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Indicated restriction enzymes

Manufactured by New England Biolabs

Indicated restriction enzymes are a class of DNA-cleaving enzymes that recognize and cleave specific DNA sequences. These enzymes can be used to cut DNA at precise locations, facilitating various molecular biology applications such as gene cloning, DNA mapping, and genetic engineering.

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3 protocols using indicated restriction enzymes

1

Aspergillus fumigatus DNA Manipulation

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Manipulation of DNA was carried out according to standard procedures (48 ). Sequence information was obtained from the Aspergillus Genome Database (AspGD; http://www.aspergillusgenome.org) (49 (link), 50 (link)). Chromosomal DNA of A. fumigatus was isolated using a MasterPure Yeast DNA purification kit (Epicentre Biotechnologies). For Southern blot analysis, chromosomal DNA of A. fumigatus was digested with the indicated restriction enzymes (New England Biolabs). DNA fragments were separated in an agarose gel and blotted onto Hybond N+ nylon membranes (GE Healthcare Bio-Sciences). Labeling of DNA probes, hybridization, and detection of DNA-DNA hybrids were performed using digoxigenin (DIG) labeling mix, DIG Easy Hyb, and a CDP-Star ready-to-use kit (Roche Applied Science), respectively, according to the manufacturer’s recommendations.
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2

Genomic DNA Digestion and Southern Blotting

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Genomic DNA was prepared from 2 × 108 cells according to standard protocols and digested with the indicated restriction enzymes (New England Biolabs). The digested DNA was resolved in a 1.2% agarose gel and blotted onto a Hybond-XL membrane (GE Healthcare). After transfer, the membrane was cross-linked with UV and hybridized with different probes. 32P labeling of DNA probes was performed by random priming using Klenow fragment exonuclease- (New England Biolabs), in presence of [α-32P]CTP and hybridizations were performed in Church buffer at 65°C for Telo/STE1 and STE1 (STE1 = Subtelomeric Element 1) probes and 55°C for chromosomal probe. For spotting assays, genomic DNA were directly spotted onto a Hybond-XL membrane (GE Healthcare). Radioactive signal was detected using a Biorad molecular imager FX.
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3

Overexpression of CD70-mCherry in HPAECs

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We constructed a plasmid to overexpress CD70 linked to the fluorescent protein mCherry. The coding sequence of CD70 was amplified from HUVEC cDNA by PCR using a Q5 High-Fidelity DNA Polymerase (New England Biolabs Inc., NEB, Ipswich, MA) with gene specific primers including recognition sites for NheI and EcoRI as follows: forward 5’-AAAGCTAGCATGCCGGAGGAGGGTTCGGG-3’ and reverse 5’-AAAGAATTCGGGGCGCACCCACTGCACTCC-3’. The PCR product was digested with indicated restriction enzymes (NEB) and N-terminally fused to a mCherry-myc-HIS tag into a pcDNA3.1(-) vector using the Quick Ligation Kit (NEB). HPAECs were transfected with this construct versus a control plasmid of the same vector backbone using Lipofectamine 3000. The manufacturer’s protocol was modified by performing transfection overnight in regular media followed by replacement with fresh media.
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