A Protein-Driven DNA Device That Measures the Excess Binding Energy of Proteins That Distort DNA

摘要

Nanomechanical devices hold the promise of controlling structure and performing exquisitely fine measurements on the molecular scale.We previously have reported three nanoscale devices that were built from DNA.The first device extrudes or withdraws a portion of a DNA cruciform from a cyclic molecule in response to the presence of an intercalator.The second device is powered by the B-Z transition :it switches a DNA domain from one side of a double-helical shaft to the other in response to the presence or absence of [Co(NH_3)_6]~(3+) in its environment.The third device is sequence-dependent ;it changes structure as a function of DNA strands that are in solution with it.All of these devices change their states in response to an external stimulus,but they do not report new information about any other molecular system.Here we describe a new DNA device that changes shape when a DNA-distorting protein is added to the system.In this case,we used E.coli integration host factor (IHF),which bends DNA significantly when it binds to an appropriate recognition site.Thus,we have developed a nanomechanical device for which the stimulus is a protein.However,this device does not merely have a different kind of activation signal.A second part of the device contains a series of nucleotide pairs that must be disrupted when the device is distorted by IHF.Consequently,this is a measuring device that enables us to estimate the amount of additional work that the protein can do when it binds to DNA.