Geneart gene synthesis service

Manufactured by Thermo Fisher Scientific

Sourced in United States, Germany

The GeneArt gene synthesis service is a laboratory tool that enables the custom synthesis of DNA sequences. It allows users to design and order synthetic DNA fragments for a variety of applications in molecular biology and genetic engineering.

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40 protocols using geneart gene synthesis service

Anti-Sperm IgG Antibody Expression

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The variable light (V L ) and variable heavy (V H ) DNA sequences for anti-sperm IgG antibody were obtained from the published sequence of H6-3C4 mAb. [18, 19] For the construction of expression vector encoding light chain (LC), a gene fragment consisting of V L and C λ DNA sequences was codon-optimized and synthesized using GeneArt® gene synthesis services (ThermoFisher Scientific) and cloned into PVX viral backbone (Icon Genetics). [20] For the construction of an expression vector containing IgG1 heavy chain (HC), a gene fragment consisting of V H and C H 1-C H 2-C H 3 DNA sequences was codon-optimized and synthesized using GeneArt® gene synthesis services (ThermoFisher Scientific) and cloned into TMV viral backbone (Icon Genetics). [20] For the construction of expression vector containing FIF HC, a
DNA sequences was synthesized using GeneArt® gene synthesis services (ThermoFisher Scientific) and cloned into TMV viral backbone (Icon Genetics).

Shrestha B., Vincent K.L., Schaefer A., Zhu Y., Vargas G., Motamedi M., Swope K., Morton J., Simpson C.A., Pham H., Brennan M.B., Pauly M., Zeitlin L., Bratcher B., Whaley K.J., Moench T.R., & Lai S.K. (2021). Hexavalent Sperm-Binding IgG Antibody Released from Self-Dissolving Vaginal Film Enables Potent, On-Demand Non-Hormonal Female Contraception.

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Cloning Gymnosperm bZIP 5'-Leader Sequences

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GeneArt^® gene synthesis service (Life Technologies, Carlsbad, CA, USA) was used to custom synthesize the 5′-leader sequences Arabidopsis S1 bZIP homologous genes from gymnosperm species Picea abies and Pinus taeda. Synthesized 5′-leader sequences contained the full 5′-leader, starting 500 nucleotides upstream of the arabidopsis bZIP11 5′uORF sequence. Gateway^® cloning sites attL1 and attL2 flanked the sequences, and the resulting constructs were cloned in the pMK-RQ vector backbone. Construct sequences are shown in the Supplementary Methods. Sequences were cloned into the pUC19 based p35S-ccdB-fLUC destination vector24 (link), using Gateway^® LR cloning according to manufacturer instructions (Invitrogen, ThermoFisher Scientific, Waltham, USA) to create transient LUC expression vectors.

Peviani A., Lastdrager J., Hanson J, & Snel B. (2016). The phylogeny of C/S1 bZIP transcription factors reveals a shared algal ancestry and the pre-angiosperm translational regulation of S1 transcripts. Scientific Reports, 6, 30444.

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NCAM2 miRNA Expression and Validation

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The NCAM2 miR expression vector was developed using the BLOCK-iT PolII miR RNAi expression vector kit (Life Technologies) and designed to co-express NCAM2-specific miRNA together with emerald GFP. The following oligonucleotides were inserted into the BLOCK-iT PolII miR RNAi expression vector:
top: 5′-TGC TGT TAA GGT CAT CTC TTC TCC TCG TTT TGG CCA CTG ACT GAC GAG GAG AAG ATG ACC TTA A-3′;
bottom: 5′-CCT GTT AAG GTC ATC TTC TCC TCG TCA GTC AGT GGC CAA AAC GAG GAG AAG AGA TGA CCT TAA C-3′.
Negative control miR vector was from Life Technologies. Immunocytochemical labelling confirmed that transfection with the NCAM2 miR vector resulted in an over 80% reduction in expression of NCAM2 in cultured hippocampal neurons at 24 h after transfection (Supplementary Fig. 5).
DNA coding for the full-length transmembrane human NCAM2 and NCAM2 with aspartic acid 693 exchanged to alanine (NCAM2D693A mutant) was synthesized using the GeneArt Gene Synthesis service (Life Technologies) and subcloned into the pcDNA3 vector. Both constructs contained an HA tag inserted at the N-terminus of the protein. The expression of both constructs was confirmed by western blot and immunocytochemistry (Supplementary Fig. 2).
Hippocampal neurons were transfected before plating by electroporation using the Neon transfection system (Life Technologies).

Leshchyns'ka I., Liew H.T., Shepherd C., Halliday G.M., Stevens C.H., Ke Y.D., Ittner L.M, & Sytnyk V. (2015). Aβ-dependent reduction of NCAM2-mediated synaptic adhesion contributes to synapse loss in Alzheimer's disease. Nature Communications, 6, 8836.

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Aspergillus Cellobiohydrolase I Gene Sequence

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Example 42

The genomic DNA sequence and deduced amino acid sequence of the Aspergillus fumigatus Af293 GH7 cellobiohydrolase I gene is shown in SEQ ID NO: 87 and SEQ ID NO: 8, respectively. Genomic sequence information was generated by The Institute for Genomic Research, Rockville, Md. 20850, USA and published by Nierman, W. C. et al., 2005, Nature 438 (7071): 1151-1156. The amino acid sequence of the full-length cellobiohydrolase I is publicly available from the National Center for Biotechnology Information (NCBI) and annotated as GenBank: EAL89006.1 The cDNA sequence and deduced amino acid sequence of the Aspergillus fumigatus cellobiohydrolase I gene is shown in SEQ ID NO: 88 and SEQ ID NO: 8, respectively.

Based on the publicly available amino acid sequence, a codon-optimized synthetic gene encoding the full-length cellobiohydrolase I was generated for Aspergillus oryzae expression based on the algorithm developed by Gustafsson et al., 2004, Trends in Biotechnology 22 (7): 346-353. The codon-optimized coding sequence (SEQ ID NO: 89) was synthesized by the GENEART® Gene Synthesis service (Life Technologies Corp., San Diego. Calif., USA) with a 5′ Bam HI restriction site, a 3′ Hind III restriction site, and a Kozac consensus sequence (CACC) situated between the start codon and the Bam HI restriction site.

US10676769B2. Cellobiohydrolase variants and polynucleotides encoding same (2020-06-09). Novozymes A/S [DK]. Inventors: Peter Westh [DK], Kim Borch [DK], Trine Soerensen [DK], Michael Windahl [DK], Brett McBrayer [US].

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Expressing TLRs and Unc93b1 in Cell Lines

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AccuPrime Pfx DNA polymerase (Invitrogen) was used for site directed mutagenesis using the QuikChange II Site-directed Mutagenesis protocol from Agilent Technologies. The following murine stem cell virus (MSCV)-based retroviral vectors were used to express Unc93b1, TLR9, TLR7, and TLR3 in cell lines: MSCV-PuromCherry (IRES-PuromycinR-T2A-mCherry), MSCV2.2 (IRES-GFP), MSCV-Thy1.1 (IRES-Thy1.1), and MIGR2 (IRES-hCD2). 3×FLAG (DYKDHDGDYKDHDIDYKDDDDK) was fused to the C-terminus of Unc93b1. TLR9, TLR7, and TLR3 were fused to HA (YPYDVPDYA) at the C-terminal end. TLR7 sequence was synthesized after codon optimization by Invitrogen’s GeneArt Gene Synthesis service as previously described^{10 (link)}. TLR9 chimeras of the juxtamembrane and transmembrane regions were previously described^{4 (link)}.

Majer O., Liu B., Woo B.J., Kreuk L.S., Van Dis E, & Barton G.M. (2019). Release from Unc93b1 reinforces the compartmentalized activation of select TLRs. Nature, 575(7782), 371-374.

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Expressing TLRs and Unc93b1 in Cell Lines

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Majer O., Liu B., Woo B.J., Kreuk L.S., Van Dis E, & Barton G.M. (2019). Release from Unc93b1 reinforces the compartmentalized activation of select TLRs. Nature, 575(7782), 371-374.

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Synthetic ZIKV Promoter Optimization

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Cryptic E. coli promoters were predicted with the publicly available Neural Network promoter program from the Berkeley Drosophila Genome Project [20 ,21 (link)] similar to an earlier report [11 (link)]. The ZIKV sequences were analysed for CEPs from nucleotide position 1–2683 for H/PF/2013 and 1–2664 for MR766. Putative promoters with a score >0.85 were eliminated by silent nucleotide exchanges introduced into the −10 regions (Pribnow/Schaller box) and/or the −35 regions (Figure S1). CEPs in the 5′UTR were not modified to avoid changes in RNA secondary structures (Acosta et al., 2014 [22 ]). In addition, in order to facilitate assembly and reverse genetic studies, several restriction sites were inserted or removed by silent nucleotide exchanges (Tables S1 and S2). The T7 promoter sequence (5′-TAATACGACTCACTATAG-3′) was inserted upstream of the 5′UTR to allow for in vitro transcription of viral RNA. The final sequences were re-analysed with the Neural Network promoter program to confirm that the scores were below 0.85. The sequences were ordered as synthetic DNA fragments (four fragments/strain) from the GeneArt Gene Synthesis service (Invitrogen, Darmstadt, Germany).

Münster M., Płaszczyca A., Cortese M., Neufeldt C.J., Goellner S., Long G, & Bartenschlager R. (2018). A Reverse Genetics System for Zika Virus Based on a Simple Molecular Cloning Strategy. Viruses, 10(7), 368.

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Cloning of acrA and acrE Mutants

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The acrA and acrE point mutants were generated using the GeneArt^Ⓡ Gene Synthesis Service (Invitrogen, Germany) and subsequently cloned into the pACYC177 plasmid using the Subcloning Service (Invitrogen). All plasmids were sequenced to check for the presence of the desired point mutations and to ensure there were no unwanted secondary mutations.

Alav I., Bavro V.N, & Blair J.M. (2021). Interchangeability of periplasmic adaptor proteins AcrA and AcrE in forming functional efflux pumps with AcrD in Salmonella enterica serovar Typhimurium. Journal of Antimicrobial Chemotherapy, 76(10), 2558-2564.

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Recombinant PD-L1 Extracellular Domain Expression

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The construct carrying the extracellular domain of PD-L1 (Phe19-Thr239) with C-terminal twin-Strep-10x His dual tag followed by a stop codon was synthesized using GeneArt Gene Synthesis service (Invitrogen, Carlsbad, CA) with SgfI and MluI restriction sites at the beginning and the end of the ORF sequence, respectively. For mammalian expression, the ORF was subcloned to pCM6-Entry vector (Origene, Rockville, MD) and transfected to wild-type MDA-MB-231 cells using Lipofectamine 3000 (Invitrogen) in serum-free OptiMEM medium (Invitrogen) according to manufacturer’s instructions. The conditioned media were harvested 72 hrs post-transfection and subjected to IMAC purification as described below.

Benicky J., Sanda M., Kennedy Z.B., Grant O.C., Woods R.J., Zwart A, & Goldman R. (2020). PD-L1 glycosylation and its impact on binding to clinical antibodies. Journal of proteome research, 20(1), 485-497.

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Generation and Cloning of acrA and acrE Mutants

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The acrA and acrE point mutants were generated using the GeneArt Gene Synthesis Service (Invitrogen, Germany) and subsequently cloned into the pACYC177 plasmid using the Subcloning Service (Invitrogen, Germany). All plasmids were sequenced to check for the presence of the desired point mutations and to ensure there were no unwanted secondary mutations.

Alav I., Bavro V.N., & Blair J.M.A. (2021). Interchangeability of Periplasmic Adaptor Proteins AcrA and AcrE in forming functional efflux pumps with AcrD in Salmonella Typhimurium.

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