BioWizard

I think it has to do with ramachandran allowed angles in secondary structures. The beloved right handed alpha helices cannot form with D-aminoacids, as the side chains would stick in to the inside and disrupt hydrogen bond and VdW packing. But I suppose if all amino acids were D-, you would just have left handed helices. My opinion is that it all depends on initial conditions of the evolution of the enzymes that processes these biomolecules. Once some efficiency was established with the L-isomers, it would be very difficult for other systems to outcompete them, and then everything else would build on L-forms, since they are the currency now. As to why we dont have a mixture of L and D, I would speculate that proteins structures containing such mixtures would not be as stable, for the aforementioned reason, and thus stereoselectivity for either the L or the R would reign, in this case, the L.

There is a method described in this paper which might be helpful: http://www.pnas.org/cgi/content/full/98/25/14601 Scicop, what you said is true, but HPLC can indeed be used for quantitative analysis as well.

For your purposes, you might be interested to look into interfering RNA (RNAi) instead of restriction enzymes, which as everyone has pointed out, might be a bit troublesome.