APOG is a hypothetical polymorphic short tandem repeat (STR) locus in humans with a
repeating unit of [CAGA]. The polymorphic region is shown below as a box with 25 bp of
flanking DNA sequence on each side. The n represents the number of times [CACA] on the top
strand is repeated (the polymorphic part of STR locus). (a) You plan to use PCR to genotype
individuals for the APOG locus. If PCR primers must be 18 nucleotides long, design a pair of
primers to amplify the APOG locus? Design the primers such that they are immediately adjacent
to the [CAGA] repeat (i.e. don\'t worry about optimizing annealing temperature, GC content, etc.
-everybody\'s primer sequences should be the same). (b) Consider APOG alleles with 9 and 7
copies of the repeating (CAGA) unit. Using the primers you have designed, what will be the
sizes in base pairs of the PCR products for each allele? In other words, if run on an
electrophoresis gel, what would be the sizes of the two bands? (c) There arc five known alleles
of APOG with 14, 11, 10.9 and 7 copies of the repeating unit. How many possible human
genotypes are there for these alleles, and what are they?
Solution
Rv primer 5’ TCACGTAACGAATGGTAC 3’
18 + 18 + 36 = 72 bp
In case of 9 copies repeating units the PCR product will be length of both the primer + 5* 4
18 + 18 + 20 = 56 bp
They will be 14-11, 14-10, 14-9, 14-7, 11-10, 11-9, 11-7, 10-9, 10-7, and 9-7
repeating unit of [CAGA]. The polymorphic region is shown below as a box with 25 bp of
flanking DNA sequence on each side. The n represents the number of times [CACA] on the top
strand is repeated (the polymorphic part of STR locus). (a) You plan to use PCR to genotype
individuals for the APOG locus. If PCR primers must be 18 nucleotides long, design a pair of
primers to amplify the APOG locus? Design the primers such that they are immediately adjacent
to the [CAGA] repeat (i.e. don\'t worry about optimizing annealing temperature, GC content, etc.
-everybody\'s primer sequences should be the same). (b) Consider APOG alleles with 9 and 7
copies of the repeating (CAGA) unit. Using the primers you have designed, what will be the
sizes in base pairs of the PCR products for each allele? In other words, if run on an
electrophoresis gel, what would be the sizes of the two bands? (c) There arc five known alleles
of APOG with 14, 11, 10.9 and 7 copies of the repeating unit. How many possible human
genotypes are there for these alleles, and what are they?
Solution
Rv primer 5’ TCACGTAACGAATGGTAC 3’
18 + 18 + 36 = 72 bp
In case of 9 copies repeating units the PCR product will be length of both the primer + 5* 4
18 + 18 + 20 = 56 bp
They will be 14-11, 14-10, 14-9, 14-7, 11-10, 11-9, 11-7, 10-9, 10-7, and 9-7
