I am trying to amplify a PCR product from a cDNA library using a
vector primer (T7) and a degenerate oligonucleotide for the center of the
gene. I get two products which are faint and want to gene clean them and
re-amplify using the products as a template. However, when I attempt to
do so using the same primers I tend to get a smear. Do you have any
recommendations as to how to clean and re-amplify these fragments using
degenerate oligonucleotides in order to get a sharp clean fragment?