Nanomechanical devices based on DNA.

Biomolecular compounds, such as proteins and nucleic acids, which are evolutionary optimized, with respect to specificity of binding to their target structure as well as to functionality, for distinct biochemical transformation and translocation, are currently explored as building blocks in the ™bottom-up∫ self-assembly of nanometer-scale functional devices. [1] So far, applications include the organization of metal and semiconductor nanoclusters, [2] numerous bioana-lytical techniques, [1] as well as biomolecular electronics [3] and nanomechanical devices. While the development of the latter was, in past years, mainly focused on motor proteins, such as actin, kinesin, and myosin, [4] nowadays an increasing number of reports are being devoted to the construction of nano-mechanical devices from DNA. This biomolecule plays an outstanding role in the development of artificial biomolecular hybrid elements, since the specificity of simple AT and G-C base pairing as well as its robust physicochemical nature allows for the fabrication of nanostructured molecular scaffolding and surface architecture, [5] and to selectively position proteins, [6] inorganic colloidal components, [2] carbohydrates , [7] organometallics, [8] and reactive chemical compounds [9] on the nanometer length scale. Another interesting property of the DNA double helix is its intrinsic susceptibility to external stimuli mediated by small molecules or ions, which opens up ways to fabricate nano-mechanical devices. For example, the contour length and the flexibility of a DNA molecule can be effectively altered by use of intercalators, such as acridinium or ethidium bromide derivatives, which bind in between the stacked nucleobases of the double helix and thereby significantly increase the DNA contour length. [10] Seeman and co-workers made use of this phenomenon: They reported on the induced change in torque of a circular DNA molecule containing a partially mobile branched DNA junction on intercalation of ethidium bromide as a potential supercoiling motion for nanomechanical elements. More recently, the Seeman group established an elegant means to utilize electrostatic interaction of Co 3‡ ions for switching a DNA device comprised of two rigid DNA double-crossover motifs. The latter were covalently linked to each other by a short d(CG) 10 proto-Z sequence which is capable of changing its conformation from a right-handed B-to a left-handed Z-DNA double helix (Figure 1 A). [12] The conforma-tional change leads to a spatial separation of two fluorescent labels, attached to each of the two double-crossover moieties, which can be measured by fluorescence resonance energy transfer (FRET). In a different approach, the increase in concentration of …