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Agei hf

Manufactured by New England Biolabs
Sourced in United States, Morocco

AgeI-HF is a Type II restriction endonuclease enzyme that recognizes and cleaves the DNA sequence 5'-ACCGGT-3'. It is a high-fidelity (HF) variant of the original AgeI enzyme, with increased specificity and reduced star activity.

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20 protocols using agei hf

1

Cloning and Expression of Anti-AcSTn Antibody

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Purified variable regions were first cloned into pGEM-T easy vector (Promega). First, dATPs were added to the insert edges using BIOTAQ DNA Polymerase (bioline) according to manufacturer’s instructions. Then, inserts with A-overhang were ligated to pGEM-T easy vector. DH5α cells were transformed with pGEM-T easy vector containing anti-AcSTn variable inserts. In order to purify the variable inserts, light chain plasmids were digested by AgeI-HF (New England BioLabs), and BsiWI (New England BioLabs), heavy chain plasmids were digested by AgeI-HF (New England BioLabs) and SalI-HF (New England BioLabs). Digested products were extracted from 1% agarose gel. Human IgG (hIgG) expression vectors (FJ475055, FJ475056) were kindly provided by Prof. Patrick Wilson (University of Chicago). Plasmids for heavy and kappa light chain were digested with restriction enzymes (heavy chain expression vector with AgeI-HF and SalI-HF, light chain expression vector with AgeIF-HF and BsiWI). Vectors were then treated with Antarctic Phosphatase (New England BioLabs) in order to prevent self-closure of the vector. Inserts were ligated with hIgG expression vectors using T4 DNA Ligase (New England BioLabs) and plasmids were transformed into DH5α cells.
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2

Generating a snpSTARRseq capture library

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Pooled human genomic DNA (NA13421; consisted of 27 males and 27 females from CEPH Utah pedigrees) obtained from Coriell Institute for Medical Research (58 (link)) (Supplementary Table S3) was fragmented (500–800 bp), end-repaired and ligated with xGen stubby adaptors (IDT) containing random i7 3bp UMI. The captured regions were enriched using xGen biotinylated oligonucleotide probe pool (IDT) (59 (link)) and Dynabeads M-270 Streptavidin beads (IDT). Post-capture was PCR-amplified with STARR_in-fusion_F primer and STARR_in-fusion_R primer, and then cloned into AgeI-HF (NEB) and SalI-HF (NEB) digested hSTARR-ORI plasmid (Addgene plasmid #99296) with NEBuilder HiFi DNA Assembly Master Mix (NEB). The snpSTARRseq capture library was then transformed into MegaX DH10B T1R electrocompetent cells (Invitrogen) and the plasmid DNA was extracted using the Qiagen Plasmid Maxi Kit. The sequences of all the primers used for generating the snpSTARRseq capture library were listed (Supplementary Table S4).
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3

Gaussia Luciferase Reporter Plasmid Construction

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The Gaussia luciferase reporter plasmid was generated by removing the firefly luciferase sequence from the pGL4.31 plasmid using FseI and HindIII-HF enzymes (New England Biolabs) and replacing it with the Gaussia luciferase sequence. Then, two complementary oligonucleotides containing an AflII restriction site were inserted upstream of the MLP promoter using EcoRI-HF and NheI enzymes (New England Biolabs). Finally, complementary oligonucleotides containing the three LANA DNA binding sites (LBS2-LBS1-LBS3) were inserted upstream of the MLP promoter using AflII and NheI enzymes (New England Biolabs). The RMCE-HILO donor plasmid was generated by digesting the pEM791 plasmid [65 (link)] with AgeI-HF and BsrGI-HF enzymes (New England Biolabs) and inserting two PCR amplified sequences containing the FLAG tag fused to the VP16 activation domain and the LANA DNA-binding domain by Gibson Assembly (New England Biolabs).
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4

Cloning Trastuzumab Light and Heavy Chains

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The plasmid pcDNA3.4-TOPO (Thermo Fisher Scientific) was used as a backbone to subclone the trastuzumab LC (light chain) and HC (heavy chain) upstream of the WPRE sequence. The pcDNA3.4-TOPO was digested with AgeI-HF (NEB), the restriction site was blunted using Klenow (NEB), followed by digestion with XbaI (NEB). LC and HC were amplified by PCR using the phosphorylated primer pair LC+XbaI F; LC-R and HC+XbaI F; HC-R (Supplementary Table S1), pVITRO1-Trastuzumab-IgG1/κ [a gift from Andrew Beavil, Addgene plasmid #61883 (Dodev et al., 2014 (link))] as the template DNA, and Phusion High Fidelity DNA polymerase (ThermoFisher Scientific) following manufacturer recommendations, for cloning in pcDNA3.4-TOPO in the XbaI and blunted AgeI restriction sites.
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5

Enrichment and Cloning of ARBS Regions

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Common clinical ARBS were defined as those sites that were present in all normal prostate (n = 3) or independent PCa tumors (n = 13) [2 (link)]. Pooled human male genomic DNA (Promega) was randomly sheared (500–800 bp) using a Covaris M220 Focused-ultrasonicator. The fragments were end-repaired and ligated with Illumina compatible adaptors using the NEBNext Ultra™ II DNA Library Prep Kit (NEB). The adaptor-ligated DNA was hybridized to custom Agilent biotinylated oligonucleotide probes across a 700-bp region (53,032 probes; 4.684 Mbp oligo) and then pulled down by Dynabeads M-270 Streptavidin beads (NEB). The post-capture DNA library was amplified with STARR_in-fusion_F and STARR_in-fusion_R primers (Additional file 3: Table S1) and then cloned into AgeI-HF (NEB) and SalI-HF (NEB) digested hSTARR-ORI plasmid (Addgene plasmid #99296) with NEBuilder HiFi DNA Assembly Master Mix (NEB). The ARBS STARRseq library was transformed into MegaX DH10B T1R electrocompetent cells (Invitrogen). Plasmid DNA was extracted using the Qiagen Plasmid Maxi Kit.
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6

Detecting Green Cotyledon Trait in Faba Beans

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Primers of dCaps marker were designed with the help of dCAPs Finder 2.0 (http://helix.wustl.edu/dcaps/dcaps.html, accessed on 12 August 2020) [43 (link)]. The primers were dCaps_F: AAGTGTTTGATTTGATTTGATTAGG and dCaps_R: TACCCAAACTAATGACTCCTCTAATACCGG. A mismatched ‘A’ (underlined) was introduced into the dCaps_R primer to form an AgeI recognition site (ACCGGT) in the PCR product of green-cotyledon faba beans. PCR was carried out using TSINGKE® 2× Master Mix (Tsingke, Henan, China, TSE003). After that, 3 μL of PCR products was digested using endonuclease AgeI-HF (NEB, Massachusetts, MA, USA, R3552). Those PCR products from green-cotyledon faba beans were recognized and digested by AgeI-HF and produced shorter bands on 3% agarose gel.
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7

Apoptosis Assessment in Cell Culture

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Cell culture products were provided by Hyclone (Logan, UT). Puromycin, streptomycin and penicillin were provided by Life Technologies, Inc. (Gaithersburg, MD). AO-EB, Caspase-8 and Caspase-3 fluorometric assay kits were provided by Beyotime Biotech (Jiangsu, China). Caspase-8 inhibitor (Z-IETD-FMK) were from MedChem Epress (Princeton, NJ). RT reagent Kit and qRT-PCR kits were from Takara Bio (Dalian, China). FuGENE®HD Transfection Reagent was from Promega Corporation (Madison, WI). Restriction enzymes NcoI, AgeI-HF and EcoRI-HF were from New England Biolabs (Ipswich, Ma). Lactobacillus plantarum NCU116, E. coli Dh5α and pLKO.pig-puro vector were stored at −80 °C.
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8

Efficient Antibody Cloning Protocol

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The cloning method was adapted from a protocol published by Smith et al (2009)(13 (link)). Briefly, 96-well PCR plates containing sorted plasmablast were thawed and used directly for reverse transcription PCR by the addition of dNTPs, RT-PCR buffer, RNAase-free H2O, reverse transcriptase, and two primer pools containing forward and reverse primers for the heavy and light chains (RT-PCR reagents purchased from Qiagen, primers purchased from Geneart, Invitrogen). These PCR products were used in 3 separate nested PCR reactions to amplify the heavy and light chains separately, and to introduce restriction sites to the ends of the PCR products. Next the PCR products were digested using their respective restriction enzymes (AgeI-HF, SalI, XhoI, and BsiWI, all purchased from New England Biolabs) and ligated into human IgH, IgK, and IgL vectors containing a CMV promotor and ampicillin resistance (all expression vectors were kindly provided by Dr Juthathip Mongkolsapaya) using T4 DNA ligase (New England Biolabs). Vectors were expanded using TOP10 chemically competent E. Coli (Invitrogen), purified using QIAprep Spin Miniprep Kit (Qiagen), and transfected into HEK293/T17 cells in FreeStyle 293 expression medium (Thermo Scientific). Antibody supernatants were collected after 2 days of culture and stored at 4°C for further use.
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9

Lenti-AsCpf1-Blast Vector Construction

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Human codon-optimized AsCpf1 were PCR amplified with primers containing NLS signals in NEB Q5 hot start mastermix from plasmid SQT1659 (Addgene# 78743). lenti-AsCpf1-Blast (Addgene# 84750) was digested with AgeI-HF(NEB) and BamHI-HF(NEB). NLS modified AsCpf1 and digested vector were ligated using Gibson Assembly.
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10

Isolation and Characterization of Anti-RBD Antibodies

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From the nine different RBD-specific B cells isolated from the patient, 7 were successfully sequenced. Two sequences were identical, leading to a total of 6 different sequences. These assembled BCR sequences were synthesized into GeneBlocks (IDT DNA) and then cloned in the pTRIOZ-hIgG1 plasmid (InvivoGen) using the restriction enzymes SgrAI (NEB) and BsiWI-HF (NEB) for the variable domain of light chain, as well as AgeI-HF (NEB) and NheI-HF (NEB) for the variable domain of heavy chain. A sanger sequencing has been performed to ensure the quality of the cloned sequences. Using these vectors, anti-RBD antibodies (EH1, EH2, EH3, EH5 and EH8) were then produced, purified, and validated.
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