2.6 Making a Genetic Probe

Often we may know the amino acid sequence (or part of it) of a protein of interest, and frequently we will wish to synthesize a short nucleic acid sequence that might correspond to the gene sequence used by the cell. Such polynucleotides may be used as molecular probes to help locate the gene and as primers for polymerase reactions.

The redundancy of the genetic code complicates our problem because we have no real way of guessing which codon the cell may be using for a particular amino acid (Figure 12), although a given organism often uses some redundant codons more efficiently that others. In this case, we would choose the sequence starting with glu which uses two codons and proceed through a region where there is a minimal number of possible codons. We still need to consider ten possible sequences in this stretch of 15 nucleotides.

Figure12. A nucleic acid probe should be selected around the least redundant sequece of possible codons. This sequence of amino acids is taken from the insulin molecule. (see FIG 14)