How do I design an oligonucleotide that contains a translationally silent restriction site?
Starting with a known coding region, use the MAP command with the /SILent switch. This will produce a restriction map with the extra silent sites shown (along with the sites that don’t require sequence modification). The /SILent command line option tells MAP, that in addition to checking for enzymes the way it usually does, to also modify the sequence at each position to accommodate each enzyme being tested, and to accept those where the resulting sequence changes do not alter the coded product. Often you want to also restrict the enzymes checked to be only six cutters, here is an example: $ MAP/infile=my_sequence.seq/SIX/SILENT – _$ /begin=2/end=100/outf=my_sequence.map/default Note 1: MAP figures out which frame to translate in, with respect to /SILENT, from the first base specified. In the example frame 2 was coding. If /begin had NOT been specified it would have defaulted to /begin=1, which means frame=1, and the resulting tests for silent restriction sites would have been incorrec
