I am using degenerate primers for amplifying viral genome. At the beginning, the bands appeared at appropriate size but now nothing appears except for unspecific bands.
Susan L Payne
There is no single suitable condition for PCR. You must test many parameters including annealing temperature, Mg concentration, template DNA concentration. Had you changed any reagents (different enzyme, new primer stock, different virus stock, dNTPs?) when the reaction stopped giving you the appropriate sized bands? You might also try a few PCR cycles at a lower annealing temperature (so that the degenerate primers can bind), followed by a higher annealing temperature for additional cycles).
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