I need to synthesize this primer: GACCATCTAGCGACCTCCACNNNNNNNN. This primer contains eight random nucleotides in the 3' end. This primer can be used for viral metagenomics, and the last 8 "N" nucleotides are similar to a random primer that is used for RT-PCR. My question is if I submit this sequence for oligo synthesis, say to IDT, will they synthesize one primer that contains random 8 nucleotides at the 3' end, or will they synthesize multiple primers containing all possible nucleotides at every position?
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$\begingroup$ That's a question you should ask the IDT customer support. There may be someone on here who can answer as to what IDT can do, but your best bet is to ask the source. $\endgroup$– bob1Commented Nov 3 at 21:10
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You will get 48 different primers in a single tube.
Oligonucleotide synthesis is a cyclical process which adds nucleotides one position at a time.
All that’s happening when an N is encountered in the sequence is, during the coupling step, instead of adding a single type of nucleotide to the reaction, they add all four (which are incorporated stochastically).
