Bionanotechnology: Design of self assembling rigid DNA units

Nagarajan Vaidehi, Brian Palmer, Georgios Zamanakos, William Goddard III

The focus of nanotechnology is to produce viable atomic components and machines. The two major criteria for these molecules are the ability to self-assemble with control and accuracy and a certain degree of stability. Proteins and nucleic acids are very good systems where the accuracy in assembly very specific. Seeman and coworkers have succeeded in building a rigid DNA double crossover molecule. This orientation provides the necessary rigidity and sticky ends that form the nucleus for self-assembly. A typical self ľassembled unit is shown in the figure below. At MSC using the first principles DNA forcefield we have built many of the structures that Seeman and coworkers have made. In collaboration with their group we are optimizing the crossover points that confer the maximum stability to the self ľassembly.