DNA nanodevice for analysis of force-activated protein extension and interactions

Force-induced changes in protein structure and function mediate cellular responses to mechanical stresses that are important in human development, physiology and diseases. However, existing methods to study proteins under mechanical force are generally single-molecule techniques unsuitable for biochemical and structural analysis. Taking advantage of DNA nanotechnology, including the well-defined geometry of DNA origami and the programmable mechanics of DNA hairpins, we built a nanodevice to apply controlled forces to proteins. This device was used to study the R1-R2 segment of the talin1 rod domain as a model protein. R1-R2 consists of two α-helical bundles that reversibly unfold under tension to expose binding sites for the cytoskeletal protein vinculin. Electron microscopy confirmed tension-dependent protein extension, and biochemical analysis demonstrated enhanced vinculin binding under tension. Using the device in pull-down assays with cell lysates, we identified filamins as novel tension-dependent talin binders. The DNA nanodevice thus provides a valuable molecular tool for studying mechanosensitive proteins on a biochemical scale.