PCR on E. coli clones

pick entire colony and resuspend in 100 ulsterile water.
use 2-5 ul for standard 25 ul PCR reaction with Taq pol, run 10' soak at 94 C before cycling
use the rest of the suspension to start cultures of clones that scored positive in the PCR reaction

PCR products produced this way can be sequenced or cloned without any further cleanup.
PCR products can be used as template for in vitro transcription without cleanup if you ad RNasin (the most abundant E. coli RNases are effectively inhibited by RNasin)

PCR on yeast clones

boil yeast colony in PCR buffer for 10', then run normal 25 ul PCR reaction with Taq pol.