FAQsFrequently Asked Questions1. Why order a synthetic gene from DNA2.0 instead of cloning and manipulating it myself?
DNA-2-Go™ custom gene synthesis is faster, more cost efficient and reliable than performing the cloning yourself. See also our discussion in Newsletter Q4/2003 on the advantages of outsourcing gene synthesis in biotechnology. 2. Can you really deliver a custom synthetic gene in eight business days?
We take great pride in our current average time from receiving an order to shipping the product, which is less than ten business days for genes up to 1.5 kb. We guarantee that genes up to 1.5 kb will be delivered in 15 business days. Failing delivery within the guaranteed limit is a very rare event. 3. Is there a faster gene synthesis service available?
Yes, our expedited custom gene synthesis service, DNA-2-Day™, is twice as fast as our standard gene synthesis speed of 8–10 days. A one kb gene will be shipped in only five business days. 4. How do I get my synthetic gene designed just the way I want?
Please contact us for assistance with any synthetic gene design issues. We have years of experience designing and constructing synthetic genes with many different features, for use in various organisms. Most of our design assistance is free of charge. For more complicated bioinformatics consulting, please contact us for a quote. Also, feel free to download our free Gene Designer software, which allows you to easily design your synthetic genes on your own. 5. Which vector will my synthetic gene be cloned into?
Our own series of vectors, the pJ vectors, covers a wide range of features. 6. What antibiotics concentration should I use for the pJ series of vectors?
30 µg/ml kanamycin for kanr plasmids, and 50 µg/ml carbenicillin for ampr plasmids. 7. Can I have the synthetic DNA fragment cloned into my own vector?
The synthetic DNA fragment can be delivered in your vector of choice for an additional charge. Please provide 5 µg of purified plasmid DNA, plasmid sequence and selection information, and detailed information of the required cloning sites. You also need to be fully licensed to use the vector. This service is not guaranteed, as it depends on information and material not within our control. Please inquire for a quote. 8. How large synthetic DNA fragments can you make?
There really is no upper limit. We have made synthetic DNA fragments of over 30 kb and routinely make genes in the 5–7 kb range. 9. Why should I codon optimize my human gene for mammalian cell expression?
It often makes a big difference to the protein expression level. This is probably because codon optimization changes the DNA/mRNA sequence and removes intragenic regulatory elements as well as adjusting the codon bias. Remember, genes have often evolved to be tightly regulated, not for maximal expression 10. Any published examples on how codon optimization helps protein expression?
Yes, many. Please, enjoy: There are also many non DNA2.0 references available. A partial list can be found in table 2 of the TibTech paper above, as well as in the research community list of publications. 11. Why aren’t all optimized codons the most abundant codon for that amino acid?
Upon codon optimization you typically want the codon bias distribution for your gene to be similar to that of highly expressed genes in your host organism. This ensures that you will not deplete the tRNA pool corresponding to the most abundant codon, as well as avoid secondary mRNA structures, repeats etc. For a detailed discussion, see: “Gene Designer: A synthetic biology tool for constructing artificial DNA segments.” Published in the 2006, 7:285 issue of BMC Bioinformatics 12. What plates/media do I need to grow up the strain with the synthetic gene?
We recommend plates and media from Teknova. The Teknova products listed here have been tested and validated to work reliably with DNA2.0 synthetic genes. Gene Designer13. Where can I download Gene Designer?
Here 14. How do I initiate a new design using Gene Designer?
Click on ‘Create new design icon’ in upper left corner or choose ‘New’ from the File pull down menu or press Ctrl N. 15. How do I create a new sequence in the design window?
Click and drag (or double-click) on the appropriate object New AA (for amino acid seq.), New DNA (for DNA seq) or New ORF (for linked aa and nt sequence). 16. How do I save my own objects?
Create object in design window. Then drag it into Custom object (lower left corner) 17. How do I delete my custom objects?
Click on it to mark it and then click delete. 18. What software can I use to read my DNA sequencing tracefiles?
Free DNA sequencing softwares can be downloaded here: Chromas, Edit View, FinchTV and BioEdit 19. Why don't I get the same sequence if I redo the optimization on my
protein?
The optimization module of Gene Designer is based on a Monte Carlo algorithm, i.e the same protein sequence can be optimized thousands of times and every time come up with a new unique and equally 'good' solution based on the existing design constraints. |
