Question: 1 . Using chemical biology methods, a student isolated a novel bacterial protein that interacts with an antibiotic chemical. After trypsin digestion, several peptides from

1. Using chemical biology methods, a student isolated a novel bacterial protein that interacts with an antibiotic chemical. After trypsin digestion, several peptides from the protein were sequenced by mass spectrometry. One of them is: NH2-Leu-Met-Pro-Tyr-Ser-Ala-Ala-Pro-Cys-Leu-Trp-Glu-Ala-Gly-Asp-Arg-COOH. However, the genomic database of this bacterium is not available but the bacterium is available in the lab. To verify and clone the gene encoding this protein from this uncharacterized bacterium, the student has to purify the bacterial genomic DNA and use it as the template to isolate the DNA fragment that encodes this peptide using PCR. The student plans to design a pair of oligonucleotides as the forward and reverse primers (usually 18 nucleotides in length for each primer) to PCR the DNA fragment that encodes this peptide from the purified bacterial DNA. How does the student design these forward and reverse oligonucleotides?

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