MBB 331 Chapter Notes - Chapter 3: Bamhi, Ecori, .Ca

• School: Simon Fraser University
• Department: Molec Biol & Biochem
• Course: MBB 331
• Professor: Stephanie Vlachos

Document Summary

Primer2: 5" tc-gaattc-(t/c)tc. (t/c)tt. (a/g/t/c)gc. cca. (a/g/t/c)gc. (a/g)ta. (a/g/t)gc 3": two ways of calculating the tm of the collection of degenerate primers that would be synthesized as above: Tm = 2(#a + t) + 4(#g + c) A: calculate an average for the collection of primers: #ts = 1/4 + 1 + 1/2 + 1/2. #gs = 1 + 1/2 + 1 + 1/2 + 1/4 + 1 + 1/2 + 1. #cs = 1 + 1 + 1/4 + 1/2 + 1 + 1/2 + 1. Primer 1 #as = 1 + 1/2 + 1 + 1/2 + 1/4 + 1 + 1 + 1 + 1/2. Tm = 2(6. 75 + 2. 25) + 4(5. 75 + 5. 25) = 62 c. B. ignore degeneracies in primer and calculate the tm based only on the nucleotides you know will basepair thus, theoretically you will calculate the tm for the worst case primer pairing possible: