes were irradiated or left untreated as control. Samples were denatured, DNA digested to mono/short oligonucleotides by a mix of Mnase, DNase I, and Benzonase, and proteins digested to peptides by trypsin and Lys-C. Peptides and peptide–nucleotide cross-links were separated from free DNA on C18 StageTips 25 , and cross-links subsequently enriched with TiO 2 beads. c Peptides were measured by LC–MS/MS and data analyzed with the RNP(xl) software package implemented in the proteome discoverer software 50 followed by manual annotation of candidate spectra.

Article Snippet: One microliter of MNase (New England Biolabs, M0247S), one microliter of DNase I (New England Biolabs, M0303S), and three microliters of Benzonase (Merck Millipore, 70746) were added to every 150 pmol of DNA.

Techniques: Generated, Irradiation, Liquid Chromatography with Mass Spectroscopy, Software