Idt codon optimization tool

Manufactured by Integrated DNA Technologies

The IDT codon optimization tool is a software application designed to assist users in optimizing the codon usage of DNA sequences. It analyzes the input sequence and provides recommendations for codon changes that can improve the expression of the encoded protein in a specified host organism.

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Lab products found in correlation

Gblock, by Integrated DNA Technologies (2 mentions) Pet28a vector, by Takara Bio (1 mentions) E coli bl21 de3 cells, by New England Biolabs (1 mentions) Pet28a vector, by New England Biolabs (1 mentions) Gblock, by Takara Bio (1 mentions) In fusion hd cloning kit, by Takara Bio (1 mentions) Histrap nickel column, by Cytiva (1 mentions) Lentiviral high titer packaging mix, by Takara Bio (1 mentions) Plvsin cmv pur, by Takara Bio (1 mentions) Lenti x 293t cells, by Takara Bio (1 mentions) Transit 293 transfection reagent, by Mirus Bio (1 mentions)

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Codon Optimization Tool

4 protocols using idt codon optimization tool

Optimized Mating Receptor Expression

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As detailed in table S1, some mating receptor ORFs were synthesized as codon-optimized genes for S. cerevisiae (see table S6), and others were cloned directly from the appropriate fungal genomic DNA (ATCC) or plasmid pLPreB using primers in table S5. Codon optimization was performed with the JCat Codon Adaptation tool (38 (link)) using the default setting for S. cerevisiae and further optimized for cloning with the IDT codon optimization tool (Integrated DNA Technologies). All receptor ORFs were incorporated into expression modules containing the S. cerevisiae TDH3 promoter and STE2 terminator (see table S4). For fluorescent assays using reporter strain yMJ183, receptor expression modules were cloned into low-copy plasmids derived from pRS416 (table S3). For lycopene biosensor strains, receptor expression modules were integrated at the STE2 locus.

Ostrov N., Jimenez M., Billerbeck S., Brisbois J., Matragrano J., Ager A, & Cornish V.W. (2017). A modular yeast biosensor for low-cost point-of-care pathogen detection. Science Advances, 3(6), e1603221.

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Codon Optimization and Cloning of Bacterial Genes

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Nucleotide sequences of acbK, and nine mck genes (the names, source and sequences of which are provided in Supplementary Table 1) were codon-optimized for E. coli K12 using the IDT codon optimization tool (Integrated DNA Technologies). gBLOCKs (Integrated DNA Technologies) of the codon-optimized genes were ordered with engineered 20-bp overlaps for cloning into a double-digested pET28a vector (using the restriction enzymes Notl and Ndel, New England Biolabs). Ligation of the gBLOCK into the linearized pET28a vector was performed using the In-Fusion HD cloning kit (Takara Bio), resulting in an N-terminal hexa histidine tag. The ligation product was then transformed into chemically competent E. coli BL-21 (DE3) cells (NEB) and plasmids were purified from transformants and verified by sanger sequencing.

Balaich J., Estrella M., Wu G., Jeffrey P.D., Biswas A., Zhao L., Korennykh A, & Donia M.S. (2021). The human microbiome encodes resistance to the antidiabetic drug acarbose. Nature, 600(7887), 110-115.

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Nanobody NbC1 and NbF2 Production

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The gene for nanobody C1 (NbC1) and F2 (NbF2) and were codon-optimized using the IDT Codon Optimization Tool, synthesized as a ready-to-clone gene fragment (Integrated DNA Technologies), and cloned into the phagemid vector pADL-23c. The nanobodies were produced as previously described (Huo et al., 2021 (link)). Briefly, the plasmid was transformed into the WK6 E. coli strain and protein expression induced by 1 mM IPTG grown overnight at 28°C. Periplasmic extract was prepared by osmotic shock, and the nanobody protein was purified with a 5 mL HisTrap nickel column (Cytiva), followed by size exclusion with a Hiload 16/60 Superdex 75 column.

Nutalai R., Zhou D., Tuekprakhon A., Ginn H.M., Supasa P., Liu C., Huo J., Mentzer A.J., Duyvesteyn H.M., Dijokaite-Guraliuc A., Skelly D., Ritter T.G., Amini A., Bibi S., Adele S., Johnson S.A., Constantinides B., Webster H., Temperton N., Klenerman P., Barnes E., Dunachie S.J., Crook D., Pollard A.J., Lambe T., Goulder P., Paterson N.G., Williams M.A., Hall D.R., Mongkolsapaya J., Fry E.E., Dejnirattisai W., Ren J., Stuart D.I, & Screaton G.R. (2022). Potent cross-reactive antibodies following Omicron breakthrough in vaccinees. Cell, 185(12), 2116-2131.e18.

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Lentiviral Expression of TMPRSS Proteases

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The human TMPRSS2, human TMPRSS11D, human TMPRSS11E, and human TMPRSS13 genes were individually cloned into the self-inactivating lentiviral vector plasmid CSII-CMV-MCS-IRES2-Bsd (48 (link)), which was kindly provided by H. Miyoshi (RIKEN BRC, Tsukuba, Japan). Codon-optimized TMPRSS2 and TMPRSS11D genes were designed by the IDT codon optimization tool (Integrated DNA Technologies, Coralville, IA), were synthesized as custom-made DNA fragments (gBlocks; Integrated DNA Technologies), and were cloned into CSII-CMV-MCS-IRES2-Bsd and pLVSIN-CMV Pur (TaKaRa Bio, Kusatsu, Japan), respectively. For the preparation of lentivirus particles, the lentiviral vector plasmid and lentiviral high titer packaging mix (TaKaRa Bio) were cotransfected into Lenti-X 293T cells (TaKaRa Bio) with TransIT-293 transfection reagent (Mirus Bio, Madison, WI). The culture supernatant containing lentiviral vectors was filtered through a Minisart 0.45-μm-pore size filter (Sartorius, Göttingen, Germany) and then inoculated to MA104 cells in the presence of 10 μg/ml Polybrene. To generate T2T11D cells, MA104 cells were inoculated with lentiviral vectors expressing TMPRSS2 and TMPRSS11D and were selected with blasticidin S (for TMPRSS2-expressing cells) and puromycin (for TMPRSS11D-expressing cells).

Sasaki M., Itakura Y., Kishimoto M., Tabata K., Uemura K., Ito N., Sugiyama M., Wastika C.E., Orba Y, & Sawa H. (2021). Host Serine Proteases TMPRSS2 and TMPRSS11D Mediate Proteolytic Activation and Trypsin-Independent Infection in Group A Rotaviruses. Journal of Virology, 95(11), e00398-21.

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