Dear all
During reading in some papers about multiplex PCR primers, I have found some letters within the sequence as d, m, w and h which are referred to some bases sometimes one of three bases. The question here if I am going to request the same sequence which base I should add in stead of foreign letter or I have to try all till I got the one that give specific amplicon?
Thanks for your consideration
Best Regards
These base redundancy codes are used when the base at each position can be one of 2-4 different bases in the population being studies, You do not need to order a lot of different oligos to cover all of the many different sequences under each oligo. Just put the redundant base code in the oligo position when having the oligo made, All oligo companies know these codes and will make your oligo with all of the changes inserted into the oligo mixture. So if you have 2 positions each with 2 base possibilities the company will make 4 oligos in a mixture that they will send to you in one tube and they will describe it as one oligo but he sequence will have your letters and not a single base in the described positions/ There will be less of each individual sequence but as primers are in huge molar excess you will not need to change the amount of primer used in your pcr except in very unusual conditions with large numbers of base changes
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