Which loci can we use, which primers can we order to see a difference on an Agarose gel?
For resolution of DNA fragments on most agarose gels, it is best to have PCR products that differ by more than 20-30 bp. Thus, alleles from tetranucleotide STR loci that differ by only 4 bp will not be sufficiently resolved on an agarose gel. The D1S80 locus, which was used briefly for human identity testing in the mid-1990s, has alleles that are separated by 16 bp. The most common D1S80 alleles are 18 and 24, which differ by 96 bp. However, since this kit is no longer commercially available, obtaining an allelic ladder for allele designation purposes will be difficult. A simple laboratory protocol for analysis of D1S80 is available at http://www.hhmi.princeton.edu/Manual/04%20HHMI%20Lab_04%20D1S80.pdf.
