Hello,
My fellow postdoc took sequence of a tetra -ARMS primer for a SNP from Publication. However, mistakenly ,for the sequence of Internal forward (IF) primers, he didnt copy the last nucleotide of the sequence and sent the sequences for synthesis. We realized this mistake quite late, now the primers are synthesized and optimized and giving us required bands of expected size , but we are unsure whether this single last nucleotide absence will affect the genotyping results or should we send the IF primer sequence for re-synthesis? thanks in advance
When you say the end base of the primer do you mean the 5' end or the 3' end ?
I would expect one missing base at the 5' end of a primer to make no difference but a missing mismatched base at the 3; end of the primer would be likely always to produce a good match of primer to template dna . producing a pcr product because there is a perfect match . If you have samples with known sequences for the presence amd absence of a snp you can use these to confirm the quality of your results but if all of your samples seem to contain the f1 allele then you probably have a problem
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