DNA synthesis can be cheap, but don't get fooled by the ads: be aggressive and make them negotiating against themselves.
I had this collateral project in mind for a while, but to realize it, I should have taken a serious cloning effort, which was asking energies not available at the moment. For my scope, I needed to have in the same plasmid a reporter gene, a protein fusion, some responsive elements made from very repetitive elements, different polyA and stop codons to minimize the interference of the different ORFs, a multiple cloning site to subclone protein mojeties in frame with a second protein. Moreover, I was flanking my construct with selected restriction sites for subsequent adenovirus production, and I had to check that no others restriction sites were present in the whole plasmid. A nightmare of 3000 base pairs.
Not surprisingly, I postponed this low-priority project for almost two years. Then, at a certain point, comes Craig Venter, who used gene synthesis to make up an entire genome. Ah-ha! I searched in google "Gene Synthesis" and found encouraging ads around $0.29/bp (check now for updates).
I had never used GS before, and I was lazy to ask quotes and procedures to
piranha customer services, but the MrGene site made me happy. It just required to paste my sequence and it was giving a quote in real-time. So, I assembled my sequence in Word (don't scream, it was my best choice to annotate with colors the different gene parts, do you have alternatives?), paste it into MrGene and get a pdf quote back. The site informed me that the quote was higher than the standard because of the lenght (3000 bp) and the repetitive sequences, but was fair around $0.65/bp. For me it was fine, I just needed a few weeks to find the money (~ $2000), to discuss adenovirus production with collaborators and I was ready to start.
When I went back, MrGene was closed as it was acquired by Invitrogen. I asked again a new quote: ~ $3000! ($1/bp) I was out of the budget! I contacted my local agent, who promised to do its best, he put me in contact with another guy, who put me in contact with the guys at Gene Art (?) that actually were managing the stuff for Invitrogen. However, they asked me to send again the sequence because:
From a technical point, we would need to take the two projects from the portal and make it all a manual order, as there is basically no flexibility in the automated ordering online portal. So it would be great if you could send me the sequences (including all details) again via email and then I can see how we can arrange the two projects to match your requirements
Apparently, nobody was able to explain me how the hell the same quote was increased by 50% just because of a change in the brand, but they gave me a stupid code that I could have used to obtain a undefined 'discount' for other, more complex projects. However, my project was complex enough to have my sequence lost in their server.
At this point I was in the jungle, therefore I started asking quotes to several companies, putting one against the other, and the results of this trip in negotiation-land are summarized in the graph below.
Six weeks later, I saved the budged receiving the plasmid from Biobasic Canada. I had 4 ug of my synthetic plasmid safely shipped in a liophylized form to my collaborator for adenovirus production, the sequence was 100% correct. The project is running without any cloning from my part. Today, Genscript and DNA 2.0 are spamming my inbox with unsolicited newsletters about their services. The Invitrogen code for the discount is P754233, in case you trust it.-----------------------------------------------------------------------
Disclaimer: this post truly reflects my experience and the quotes I received. I don't have any conflict of interest to disclose. You may get better quotes for smaller sequences. Next time, you might offer better quotes to me if you want to perform better in my graphs, period.