Nanomechanical effect of enzymatic manipulation of DNA on microcantilever surfaces

Microcantilevers functionalized with DNA incorporating a Hind III restriction endonuclease site were digested with Hind III to produce DNA with a single-stranded end on the cantilever surface. Ligase was then used to link a second DNA molecule with a compatible end to the DNA on the cantilever. Nanomechanical motion of the cantilever was monitored throughout the digestion and ligation. Fluorescently labeled DNA was used to confirm that ligation and digestion occurred. The DNA was attached to the silicon side because Hind III and DNA ligase both require dithiothreitol to retain their activity. We therefore avoided the possibility that thiolated DNA on the gold side of the cantilever would be displaced by thiol-containing compounds in solution. Our results show that any natural DNA containing a restriction endonuclease site could be digested and attached to a cantilever functionalized with a compatible DNA. Our results also show that the ligated DNA can be removed, regenerating the cantilever for future use.