A single, clonable strand of DNA that folds into an octahedron

A group of scientists at The Scripps Research Institute has designed, constructed, and imaged a single strand of DNA that spontaneously folds into a highly rigid, nanoscale octahedron that is several million times smaller than the length of a standard ruler and about the size of several other common biological structures, such as a small virus or a cellular ribosome.

Making the octahedron from a single strand was a breakthrough. Because of this, the structure can be amplified with the standard tools of molecular biology and can easily be cloned, replicated, amplified, evolved, and adapted for various applications. This process also has the potential to be scaled up so that large amounts of uniform DNA nanomaterials can be produced. These octahedra are potential building blocks for future projects, from new tools for basic biomedical science to the tiny computers of tomorrow.

"Now we have biological control, and not just synthetic chemical control, over the production of rigid, wireframe DNA objects," says Research Associate William Shih, Ph.D., of Scripps Research.

Shih led the research, described in the latest issue of the journal Nature, with Professor Gerald Joyce, M.D., Ph.D., of the Department of Molecular Biology and The Skaggs Institute for Chemical Biology at Scripps Research.

Compartments and Scaffolds on the Nano-Scale

Similar to a piece of paper folded into an origami box, the strand of DNA that Shih and Joyce designed folds into a compact octahedron -- a structure consisting of twelve edges, six vertices, and eight triangular faces. The structure is about 22 nanometers in overall diameter.

These miniscule octahedral structures are the culmination of a design process that started one day when Shih was building a number of shapes with flexible ball and stick models in the laboratory. This exercise attracted his attention to an important structural principle: frames built with triangular faces are rigid, while cubes and other frames built with non-triangular faces are easily deformed.

Translating this principle to a scale over a million times smaller, Shih sought to design a DNA sequence that would fold into a triangle-faced, and therefore very rigid, object. Shih and Joyce settled on trying to build an octahedron.

Shih and Joyce constructed a 1669-nucleotide strand of DNA that they designed to have a number of self-complementary regions, which would induce the strand to fold back on itself to form a sturdy octahedron. Folding the DNA into the octahedral structures simply required the heating and then cooling of solutions containing the DNA, magnesium ions, and a few accessory molecules. And, indeed, the DNA spontaneously folded into the target structure.

The researchers used cryoelectron microscopy, in collaboration with Research Assistant Joel Quispe of the Scripps Research Automated Molecular Imaging Group, to take two-dimensional snapshots of the octahedral structures. Significantly, the structures were highly uniform in shape -- uniform enough, in fact, to allow the reconstruction of the three-dimensional structure by computational averaging of the individual particle images.

Potential Applications

Shih and Joyce note that because all twelve edges of the octahedral structures have unique sequences, they are versatile molecular building blocks that could potentially be used to self-assemble complex higher-order structures.

Possible applications include using these octahedra as artificial compartments into which proteins or other molecules could be inserted -- something Joyce likens to a virus in reverse, since in nature, viruses are self-assembling nanostructures that typically have proteins on the outside and DNA or RNA on the inside.

"With this," says Joyce, "you could in principle have DNA on the outside and proteins on the inside."

The DNA octahedra could possibly form scaffolds that host proteins for the purposes of x-ray crystallography, which depends on growing well-ordered crystals composed of arrays of molecules.

Another potential application is in the area of electronics and computing. Computers, which rely on the movement and storage of charges, can potentially be built with nano-scale transistors, but one of the big challenges to accomplishing this is organizing these components into integrated circuits. Structures like the ones that Shih and Joyce have developed might someday guide the assembly of nanoscale circuits that extend computing performance beyond the limits set by silicon integrated circuit technology.

### The article, "A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron" was authored by William M. Shih, Joel D. Quispe, and Gerald F. Joyce and appears in the February 12, 2004 issue of the journal Nature.

This work was supported by the National Aeronautics and Space Administration, The Skaggs Institute for Research, the National Institutes of Health through the National Center for Research Resources, and through a Damon Runyon Cancer Research Foundation fellowship.

About The Scripps Research Institute
The Scripps Research Institute in La Jolla, California, is one of the world's largest, private, non-profit biomedical research organizations. It stands at the forefront of basic biomedical science that seeks to comprehend the most fundamental processes of life. Scripps Research is internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases and synthetic vaccine development.

Contact: Keith McKeown
kmckeown@scripps.edu
858-784-8134
Scripps Research Institute