User:Anthony Salvagno/Notebook/Research/2009/11/06/Oligo Designing/email snippet from AlphaDNA
"Anyhow, we will send you a free replacement, but for your future orders, please use the asterisks only for phosphorothioate modifications. For all other modifications, you can safely use the “X” (upper case X), because this is how the modification is actually entered on the DNA synthesizers. Any DNA modification, be it at the 5’ end, the 3’ end, or in the middle of the sequence, each and every modification (except the phosphorothioate) is entered as an X. This is because the DNA synthesizers can “understand” only X as a modification, to be added from the extra amidite position (X position) on the machine (once again, the phosphorothioate modification is the only one that is added not as an X, i.e. not from the X-amidite bottle on the machine, but through a change of the protocol at the post-coupling steps). If you use X instead of an asterisk, we would not have the problem we are having now."