Forum 10/09/2003

“A 1.7-Kilobase Single-Stranded DNA that Folds into a Regular Octahedron”

William Shih, Research Assoc. – The Scripps Research Institute, La Jolla, CA

Rigid DNA-based nanostructures may play a role in the construction of miniaturized devices through their ability to direct the assembly of materials on the subnanometer to micrometer scale. A key property of DNA – its ability to be amplified exponentially by polymerases – facilitates both the large-scale clonal production of individual sequences and the directed evolution of sequence lineages toward optimized behaviors. Previous examples of three-dimensional geometric DNA objects, however, are not amenable to cloning because they contain opologies that prevent copying by polymerases.  Here we show the design and synthesis of a 1,669-nucleotide, single-stranded DNA molecule that is readily amplified by polymerases and that, in the presence of five 40mer oligonucleotides, can be folded into a regular octahedron structure by a simple denaturation-renaturation procedure.
The resulting octahedron, approximately 24 nanometers on a side, was visualized by cryo-electron microscopy and shown to have the redicted structure.  Sequence symmetry was minimized such that no seven base-pair sequence appears twice in the octahedron. Thus each part of the octahedron is uniquely addressable by the appropriate sequence-specific DNA binder.