Also for best clone stability, prepare plasmid DNA from fresh transformants (from plates not greater than three days old). Store unstable clones as plasmid DNA, rather than cell-based glycerol stocks.
Gibson Assembly cloning (#E2611 – Gibson Assembly Master Mix) is an especially efficient method for isolating difficult clones. (e.g. large plasmids with single or multiple inserts). Use a primer design program such as NEBuilder® to design cloning primers that anneal outside of any repeat elements.