User:Anthony Salvagno/Notebook/Research/2009/11/06/Oligo Designing/AlphaDNA explanation of how to order
The best way is to use the “language” that the DNA synthesizers “understand”. Almost all modifications, of any kind, have to be uploaded to the machines as “X”, because X is the extra reagent position on the machine, where the special reagent for your modification will be mounted.
So, it is going to be
You can even use the order form (although any other format is also acceptable). If you use the form, enter the sequence with X (see above), select from the list of modifications “other”, and explain anywhere (on the order form, or in the text of your message) the meaning of the X.
The good point about the use of X for this or any other modification is that even if, for some reason, you forget to explain the X, the oligo will not be synthesized, because the lab would want to know what reagent to use for the X position. By contrast, if you use *, the lab is likely to synthesize your oligo with phosphorothioate modification (one of the very few modifications, for which we do not use « X »).
From: Steven J. Koch  Sent: April-15-09 5:28 PM To: 'Alpha DNA' Subject: Help with ordering
We’re interested in ordering another oligo with an internal biotin-dT modification. Last time, I used an “*” to represent this, which caused trouble, and which you graciously fixed for free. This time I want to order in a way that doesn’t confuse your technicians! So, I’m sending a pre-email to ask how to do it. (Assuming the excel sheet still doesn’t work for this modification.) Let’s say I wanted to order the following oligo:
and I wanted the middle “T” (the 5th nucleotide) to be biotinylated. What would be the best way to convey this information?