PCR primers commonly used by the FBI Laboratory for mtDNA sequencing are shown as arrows on Figure 10.6 (Wilson et al. 1995b). Their primer nomenclature uses the strand corresponding to the primer (L for light and H for heavy) and the 3' nucleotide position. Thus, primer A1 is designated as L15997 so it corresponds to the light strand of the Anderson reference sequence and ends at position 15997. Note that this nomenclature system does not indicate the 5'-end of the primer and therefore can make it more difficult to determine the overall PCR product size.
Another approach to mtDNA primer nomenclature is that used by the Armed Forces DNA Identification Laboratory. The primer positions for their primer sets (PS) I-IV are indicated in Figure 10.3. Strand designation in this case is by forward (F) and reverse (R) rather than light (L) and heavy (H). Also different is the fact that the 5' nucleotide position is noted rather than the 3' nucleotide as done by the FBI Laboratory. This approach permits an easier determination of the overall PCR product size defined by a primer pair. It is worth noting that two of the primers between the FBI and AFDIL sets are identical even though their names are different: FBI B1 (H16391) is the same primer as AFDIL R16410 used in PSII.
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