The pALS anchor is special in that it has two purposes. The first is that it is immediately usable in DNA stretching experiments because it has a dig molecule (to stick to glass) on one end and a biotin (to stick to microspheres) on the other. The second is that I can digest it with BstXI restriction enzyme and use it as the anchor segment for unzipping DNA.
And when it all works well, pALS is much more useful than the pRL574 anchor (1.1kb). It’s extra length makes it easier to calibrate the optical tweezers for unzipping and we can get higher forces in the optical trap by using bigger beads. (Note: The tweezers are the entire device, and the trap is the focal point of the laser in the microscope. So the trap is a subset of the tweezers.)
With the huge success of the pALS PCR yesterday, I’m going to digest some of it and then ligate this piece to EpBR and both adapters. But first here is my digestion reaction: