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Gibson assembly mix

Manufactured by New England Biolabs
Sourced in United States

The Gibson assembly mix is a proprietary DNA assembly method developed by New England Biolabs. It enables the seamless joining of multiple DNA fragments in a single isothermal reaction. The mix contains the necessary enzymes and buffers to perform the assembly process.

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32 protocols using gibson assembly mix

1

Comprehensive Biochemical Assay Protocol

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ATP (A2383), CTP, GTP, ɑ-ketoglutaric acid (75890) L-glutamic acid (G1626), NAD+ (10127965001) Etheno-NAD+ (N2630) NADH (10107735001) NADP+ (93205), protease inhibitor cocktail (PIC; 11873580001), and nicotinamide (N3376) were from Sigma. Six-biotin-17-NAD+ (4670-500-01) was from Trevigen (for capture of Lart1 substrate in yeast lysate) and Amsbio (AMS.80610, for assays with Lart1 orthologs). [32P]-NAD (NEG023X250UC) was from Perkin Elmer. Tris (2-carboxyethyl) phosphine hydrochloride (TCEP; 20490), PfuTurbo DNA polymerase (50-125-946), and high-capacity streptavidin agarose (20357) were purchased from Thermo Fisher Scientific. High-sensitivity streptavidin HRP (21130) was from Pierce. The ethenoadenosine antibody 1G4 (sc-52666) was from Santa Cruz Biotechnology. Q5 DNA polymerase, 2X Gibson assembly mix, and all restriction enzymes used for cloning were from New England Biolabs.
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2

Assembling TCR Gene Fragments

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Individual CDR3 gene fragments generated by PCR contained a 15-bp overlap sequence at the 3’ end of each oligonucleotide. To assemble the 4 gene fragments, we mixed 50 ng of TRAV-TRBC2-pSB linear DNA, 9.4 ng of TRAC-TRBV linear DNA, 1.4 ng of TCRα CDR3, 1.4 ng of TCRβ CDR3, and 2x Gibson Assembly mix (New England Biolabs, Ipswich, MA) in a 0.2-mL PCR tube. After 1 hour of incubation at 50°C, 5 μL of the sample was used to chemically transform 25 μL of competent cells (E. Cloni; Lucigen, Middleton, WI). Colonies were selected and expanded in lysogeny broth containing kanamycin. SB DNA plasmids were isolated using the Miniprep kit or Midiprep kit (Qiagen), and coding sequences were verified by Sanger sequencing.
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3

Optimized DNA Construct Generation

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All constructs were generated using either PCR with NEB Phusion polymerase or IDT gene blocks. Cloning into transgenic vector plasmids was performed using Gibson assembly mix from NEB. The sequences of the constructs used to generate the data shown in main text (ID3 dNRR dNotch1 TMD dnlng2 esn V5, nSyb::CD19, and CD19::sdc) are shown in Supplementary file 1, including maps indicating their key elements).
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4

Kanamycin Resistance Cassette Insertion

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The strain carrying the kanamycin resistance cassette was obtained by PCR amplifying a plasmid obtained from the Gene Synthesis services from Genscript Inc. found in Supplementary Table S2 with primers ResistanceF and ResistanceR (Supplementary Table S1). Roughly 400 bps on either side of the AR (Antibiotic Resistance) insertion point were PCR amplified with primer pairs UpGCF and UpGCR_resistance on one hand and DownGCF_resistance and DownGCR on the other hand. Fragments were joined by using Gibson Assembly Mix (New England Biolabs). The assembled product was further amplified by the external primers, transformed into MS11 and selected to obtain the AR::Kan MS11 strain (MS11AR::Kan).
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5

Cloning of Glycosyl Hydrolase Genes

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All oligonucleotide primers used for cloning are listed in S1 Table and were obtained from Integrated DNA Technologies (Coralville, IA, USA). For plasmid construction, the vector backbone and gene fragments were amplified by PCR using Q5 DNA polymerase (New England Biolabs, Ipswich, MA, USA) following the manufacturer’s protocol. DNA fragments were purified by agarose gel electrophoresis and assembled using Gibson Assembly mix (New England Biolabs, Ipswich, MA, USA) following the manufacturer’s protocol. All plasmids used in this study were verified by DNA sequencing and restriction enzyme digestion analysis and are listed in S2 Table.
The plasmids pCel3A and pGH3 were constructed by cloning the respective glycosyl hydrolases encoded by cel3A from Cellvibrio japonicus and CC_0968 from Caulobacter crescentus in pIND4-spec (pVector). The predicted localizations of Cel3A and CC_0968 are shown in S3 Table.
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6

Heterologous Expression of Terpene Synthases

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For in vivo diterpenoid synthase activity, 8 TSs listed in Table 1 were amplified by pETM11-fw and pETM11-rev using a pETM11-TS as a template containing homologous sequences at both ends for Gibson assembly [33 (link)]. IspAM22 (D2G, C155G) inserts were created by amplification of the ispA gene from E. coli DH5α with primers containing the desired base changes (S1 Table). A primer extension method was used to amplify the full-length gene which was inserted into pBbA2k-ispAM22-TS (for full list see S1 Table) by annealing at 50°C using Gibson assembly mix (NEB). For mono- or sesqui-terpene production pBbb2a-GPPS plasmid backbone was used for cloning and TSs (S1 Table) were amplified by pETM11-fw and pETM11-rev using a pETM11-TS as a template containing homologous sequences at both ends for Gibson assembly.
Genes encoding selected TS from different bacteria were codon optimised for expression in E. coli (S1 Table), synthesized, and sub-cloned into pETM11 with N-terminal His-tag (GeneArt, Life Technologies). Protein sequence of the selected TSs are shown S2 Table.
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7

Cloning and Expression in KL235

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Pfu Ultra II DNA polymerase was obtained from Agilent Technologies; restriction enzymes, T4 DNA ligase, and the Gibson Assembly mix were from New England Biolabs. In-Fusion cloning kit was from Clontech. The thermosensitive E. coli strain KL235 [14 (link)] was obtained from the Coli Genetic Stock Center (Yale University).
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8

Plasmid Constructs for TRPV4 and RhoA

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TRPV4-FLAG in pcDNA3.1 was previously described88 (link). TRPV4-GFP was generated by replacing the FLAG epitope tag with EGFP amplified from pEGFP-C1 (Clontech). TRPV4-M680K, TRPV4-R232C, TRPV4-R237L, TRPV4-R269C, TRPV4-I331F, TRPV4-D333G, TRPV4 P142A/P143L, TRPV4 121AAWAA125, RhoA E47A, and RhoA E54A with either FLAG or EGFP tags were generated by site directed mutagenesis using the Quikchange XL-II kit (Agilent, 200521) according to manufacturer protocols. TRPV4-mScarlet was generated from TRPV4-FLAG in pcDNA3.1 using Gibson assembly mix (New England Biolabs, E2611S) and PCR amplification of the mScarlet coding sequence from pmScarlet-C1 (Addgene, 85042). Primers used for mutagenesis and subcloning are listed in Supplementary Table 2. The following additional plasmids were obtained from Addgene: WT RhoA-GFP WT (12965), T19N RhoA-GFP (12967), Q63L RhoA-GFP (12968), WT RhoA-Myc (12962), T19N RhoA-Myc (12963), Q63L RhoA-Myc (12964), Cdc42-Myc (12972), RhoA2G-mTFP-mVenus (40176), mTFP-N1 (54521), mVenus-N1 (54640), and LifeAct-mCherry (67302). Expression plasmids for p63RhoGEF-mVenus and p63RhoGEF-Myc were a generous gift from Dr. Thomas Wieland (Universität Heidelberg). The expression plasmid for PACSIN1-Myc was a generous gift from Dr. Markus Plomann (University of Cologne).
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9

Cloning and Expressing R15 Mb Fusion Proteins

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R15 Mb was cloned either into CFP-tagged, pECFP-C1 for transient expression and pCW5.1 for stable cell expression using Gibson assembly. Briefly, R15 was PCR amplified from the from bacterial expression vector pHBT by two separate PCRs using 5′ Mb Gibson primer (GACGATGACGACAAGGGATCCGTTTCTTCTGTTCC) and a 3′ Mb Gibson primer (TCAGTTATCTAGATCCGGTGGATCCCTAGGTACGGTAGTT AATCGAGATTGG) in one reaction and 5′ Mb Gibson primer and 3′ pCW Mb Gibson primer (GGCGCAACCCCAACCCCGGCCTAGGTACGGTAGTTAATCGAGATTGG) in the other. The two resulting amplicons (325 and 320 bp respectively) were mixed with BamH1 digested vectors (pECFP-NS1 and pCW5.1-CFP-NS1) and ligated using Gibson Assembly Mix (New England Biolabs) and then used to transform E. coli. The resulting transformants were screened for inserts and sequenced to confirm mutants.
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10

Engineered Stem Cell Reprogramming

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The cDNAs from chicken POUV (POU5F3), SOX2, SOX3, KLF4, c-MYC, NANOG, and LIN28 were cloned, sequenced, inserted into the pGAE lentivirus or pPB transposon backbones, and deposited to Addgene. All constructs were generated using the Gibson Assembly Mix (NEB) and sequenced to validate the cDNA insertion. Viral ready-to-use stocks were purchased for the polycistronic pLentG-mKOSM lentiviral vector expressing mouse genes (Cell Biolabs) and for the Sendai viral vectors expressing the human genes (Cytotune Kit, Life Technologies). pMX reprogramming vectors were purchased from Addgene (nos. 13366, 13367, 13375, and 13370).
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