(a) Using the amino acid sequence provided ( MVSKGEELFT ), you set out to design

Question

(a) Using the amino acid sequence provided (MVSKGEELFT), you set out to design a set of degenerate primers in order to amplify the cDNA sequence corresponding to your protein of interest from a cDNA library. In order to do so, you need to synthesize all the oligonucleotide primers that may possess complementary to the 5’ and 3’ ends of your targeted gene. Assuming you chose a length of 20 bases for your “forward” primer, how many possible degenerate sequences would you need to create in order to cover all possible sequences corresponding to your protein? List the nucleotide sequence of one of your designed primers below. Be sure to label the 5’ and 3’ ends.

Explanation / Answer

Given protein sequence: MVSKGEELFT
Number of codons for M = 1
Number of codons for V = 4
Number of codons for S = 6
Number of codons for K = 2
Number of codons for G = 4
Number of codons for E = 2
Number of codons for F = 2
Number of codons for T = 4
Number of codons for L = 6

Number of probabilities for the degenerate primer = 1 X 4 X 6 X 2 X 4 X 2 X 2 X 4 X 6
= 18432 different combinations.

Sample sequence: 5'-AUGGUUUCUAAAGGGGAAGAAUUAUUUACC-3'

Related Questions

Navigate

• Browse (All)
• Browse #
• Subjects

Integrity-first tutoring: explanations and feedback only — we do not complete graded work. Learn more.