Smallest Mona Lisa Panted on Largest
January 9, 2018
2006, Caltech's Paul Rothemund (BS '94)—now research professor of
bioengineering, computing and mathematical sciences, and computation and
neural systems—developed a method to fold a long strand of DNA into a
prescribed shape. The technique, dubbed DNA origami, enabled scientists
to create self-assembling DNA structures that could carry any specified
pattern, such as a 100-nanometer-wide smiley face.
DNA origami revolutionized the field of nanotechnology, opening up
possibilities of building tiny molecular devices or "smart" programmable
materials. However, some of these applications require much larger DNA
The process of fractal assembly,
using wooden puzzle pieces.
Now, scientists in the laboratory of
Lulu Qian, assistant professor of bioengineering at Caltech, have
developed an inexpensive method by which DNA origami self-assembles into
large arrays with entirely customizable patterns, creating a sort of
canvas that can display any image. To demonstrate this, the team created
the world's smallest recreation of Leonardo da Vinci's Mona Lisa—out of
The work is described in a paper appearing in the December 7 issue of
the journal Nature.
While DNA is perhaps best known for encoding the genetic information of
living things, the molecule is also an excellent chemical building
block. A single-stranded DNA molecule is composed of smaller molecules
called nucleotides—abbreviated A, T, C, and G—arranged in a string, or
sequence. The nucleotides in a single-stranded DNA molecule can bond
with those of another single strand to form double-stranded DNA, but the
nucleotides bind only in very specific ways: an A nucleotide with a T or
a C nucleotide with a G. These strict base-pairing "rules" make it
possible to design DNA origami.
To make a single square of DNA origami, one just needs a long single
strand of DNA and many shorter single strands—called staples—designed to
bind to multiple designated places on the long strand. When the short
staples and the long strand are combined in a test tube, the staples
pull regions of the long strand together, causing it to fold over itself
into the desired shape. A large DNA canvas is assembled out of many
smaller square origami tiles, like putting together a puzzle. Molecules
can be selectively attached to the staples in order to create a raised
pattern that can be seen using atomic force microscopy.
The Caltech team developed software that can take an image such as the
Mona Lisa, divide it up into small square sections, and determine the
DNA sequences needed to make up those squares. Next, their challenge was
to get those sections to self-assemble into a superstructure that
recreates the Mona Lisa.
"We could make each tile with unique edge staples so that they could
only bind to certain other tiles and self-assemble into a unique
position in the superstructure," explains Grigory Tikhomirov, senior
postdoctoral scholar and the paper's lead author, "but then we would
have to have hundreds of unique edges, which would be not only very
difficult to design but also extremely expensive to synthesize. We
wanted to only use a small number of different edge staples but still
get all the tiles in the right places."
The key to doing this was to assemble the tiles in stages, like
assembling small regions of a puzzle and then assembling those to make
larger regions before finally putting the larger regions together to
make the completed puzzle. Each mini puzzle utilizes the same four
edges, but because these puzzles are assembled separately, there is no
risk, for example, of a corner tile attaching in the wrong corner. The
team has called the method "fractal assembly" because the same set of
assembly rules is applied at different scales.
"Once we have synthesized each individual tile, we place each one into
its own test tube for a total of 64 tubes," says Philip Petersen, a
graduate student and co-first author on the paper. "We know exactly
which tiles are in which tubes, so we know how to combine them to
assemble the final product. First, we combine the contents of four
particular tubes together until we get 16 two-by-two squares. Then those
are combined in a certain way to get four tubes each with a four-by-four
square. And then the final four tubes are combined to create one large,
eight-by-eight square composed of 64 tiles. We design the edges of each
tile so that we know exactly how they will combine."
The Qian team's final structure was 64 times larger than the original
DNA origami structure designed by Rothemund in 2006. Remarkably, thanks
to the recycling of the same edge interactions, the number of different
DNA strands required for the assembly of this DNA superstructure was
about the same as for Rothemund's original origami. This should make the
new method similarly affordable, according to Qian.
"The hierarchical nature of our approach allows using only a small and
constant set of unique building blocks, in this case DNA strands with
unique sequences, to build structures with increasing sizes and, in
principle, an unlimited number of different paintings," says Tikhomirov.
"This economical approach of building more with less is similar to how
our bodies are built. All our cells have the same genome and are built
using the same set of building blocks, such as amino acids,
carbohydrates, and lipids. However, via varying gene expression, each
cell uses the same building blocks to build different machinery, for
example, muscle cells and cells in the retina."
The team also created software to enable scientists everywhere to create
DNA nanostructures using fractal assembly.
"To make our technique readily accessible to other researchers who are
interested in exploring applications using micrometer-scale flat DNA
nanostructures, we developed an online software tool that converts the
user's desired image to DNA strands and wet-lab protocols," says Qian.
"The protocol can be directly read by a liquid-handling robot to
automatically mix the DNA strands together. The DNA nanostructure can be
this online software tool and automatic liquid-handling techniques,
several other patterns were designed and assembled from DNA strands,
including a life-sized portrait of a bacterium and a bacterium-sized
portrait of a rooster.
"Other researchers have previously worked on attaching diverse molecules
such as polymers, proteins, and nanoparticles to much smaller DNA
canvases for the purpose of building electronic circuits with tiny
features, fabricating advanced materials, or studying the interactions
between chemicals or biomolecules," says Petersen. "Our work gives them
an even larger canvas to draw upon."
The paper is titled "Fractal assembly of micrometre-scale DNA origami
arrays with arbitrary patterns." The work was funded by the Burroughs
Wellcome Fund, the National Institutes of Health's National Research
Service Award, and the National Science Foundation's Expeditions in