Guest-mediated access to a single DNA nanostructure from a library of multiple assemblies

We present a method in which a small molecule template is used to access a single DNA nanostructure from a library of multiple assemblies. DNA building blocks 2 and 2', in which two identical DNA arms branch from a fully rigid organic vertex, were synthesized and their self-assembly was found to generate a small dynamic library of products. The small molecule Ru(bpy)(3)(2+) was found to provide access to a single member from this library (i.e., square 5) and was also found to re-equilibrate each other already formed member into 5 quantitatively. The use of a small molecule to access a single DNA assembly from many possible combinations introduces an additional level of control in DNA construction. In addition, the ability of this template to transform the other members into the same single product provides a built-in correction mechanism that helps ensure the integrity of the construction process, even when errors are made. We apply this approach to predictably generate periodic 1D DNA fibers extending over tens of microns, using two trifunctional symmetrical DNA building blocks that otherwise assemble into ill-defined oligomeric networks.