Why use degenerate PCR?
Degenerate PCR has proven to be a very powerful tool to find “new” genes or gene families. Most genes come in families which share structural similarities. By aligning the sequences from a number of related proteins you can determine which parts are conserved and which are variable. Based on this information you can use conserved protein motifs for starting points for designing degenerate PCR primers. Degenerate PCR applies to a number of scientific settings: • You have isolated a protein and managed to sequence some amino acids from it. You want to find the corresponding gene! Why not try with degenerate PCR? • You have found a human gene and want to clone the homolog gene from e.g. mouse or Drosophila. Of course, you can try with low stringency hybridizations, but how many false positives do you have to sequence before you find the correct one? • You have found an interesting gene in yeast or C. elegans and want to find the human homolog (if it exists). Why not try degenerate PCR? •
