Using Matchmaker Yeast one-hybrid screening system, I have obtained around 1.8-2 million clones and carrying forward from here, I performed colony PCR as per recommendation. However, most of the amplicons (in a batch of 50 randomly selected colonies) showed similar bands. Do I need to confirm the cDNA insert via restriction digestion first and then proceed for selection or should I screen many colonies (there might be more than 10K colonies, so selecting many would be impossible). If yes, which RE should I prefer?

The kit supplies reagents only for 100 reactions and currently I have the kit only for 50 more. Kindly suggest the further steps to be taken. Thanks in advance!