I have sequences of the Cytochrome c oxidase I (COI) from several populations of Peringia ulvae (Mollusca; Gastropoda; Littorinimorpha; Hydrobiidae). I need additional COI sequences from a specific population. When using the same primers and PCR protocol as for the other populations, I do not get any PCR product for the specific population. My PI suggested me to design internal COI primers for Peringia ulvae. How can I do that? Should I use the COI sequences from the other populations?
If you are not getting amplification, there are multiple things to visit before you want to design internal primers. You should try troubleshooting your PCR reactions before designing and ordering internal primers. If you are doing the PCRs wrong, it is likely you will run into the same problems again with internal primers.
There are excellent guides to trouble shooting PCRs - Just a google search "Trouble-shooting PCRs" should give you a lot of material to go through. This is from NEB, but there are several others, each manufacturer having their own, so you could refer to one of whose reagents you are using.
Primers generally give good reads from the 5' end for about 600-700 bp and after that the quality of base calling deteriorates, so if your target amplicon is above 1500bp or so, you would need internal primers because the 'external' primers would give you good sequences for only 1400 bp or so (600-700 bp from both directions, for fwd and rev primers). So internal primers can be used to sequence the regions that cannot be reached by the main (external) forward and reverse primers. The published papers from where you are using the external primers will most likely have the internal primers if CO1 is long enough to require internal primers.
Otherwise, you would need to align the existing sequences from the other populations, and look through regions of the alignment that are conserved which could act as potential priming sites. There are other issues to be taken care of before you can consider a 'conserved region' a 'priming site' and go ahead and order primers. Again there are excellent primer design tutorials available, just a google search away.
Let me know if any parts of the answer are not clear, or sound like jargon and I will do my best to simplify it for you. However, I would strongly suggest troubleshooting the PCR first - for e.g. trying a gradient PCR to find the optimal annealing temperature.