Can I use a smaller volume for the fluorescence based assays? Can the assays be done in 384-well plates?

The assays can be scaled down for 384-well plates. Scale the volumes of all reagents and DNA proportionally. The ratios of DNA, dye, and enhancer (if applicable) should remain the same as in the standard 96-well protocol. However, using less than 200 uL reaction in a 96-well plate may result in lower signal.