Synthetic Biology

SGI-DNA is a subsidiary of Synthetic Genomics, Inc. (SGI), specializing in development, manufacturing, and commercialization of synthetic DNA. The IDT partnership with SGI-DNA will uniquely enable the research community by providing a complete solution from short genes to very large synthetic constructs with an unprecedented, fast delivery time.

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Custom Gene Synthesis

IDT and SGI-DNA have partnered to offer custom gene synthesis. Synthetic gene products manufactured by IDT and SGI-DNA can be ordered through the IDT website, allowing researchers to save money spent on construction and cloning, and saving significant time and effort by outsourcing the production of hard-to-clone sequences that often result in repeated failures.

All genes are constructed using the highest quality oligonucleotides from IDT. Genes arrive in a plasmid cloning vector and are ready for use in a variety of applications.

Sequence information is always secure and confidential at IDT. Non-disclosure agreements are available through IDT’s legal services upon request.



Gene sequences with added complexity (such as homopolymeric runs, critical hairpin structures or G/C content), which can interfere with assembly and/or sequencing performance may result in extra service charges. For more information about potential types of complexity, please see the Overview tab.

ProductPricing
MiniGene 25-500 bp$225.00 USD
Gene 501-1500 bp$0.45 USD / bp
Gene 1501-3000 bp$0.45 USD / bp
Gene 3001-5000 bp$0.60 USD / bp
Gene 5001+ bpInquire for Pricing
Product
Typically Shipped 1
MiniGene 25–500 bp  8 Business Days
Gene 501–1500 bp
12 Business Days
Gene 1501–3000 bp 18 Business Days
Gene 3001–5000 bp
25 Business Days
Gene 5001+ bp
Inquire


  1. The time it takes to make a gene is dependent on length, complexity, and vector choice. >85% orders are ready to ship within the number of business days indicated above. Sequences that are unstable and/or toxic to E. coli can substantially affect delivery times.

How to order Gene and MiniGene™ synthesis:

Single gene entry

  1. From the Ordering tab, click on the Order Genes Now button and select the MiniGene or Genes ordering tool according to gene size.
  2. Copy and paste, or enter your desired DNA sequence using the A, C, G, and T bases only. Degenerate (mixed bases) or modified bases are not offered with our synthetic genes products. Alternatively, customers may enter their amino acid sequence, consisting of one letter codes, into the Codon optimization tool. 
  3. Codon optimization can be performed for a variety of organisms based on either a nucleotide sequence or an amino acid sequence. More information about codon optimization  is provided below.
  4. IDT provides synthetic genes ≤5000 bp in optimized IDT cloning vectors with either ampicillin or kanamycin resistance. In addition, for in vitro transcription applications, pIDTBlue may be selected for genes ≤1500 bp in length. Information about these vectors is available on the Vectors tab. Genes >5000 bp will be provided in BACs.
  5. After submitting your order, the gene request will be reviewed for the following characteristics which may interfere with synthesis, assembly, or sequencing performance. Potential issues include:

      • Secondary structure: hairpins >10 bases and G/C-rich secondary structure
      • Repeats and homo-polymeric runs: long repeats, >10 bases for G/C, or >30 bases for A/T
      • Overall GC Content >65% and regional GC content <25%
      • Restriction site duplications and Dam/Dcm Methylation sites that may interfere with digestion by restriction endonuclease
      • If the sequence does not pass the screening criteria, you will be contacted by a gene services specialist to determine the best way to proceed

Multiple gene entry

From the Ordering tab, click on the Order Genes Now button and select the Multiple Gene Entry, or Paste Gene Entry ordering tool.

Follow the instruction and/or look up Example Excel files


Biosecurity review: Each gene will be screened to identify regulated and other potentially dangerous pathogen sequences and must be accompanied by a hazard disclosure statement from the customer. IDT reserves the right to refuse any order that does not pass this screen.

Codon Optimization Tool

IDT offers free software in our SciTools™ Suite of online tools to help with the design of gene constructs for multiple molecular biology applications. The recently updated Codon Optimization Tool can help with the design of synthetic constructs, including gBlocks® Gene Fragments to meet your application needs.

With the Codon Optimization Tool you have the ability to optimize a protein coding sequence that is derived from one species for expression in another, you can choose how many results you want to view, and there is the option to manually adjust individual codons within the optimized sequence.

Note: Confirm that the final, optimized sequence is what you require prior to placing your order.The Codon Optimization Tool ranks the least complex sequence as the first result. If your sequence contains repeated motifs or is particularly GC rich, choosing the least complex sequence may improve the manufacturing success of the construct, as well as its use in some downstream applications. 

Sequence Verification

All inserts for Genes and MiniGene Synthesis products are sequence verified on both strands prior to shipping. For genes ≤5000 bp, Sanger sequencing information including chromatograms, a plasmid map, and a FASTA file are available to the customer by logging into their online IDT customer account. In some cases, Sanger sequencing may be substituted with a  Illumina® MiSeq® system data.

A sequencing certificate of analysis will be available for genes will be provided genes ≥5001 bp.

  • To download your sequence information or certificate of analysis, login to your account, highlight the Order tab, and select Order History.  Locate your order number in the order history and expand the order using the plus button. Select the PDF Spec Sheet from the right hand column.


Guaranteed yields

For genes ≤5000 bp, IDT will provide 4 µg of purified, double-stranded DNA in a circularized plasmid, delivered dried down.

For genes >5000 bp, provided in a BAC, 1µg of material will be delivered, dried down.

Confidentiality

All gene information, including sequence entry and choice of parameters, is confidential at IDT.

IDT Cloning Vectors

All synthetic gene products manufactured by IDT and SGI-DNA are delivered in a vector, ready to be transformed into E. coli.

“Best-Fit” Vectors for Genes ≤5000 bp

Occasionally, during cloning protocols, a desired DNA insert will prove to be incompatible with a predefined vector due to unforeseen cloning or toxicity issues. This can cause unpredictable delays in manufacturing and delivery of synthetic genes to researchers.

In order to optimize manufacturing and delivery time, synthetic genes ≤5 kb in length will be provided in a “best-fit” IDT cloning vector. A choice of either ampicillin or kanamycin selection markers is available.

Providing synthetic genes ≤5 kb in best-fit IDT cloning vectors is the most reliable way for IDT to provide you with your gene of interest in the shortest time. Your high-quality, synthetic gene can then be subcloned into the vector of your choice using a variety of methods. IDT cloning vectors are provided in the table below. The identity of the cloning vector used, its sequence, and insertion site will be confirmed in the documentation accompanying the product.

pIDTBlue Option for Genes ≤1500 bp

Genes ≤1500 bp in length may be ordered in pIDTBlue when in vitro transcription of the gene is intended. Similar to the pBluescript II phagemid vector, pIDTBlue contains a multiple cloning site in the alpha fragment of the LacZα gene and T3 and T7 promoters flanking the insertion site. PIDTBlue is Ampicillin resistant.

BACs and Genes >5000 bp

Genes >5000 bp are provided in a BAC with a chloramphenicol resistance marker. Instructions on how to handle and use BAC vectors can be found here.


Vector name
Size Selection marker Application Sequence
pUCIDT (Amp) 2752 bp Ampicillin Cloning
pUCIDT (Amp).txt
pUCIDT (Kan) 3409 bp Kanamycin Cloning
pUCIDT (Kan).txt
pIDTSmart (Amp)
2056 bp Ampicillin
Cloning pIDTSmart (Amp).txt
pIDTSmart (Kan) 1962 bp Kanamycin Cloning
pIDTSmart (Kan).txt
pIDTBlue 
2951 bp Ampicillin
In vitro transcription pIDTBlue.txt
pBRIDT 3170 bp Ampicillin Cloning
pBRIDT.txt
BAC 2 6944 bp Chloramphenicol
Cloning BAC 2.txt
 BAC 3 
8322 bp Chloramphenicol
Cloning BAC 3.txt

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Plasmid Resuspension

    1. Centrifuge the tube prior to opening to ensure that the DNA is at the bottom of the tube.
    2. Resuspend DNA in 80 µL of IDTE (10 mM Tris, 0.1 mM EDTA) buffer (pH 7.5–8.0) to reach an approximate concentration of 50 ng/µL for a stock concentration. Vortex for 20 seconds.
    3. Incubate the tube at room temperature for 30 minutes.
    4. Centrifuge for 1 minute.
    5. To dilute for transformation, add 2 µL of the stock concentration to 999 µL of water to reach an approximate concentration of 0.1 ng/µL. Use 1–2 µL of this working dilution for each transformation.

Recommended Storage

  • Store hydrated DNA at –20°C.
  • Lyophilized DNA is stable at room temperature for approximately 3 months. We recommend storing at –20°C for longer periods of time.

Resuspension and Storage Conditions

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Some common techniques used with our plasmids are listed below. For a more complete description of these and other methods please refer the  following publication:
Sambrook, Joseph. and Russell, David W. and Cold Spring Harbor Laboratory.  Molecular cloning : a laboratory manual, Joseph Sambrook, David W. Russell  Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y. :  2001Transformation (Chemical)

Transformation protocols vary based on the manufacturer and the cell line. For best results we recommend you follow a protocol optimized for the particular cells you are using. Below is a general protocol applicable for many commercial E. coli cell lines such as DH5α or XL1 Blue.

Transforming E. Coli

  1. Place frozen, competent cells and pre-labeled tubes on ice
  2. Pre-warm the water bath to 42°C
  3. Once cells are thawed on ice, gently aliquot 25 µL of XL1 Blue cells (Stratagene) to each of the pre-chilled tubes. Keep all the tubes on ice
  4. Add 2 µL of the diluted plasmid (0.4ng) to the cells and gently swirl the cells with pipette tip
  5. Incubate on ice for 30 minutes
  6. Heat shock tubes for 45 seconds in 42°C hot bath
  7. Return tubes to ice for 2 minutes
  8. Add 250 µL of SOC media to each tube and place tubes in a 37°C shaking incubator for 1 hour
  9. Pre-warm agar plates to 37°C in incubator
  10. Spread 125 µL of cells on agar plates containing the appropriate antibiotic
  11. After spreading cells, let plates sit for approximately 10 minutes at room temperature. Then place the plates inverted in 37°C incubator for 12–24 hours.

Inoculation and plasmid isolation

  1. For a large number of colonies, use a 2.2 mL deep well plate and add 1.6 mL of LB Broth with the appropriate antibiotic. For a small number of colonies, use a 14 mL round bottom culture tube and add 2 mL of LB Broth with the appropriate antibiotic
  2. Touch the colony with a toothpick or pipette tip and place it in the broth
  3. Cover with a gas permeable lid and place in a 37°C shaking incubator for 12–20 hours.
  4. Plasmid DNA can be purified from broth cultures by a variety of commercial kits or by the alkaline lysis method listed in the Molecular Cloning  manual by Sanbrook et al. listed above.

Restriction enzyme Digestions

The standard in-house digestion protocol is below:

Incubate for 1 hour at the temperature recommended by the enzyme manufacturer. Take 2–5 µL of the digested sample, add loading dye, and run on a gel to verify that the digestion took place. In separate lanes, also run a ladder to verify the size of the product and a sample of undigested product as a control.

* The length of running time for the gel will depend on the size of the digested insert. Smaller inserts require shorter run times or the product will run off the gel.

* The enzyme should not be more than 1/10th of total reaction

 

DNA 400 ng
Buffer 5 µL
Water X µL
Enzyme(s) 1 µL each
Total Volume 50 µL

Molecular Biology

Gene Biosecurity

Integrated DNA Technologies screens the sequence of every gene order that is received to identify regulated and other potentially dangerous pathogen sequences, and to verify that IDT’s gene customers are legitimate scientists engaged in beneficial research.

IDT is among the five founding members of the International Gene Synthesis Consortium (IGSC), and helped to create the IGSC’s Harmonized Screening Protocol. The Harmonized Screening Protocol describes the gene sequence and customer screening practices that IGSC member companies employ to prevent the misuse of synthetic genes. IDT takes the steps set out in the Harmonized Screening Protocol to screen the sequences of ordered genes and the prospective customers who submit those orders.

For more information about the IGSC and the Harmonized Screening Protocol, please visit the website at http://www.genesynthesisconsortium.org.

In October of 2010, the United States government issued final Screening Framework Guidance for Providers of Synthetic Double-Stranded DNA, describing how commercial providers of synthetic genes should perform gene sequence and customer screening. IDT and the other IGSC member companies supported the adoption of the Screening Framework Guidance, and IDT follows that Guidance in its application of the Harmonized Screening Protocol. For more information, please see 75 FR 62820 (Oct. 13, 2010), or http://federalregister.gov/a/2010-25728.