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Mark Bathe, the Samuel A. Goldblith Assistant Professor of Applied Biology Photo: Dominick Reuter
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While
the primary job of DNA in cells is to carry genetic information from one
generation to the next, some scientists also see the highly stable and
programmable molecule as an ideal building material for nanoscale structures
that could be used to deliver drugs, act as biosensors, perform artificial
photosynthesis, and more.
Trying
to build DNA structures on a large scale was once considered unthinkable. But
about five years ago, Caltech computational bioengineer Paul Rothemund laid out
a new design strategy called DNA origami: the construction of two-dimensional
shapes from a DNA strand folded over on itself and secured by short "staple"
strands. Several years later, William Shih's lab at Harvard Medical
School translated this
concept to three dimensions, allowing design of complex curved and bent
structures that opened new avenues for synthetic biological design at the
nanoscale.
A
major hurdle to these increasingly complex designs has been automation of the
design process. Now a team at MIT, led by biological engineer Mark Bathe, has
developed software that makes it easier to predict the three-dimensional shape
that will result from a given DNA template. While the software doesn't fully
automate the design process, it makes it considerably easier for designers to
create complex 3D structures, controlling their flexibility and potentially
their folding stability.
"We
ultimately seek a design tool where you can start with a picture of the complex
three-dimensional shape of interest, and the algorithm searches for optimal
sequence combinations," says Bathe, the Samuel A. Goldblith Assistant Professor
of Applied Biology. "In order to make this technology for nanoassembly available
to the broader community—including biologists, chemists, and materials scientists
without expertise in the DNA origami technique—the computational tool needs to
be fully automated, with a minimum of human input or intervention."
Bathe
and his colleagues described their new software in Nature Methods. In that paper, they also provide a primer on
creating DNA origami with collaborator Hendrik Dietz
at the Technische Universitaet Muenchen. "One bottleneck for making the
technology more broadly useful is that only a small group of specialized
researchers are trained in scaffolded DNA origami design," Bathe says.
Programming DNA
DNA consists of a string of four nucleotide bases known as A, T, G, and C,
which make the molecule easy to program. According to nature's rules, A binds
only with T, and G only with C. "With DNA, at the small scale, you can program
these sequences to self-assemble and fold into a very specific final structure,
with separate strands brought together to make larger-scale objects," Bathe
says.
Rothemund's
origami design strategy is based on the idea of getting a long strand of DNA to
fold in two dimensions, as if laid on a flat surface. In his first paper
outlining the method, he used a viral genome consisting of approximately 8,000
nucleotides to create 2D stars, triangles and smiley faces.
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The CanDo (computer-aided engineering for DNA origami) program can convert a 2D DNA origami blueprint into a complex 3D shape, seen here. Image: Do-Nyun Kim
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That
single strand of DNA serves as a "scaffold" for the rest of the structure.
Hundreds of shorter strands, each about 20 to 40 bases in length, combine with
the scaffold to hold it in its final, folded shape.
"DNA
is in many ways better suited to self-assembly than proteins, whose physical
properties are both difficult to control and sensitive to their environment,"
Bathe says.
Bathe's
new software program interfaces with a software program from Shih's lab called
caDNAno, which allows users to manually create scaffolded DNA origami from a
two-dimensional layout. The new program, dubbed CanDo, takes caDNAno's 2D
blueprint and predicts the ultimate 3D shape of the design. This resulting
shape is often unintuitive, Bathe says, because DNA is a flexible object that
twists, bends and stretches as it folds to form a complex 3D shape.
According
to Rothemund, the CanDo program should allow DNA origami designers to more
thoroughly test their DNA structures and tweak them to fold correctly. "While
we have been able to design the shape of things, we have had no tools to easily
design and analyze the stresses and strains in those shapes or to design them
for specific purposes," he says.
At
the molecular-level, stress in the double helix of DNA decreases the folding
stability of the structure and introduces local defects, both of which have
hampered progress in the scaffolded DNA origami field.
Postdoctoral
researcher Do-Nyun Kim and graduate student Matthew Adendorff, both of the
Bathe lab, are now furthering CanDo's capabilities and optimizing the
scaffolded DNA origami design process.
Building nanoscale tools
Once scientists have a reliable way to assemble DNA structures, the next
question is what to do with them. One application scientists are excited about
is a "DNA carrier" that can transport drugs to specific destinations in the
body such as tumors, where the carrier would release the cargo based on a
specific chemical signal from the target cancer cell.
Another
possible application of scaffolded DNA origami could help reproduce part of the
light-harvesting apparatus of photosynthetic plant cells. Researchers hope to
recreate that complex series of about 20 protein subunits, but to do that,
components must be held together in specific positions and orientations. That’s
where DNA origami could come in.
"DNA
origami enables the nanoscale construction of very precise architectural
arrangements. Researchers are exploiting this unique property to pursue a
number of applications at the nanoscale, including a synthetic photocell,"
Bathe says. "While applications such as this are still quite far off on the
horizon, we believe that predictive engineering software tools are essential for
progress in this direction."
Novel
applications may also grow out of a new competition being held at Harvard this
summer, called BIOMOD. Undergraduate teams from about a dozen schools,
including MIT, Harvard and Caltech, will try to design nanoscale biomolecules
for robotics, computing and other applications.
In
the meantime, Bathe is focusing on further developing CanDo to enable automated
DNA origami design. "Once you have an automated computational tool that allows
you to design complex shapes in a precise way, I think we’re in a much better
position to exploit this technology for interesting applications," he says.
For
DNA origami to have a broad impact, it needs to become routine to simply order
up DNA parts to build any configuration you can dream up, Bathe says. He notes: "Once non-specialists can design arbitrary 3D nanostructures using DNA origami,
their imaginations can run free."
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