| Nanomechanical devices hold the promise of controlling structure and performing exquisitely fine measurements on the molecular scale. DNA, the substance carrying the genetic information of living systems, has also been proved to be an intriguing construction material for nanotechnology. Several DNA nanomechanical devices based on different biochemistry phenomena have been reported before, here we will present two types of protein-driven DNA triple crossover (TX) molecular nanomechanical devices, which can also serve as measuring devices to investigate the behavior of proteins upon binding to DNA.; In Chapter 2, a DNA nanomechanical device has been developed by linking two DNA TX motifs by a shaft of conventional double helical DNA that connects their top domains. This shaft contains the binding site for integration host factor, IHF. When IHF binds to its site on the DNA shaft, it bends it markedly. This bending is monitored by fluorescence resonance energy transfer. We have added a second double helical portion to the bottom domains. This second double helix is nicked near its central region on both strands, creating a 'sticky end'. By relocating the nicks, we are able to estimate the amount of free energy available to do work when IHF binds to the device. We find that the available free energy is about 7 kcal/mol.; In Chapter 3, a topologically closed version of the DNA TX molecular nanomechanical device has been constructed and characterized. It could be used to investigate proteins that function by unwinding DNA, such as SoxR protein. |
