gene coding

[featherstars]

Question:

 

 

 

 

Design a minimum numbers of probes (20 nucleotides in length) to detect gene coding for the protein of the amino acid sequence shown below.

 

 

 

 

Picture of problem with solution: http://imgur.com/RFMH7.

 

 

 

 

I understand how to get the possible codons but how are the synthetic probes derived from them?

 

 

 

 

 

 

 

 

 

 

Thank You

 

[D.Smalley]

The most important piece of information given in the question is minimum number of probes. So you work out the possible codons for each amino acid and then choose a 20 nucleotide long segment that has the lowest number of possible codons. This is all to do with degeneracy in the genetic code. When designing DNA probes for an experiment, you must take into account all possibilities, as from the amino acid sequence you have no idea what the actual codon was that coded for, lets say, leucine, as leucine has 6 possible codons.So the first thing to do is to discount those amino acids with the highest no. of possibilities. In this case leucine and arginine. Next look at which amino acids have the lowest: met and 2x trp. From this you should see you only have 2 possibilities to get 20 nucleotides without including Leu or Arg; either start at Pro and end at Phe or start at Trp and end on Val. How do you decide which, when both Pro and Val have 4 options? Well, as you only want 20 nucleotides, the last amino acid of the last codon gets left off. So if we ended on Val then the degenerate nucleotide gets left off, meaning overall we will only have 8 probes.Oh and when writing out the probes you must write out every possibility as shown. I hope that helps