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I would like to synthesize a 3.4kb gene (originally isolated from soil bacteria) and transform it into E. coli. There are several companies (DNA2.0, GeneScript, BlueHeron) which will synthesize the gene for you. I would like to know how these companies (or others) compare with each other in terms of:

  1. Codon optimization - most of the companies are going to codon optimize the sequence and thus increase the protein expression in the desired host. Recently I learned that there are different algorithms that can be applied. I am mostly interested in how the codon-optimization is performed in the different companies and whether there are some direct comparisons of protein expression between them.

  2. cost per base - I would like to find the cheapest one. In general, the cost of gene synthesis usually depends on the size of the fragment, as well as the complexity of the sequence. But on the other hand, DNA2.0 can synthesize 1kb fragment and 5kb fragment for the same price.

  3. Turn-around time - which company will synthesize the fragment the fastest? I think that this mainly depends on size. Of course I have an option of ordering 3 x 1.1kb fragments and joining them myself, but then I have to sequence-verify the final product. So, I need to find the trade-off.

Please, keep in mind that I am not asking about your favorite company, but about specific characteristics of the companies.

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    $\begingroup$ The question about price is probably too localized, it changes too fast and those questions are discouraged across the SE network. For the turn-around time you'll only get anecdotes here, which probably won't help much. I'd focus the question on the codon optimization, though I fear the answer will be that the algorithms are prorietary and they won't tell you how they work exactly. $\endgroup$
    – Mad Scientist
    Commented Jan 30, 2012 at 7:22
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    $\begingroup$ These are good points. I would thing that the information about cost will be valid once you match it with the date on which the answers are posted. As for turn-around time, I came across a blog, where there was a plot of turn-around time vs length of DNA construct for several companies, so average values can be definitely taken into account. But mostly, I really would love to know about their codon-optimization algorithms but perhaps you are right and they are proprietary. Hopefully, the main ideas are not. $\endgroup$
    – Gergana Vandova
    Commented Jan 30, 2012 at 18:30

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Are you working in academia? It might be worthwhile to call the companies directly and see if there is a discounted rate for your institution (another lab or department may have already set something up).

You won't be able to get information on the different algorithms if they are proprietary. However considering that codon usage data is public and shared knowledge, I can't imagine that the different algorithms are that much different. I think there are some tricks for choosing certain codons near the transcription start site in some organisms? From what I hear, the algorithms are constantly changing. I could tell you how my E. coli optimized gene from GenScript worked two years ago, but they'd probably design it differently now.

Okay - GenScript calls their algorithm "proprietary", so they are not sharing the details. DNA2.0 says their algorithm is patented, so it's out there for inspection. They published a PLOS paper on their E. coli algorithm: Welch et al..

Although, maybe all they do these days is spit out codon sequence randomly:

The results obtained in this study indicate that the codon randomization method is a superior strategy for codon optimization. A significant improvement in protein expression was obtained for the largely established process of chymosin production, showing the power of this strategy to reduce production costs of industrial enzymes in microbial hosts. (Menzella 2011)

Stitching smaller synthesized fragments works well if you're pressed for time, but it's usually more expensive. However, sometimes these companies do special pricing on synthesis for <1kb, which makes stitching a great choice. Turnaround is generally faster for three 1kb fragments than one 3kb fragment.

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  • $\begingroup$ Thanks for your answer @Amy. So, you have experience with GenScript. I would like to ask you some specific questions. Would you mind emailing me so that I don't extend my comment into long discussion? My email is [email protected] $\endgroup$
    – Gergana Vandova
    Commented Feb 1, 2012 at 23:28
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Here is a blog post from Ginkgo BioWorks that graphs the turn-times from 3 major suppliers: http://blog.ginkgobioworks.com/2012/01/14/commercial-gene-synthesis/

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  • $\begingroup$ Thanks, I already looked at it, but yeah, it is really useful. $\endgroup$
    – Gergana Vandova
    Commented Feb 2, 2012 at 6:38
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And here is a blog post from Reportergene that compares actual prices, even do I agree with Mad Scientist that the question about prize is probably too localized.

http://www.reportergene.com/2011/08/gene-synthesis-review.html

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