Microsatellites, also known as Simple Sequence Repeats (SSRs), or sometimes Shor
ID: 29731 • Letter: M
Question
Microsatellites, also known as Simple Sequence Repeats (SSRs), or sometimes Short Tandem Repeats (STRs) are repeating sequences of 1-6 base pairs of DNA. ROC is a hypothetical microsatellite locus in humans with a repeating unit of CAGA. The locus is shown underlined in the figure with 18 bp of flanking DNA sequences that can serve as primers for amplification of the locus via PCR. 5 TTGATCTCCT TTAG CTTC ROC GTATAATTCAT TATGTGA 3 3AACTAGAGGAAATCGAAG LOCUS CATATTAAGTAATACACT 5 A)You plan to use PCR to genotype individuals for the ROC locus. If PCR primers must be 18 nucleotides long, what are sequences of the pair of primers required to amplify the ROC locus? Please note that that primers must be of the correct polarity to amplify the DNA between them, so do label the 5' and 3' ends of both the primers. Also primer sequences by designation are always written in the 5 to 3 direction. B)Consider ROC alleles with 10 and 7 copies of the repeating unit. Using the primers you have designed, what will be the sizes of the amplified PCR products for each allele? C)There are four known alleles of the ROC locus with 15, 12, 10, and 7 copies of the repeating unit. How many possible genotypes are there for these alleles, and what are they? D) One parent is heterozygous for the 15 and 10 alleles of the ROC locus and the other parent is heterozygous for the 10 and 7 alleles. Growing up in the house with the two parents are three children. When you type them for the ROC locus, you find that their genotypes are (10,10), (15,10) and (12,7). What can you conclude?Explanation / Answer
A)
Primers for the given sequences:
5’-TCACATAATGAATTATAC-3’
5’-TTGATCTCCTTTAGCTTC-3’
B)
5’-TTGATCTCCTTTAGCTTCCAGACAGACAGACAGACAGACAGACAGACA
GACAGACAGAGTATAATTCATTATGTGA-3’
This sequence having 10 ROC repeats gives 77 nucleotides long PCR products.
The sequence having 7 ROC repeats gives 65 nucleotides long PCR products.