bstyi  (New England Biolabs)

Journal: The Scientific World Journal

Article Title: Distribution of BoLA-DRB3 Allelic Frequencies and Identification of Two New Alleles in Iranian Buffalo Breed

doi: 10.1100/2012/863024

Figure Lengend Snippet: Electrophoresis in 8% polyacrylamide gel of exon 2 amplification products of gene BoLA-DRB3 digested by endonucleases Rsa I (b), Hae III (a), and BstYI (c). Msp I fragments of plasmid pUC19 are used as a molecular marker. The length of fragments composing Rsa I, Hae III, or Bst YI DNA patterns is shown on pictures.

Article Snippet: Restriction Endonuclease Digestion The PCR-amplified DNA fragments from the second PCR restriction were digested with restriction endonuclease Rsa I, BstYI , and Hae III (New England Biolabs, Beverly, Mass).

Techniques: Electrophoresis, Amplification, Plasmid Preparation, Marker

Journal: Nature Communications

Article Title: A recurrent point mutation in PRKCA is a hallmark of chordoid gliomas

doi: 10.1038/s41467-018-04622-w

Figure Lengend Snippet: Characterization of PRKCA D463H mutation in chordoid glioma. a Left panel: gadolinium T1 weighted MRI showing a well-limited, strongly enhancing mass developed at the anterior part of the third ventricule (patient 2123). Right panel: Pan-cancer PRKCA somatic mutations in TCGA cohort. D463H was not identified in this cohort and its position is marked by the straight line. b Somatic mutations in PRKCA in Cosmic census genes for the ChG samples with matched blood (G1 group). The predicted impact of the mutations according to Sift 7 and Polyphen 8 scores are given. c Three-dimensional structure of the catalytic site of PKCα showing the positions of D463 in the wild-type, H463 in the mutant protein, and the amino acids predicted to interact via hydrogen bonds with wild-type and mutant 463 residue. Hydrogen bonds identified using CHARMM software and Baker and Hubbard algorithm in MDTraj 70 python package (see Methods) are indicated by arrows: orange (common to both WT and mutant), blue (present only in WT), red (present only in the mutant). d PRKCA D463H transcript is overexpressed in ChG compared to PRKCA WT . Left: the G to C substitution leads to the loss of BstYI restriction site in the mutant allele. PCR products from ChG cDNA were digested by BstYI then analyzed by LabChIP GX. Lanes T7033 and T7095 correspond to cDNA from low-grade glioma wild type for PRKCA , which shows that digestion efficiency is 100%. Mutant product size appears arround 418 bp; wild type digested product sizes appears around 227 and 185 bp. The last two lanes correspond to pcDNA plasmid controls, either WT or D463H mutant (MUT). Right: concentration ratio of mutant to wild-type bands is indicated (mean = 1.8)

Article Snippet: PCR reactions were split and half was digested with BstYI (New England Biolabs), when the other half was incubated in the digestion mix without BstYI, and left over night at 60 °C.

Techniques: Mutagenesis, Magnetic Resonance Imaging, Software, Polymerase Chain Reaction, Plasmid Preparation, Concentration Assay

Journal:

Article Title: Activation-dependent intrachromosomal interactions formed by the TNF gene promoter and two distal enhancers

doi: 10.1073/pnas.0708210104

Figure Lengend Snippet: 3C assay. ( A ) Genomic DNA products of BstY I digestion (arrows), with areas of interest (HSS and gene promoters) labeled A–F and PCR primers numbered 1 and 2. ( B and C ) Relative cross-linking frequencies (±SEM) between the indicated fragments

Article Snippet: Nuclei were pelleted and digested with BstY I (New England BioLabs) for 3 h at 60°C (inactivated at 80°C for 20 min).

Techniques: Labeling, Polymerase Chain Reaction