A Brief Overview of DNA Origami and Its Applications
Tatiana H. RiordanMath 89S Duke University
September 27th, 2016
A BRIEF OVERVIEW OF DNA ORIGAMI AND ITS APPLICATION
Introduction/Foundation of DNA Origami
Imagine injecting a minute robot into your body, it travelling harmlessly through your
bloodstream, until it comes into direct contact with a tumor, at which point it would open up and
attack the cancerous cells. DNA “origami” technology could make this magical robot a reality in
the foreseeable future. The idea of manipulating DNA to form new structures originated from
Ned Seeman, a nanotechnologist and crystallographer. Seeman’s inspiration came from his
desire to create DNA “prisons” that would be rigid and stable enough to hold proteins still so that
he could take X-Ray “mugshots” of them, a process that required the use of nanotechnology.
Seeman’s creation of various geometric forms of DNA showed that DNA doesn’t just have to be
in the shape of a double helix. More specifically, it showed the DNA could have joints, where
three strands of DNA double helices could come together and wind along one helix and jump to
another helix, as seen in Figure 1 (Rothemund, P. (2016)).
Figure 1. Ned Seeman’s Geometric Forms
This process of “joining, coupling or weaving two molecules together to produce a
structure of the same certainty enjoyed by a carpenter”, came to be known as DNA carpentry
(Seeman, N. Zhang, Y., Du, S. & Chen, J. (1995)). However, the process of DNA carpentry is
complex and very time consuming. In 2006, Paul W.K. Rothemund, a senior research fellow at
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A BRIEF OVERVIEW OF DNA ORIGAMI AND ITS APPLICATION
the Computation and Neural System Department at Caltech came up with a faster and simpler
process of taking a long string of DNA and folding it into any shape or pattern, now known as
DNA origami.
What is DNA Origami?
DNA origami is the process of folding DNA to make systematic, two and three
dimensional nanoscale shapes. DNA is the ideal construction material due to its predictable and
programmable nature and the specificity of the connections between its base pairs. (Zadegan, R.
M., & Norton, M. L. (2012). DNA also has “well-known nanometer structural geometry”, has
combined “stiffness and flexibility”, and can easily be manipulated by commercially available
enzymes (Lin, C., Liu, Y., Rinker, S., & Yan, H. (2006).
Process of Folding DNA
In order to create DNA origami, one would need a natural source of a single long strand
of DNA. The current dominating scaffold strand in the field is M13mp18, a mass bred, relatively
affordable bacteriophage (Said, H., Schüller, V. J., Eber, F. J., Wege, C., Liedl, T., & Richert, C.
(2013)). Around this long strand, about 200 programmable short strands of DNA are placed, and
are there to act as “staples” (Rothemund, P. (2016)). Each of the staple strands have a left half
and a right half; because the double helix habitually forms in agreement with the complimentary
rule of the Watson-Crick base pairing – adenine (A) pairs with thymine (T) and that guanine (G)
pairs with cytosine (C) – the left half of the staple strand binds to one position on the scaffold
strand, while the right half of the staple strand binds to a distant position on the scaffold,
bringing the two distant points of the strand together. This creates a constraint or “crease” in the
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A BRIEF OVERVIEW OF DNA ORIGAMI AND ITS APPLICATION
DNA origami, as seen in figure 2. The action of the staples pulling the long strands together
occurs after the DNA is mixed and heated, while it is cooling. The net action of the 200 staple
strands creating creases, folds the long strand into various shapes (Seeman, N. C., Zhang, Y., Du,
S. M., & Chen, J. (1995)).
Figure 2. Staple Strands Folding Long Scaffold Strand
In order to produce a desired shape or pattern, an image is drawn with a raster fill,
folding a long scaffold strand. Then a computer program calculates the placement of individual
staple strands. This is possible due to the well understood intermolecular interactions of DNA.
The first design Rothemund created was the smiley face nanostructures, as seen in Figure 3. This
process if often referred to as ‘bottom-up fabrication’, as opposed to Seeman’s top-down
method. This method of self-assembly offers an inexpensive, equivalent synthesis of
nanostructures under comparatively mild conditions (Rothemund, P. W. (2006)).
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A BRIEF OVERVIEW OF DNA ORIGAMI AND ITS APPLICATION
Figure 3. Nanoscale Smiley Face DNA origami
Observing DNA Origami Structure and its Intracellular Interactions
The nanostructures created by DNA origami are so miniscule that 70 of these structures
would fit across the width of just one blood cell. Because of their minuteness, the nanostructures
cannot be observed through normal light microscopy. The main method used to measure these
molecules is through atomic force microscopy, a method of measuring molecules invented in the
eighties. This process begins by immobilizing the molecules on a hard substrate. As seen in
Figure 4, they are stuck down firmly on a rectangular platform. Then a very fine needle is
dragged back and forth over the surface with a laser beam shining at the tip of the needle. As the
needle bumps up and down the platform, a computer measures the deflection of the needle,
recording a white pixel when the needle goes up and a black pixel when the needle goes own.
The image formed on the computer shows the structure of the folded DNA.
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A BRIEF OVERVIEW OF DNA ORIGAMI AND ITS APPLICATION
Figure 4. Atomic Force Microscopy
Applications
As of now, DNA origami is still in the experimentation process, with researchers creating
microscopic smiley faces and three dimensional cubes. However, as the technology progresses
DNA origami has many potential applications, particularly with specifically constructed DNA
lockboxes – a cage or basket that protects a fragile, toxic, or precious payload – that could be
used to deliver drugs directly to tumors.
DNA lockboxes are being heavily researched due to their ability to attack target cells and
leave other cells alone. This technology is possible due to the “locks” on the DNA origami
boxes. The locks are made of double helix DNA strands that are designed to be complementary
to tumorous cells. Because of this, the DNA strands remain attached, closing the lid of the box,
until it’s in contact with a tumorous cell, where it will unwind and open up the box. This same
technology can also be used to create jails for viruses or be used as a way to immobilize enzymes
(Kean, S. (2016, September)). Another major application for DNA origami is attaching
conductors to the DNA and creating tiny computer chips. Below is an overview of the current
research done on these possible applications (“DNA 'origami' could help build faster, cheaper
computer chips” - American Chemical Society. (2016, March 13)).
Researchers at the Hansjörg Wyss Institute for Biologically Inspired Engineering at
Harvard University created cell-targeted, payload-delivering DNA nanorobots. Ido Bachelet, one
of the researchers in the study stated that "the nanorobot we designed and fabricated is a machine
that can be programmed to autonomously recognize target cells and deliver payloads to those
cells". The nanorobot they created looks like an open ended barrel, as seen in figure 5, that has
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A BRIEF OVERVIEW OF DNA ORIGAMI AND ITS APPLICATION
anchor strands and linker strands attached to the ends, which are computed to be complementary
to the payload and connects the barrel to the payload.
Figure 5. Visual of Nanorobot
The locks on the lockboxes are DNA double helices. In the absence of the key, the
helixes are held strong enough to maintain the structure in a closed position. However, when the
key is present, the DNA lock is designed to recognize that key and switch to bind to the key,
unzipping the double helices and opening the box. Their findings showed that a "nanorobot can
recognize a small population of target cells within a larger population of bystander cells, which
should be left alone". This is because while all cells share the same drug target that they wanted
to attack, only the target cells possessed the proper set of keys to open the lock and therefore
only they will be attacked by the nanorobot and the drug. The nanorobot they designed was
bearing a functional payload, so it had antibodies fragments that were able to communicate with
a cell and induce it to apoptosis (DNA Nanorobot [Video file]. (2012)). The first models the
researchers used were leukemia and lymphoma (Garde, D. (2012, May 15)).
In another study conducted by bioengineers at the Hansjörg Wyss Institute for
Biologically Inspired Engineering at Harvard University, collaborated with Bar-Ilan University
to fabricate “nanoscale robots that are capable of dynamically interacting with each other in a
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A BRIEF OVERVIEW OF DNA ORIGAMI AND ITS APPLICATION
living animal” (Amir, Ben-Ishay). The nanorobots are able to perform similar operations to a
silicon-based computer inserted into a living animal. To prove their concept, the researchers
injected cockroaches with various nanorobots and measured the nanorobots’ diffusion. The DNA
“computers” traveled around the cockroaches’ bodies and interacted with each other and with the
insects’ cells. The team of researchers then injected a variety of nanorobots into the cockroaches
to analyze how “different robot combinations affect where substances are delivered”
(Spickernell, S. (2014, April 8)). They found that the more nanorobots they injected, the more
complex the logic operations became, and that the accuracy of the delivery and control of the
nanorobot is equivalent to that of a computer system. They also stated that they could potentially
increase the computing power in the cockroach to match that of an 8-bit computer (Amir, Y.,
Ben-Ishay, E., Levner, D., Ittah, S., Abu-Horowitz, A., & Bachelet, I. (2014).)
Scientists from iNANO center and CDNA Centerin Aarhus University developed an
18x18x24nm3 hollow DNA origami box with a switchable lid. They noticed that there was a
“higher density of the projected stained DNA helices of boxes lying on the side”. This outcome
is probably due to a bigger surface reaction between negatively charged DNA with the positively
charged surface. The origami box had a unique “reclosing mechanism”, which permitted the box
to repeatedly open and close when exposed to DNA and RNA keys, making the box reusable.
The box can potentially be used for “controlling the function of single molecules, controlled drug
delivery, and molecular computing” (Zadegan, R. M., Jepsen, M. D., Thomsen, K. E., Okholm,
A. H., Schaffert, D. H., Andersen, E. S., . . . Kjems, J. (2012)).
Researchers in the National Center for Nanoscience and Technology in Beijing and
Arizona State University non-covalently attached Doxorubicin, a well-recognized anti-cancer
drug, to DNA origami nanostructures. This was achieved through intercalation, and resulted in
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A BRIEF OVERVIEW OF DNA ORIGAMI AND ITS APPLICATION
high loading efficiency to typically doxorubicin-resistant cancer cells, “inducing a remarkable
reversal of phenotype resistance”. With this new technology, endocytosis of the cell was
increased, which amplified cell-killing activity to doxorubicin-resistant cells. The results suggest
“DNA origami has immense potential as an efficient biocompatible drug carrier and delivery
vehicle in the treatment of cancer” (Jiang, Q., Song, C., Nangreave, J., Liu, X., Lin, L., Qiu,
D., . . . Ding, B. (2012)).
One issue with the functionality of DNA origami structures, observed by group of
researchers at the Wyss Institute at Harvard University, are their susceptibility to nuclease
degradation, and their capability to trigger an inflammatory immune response. Addressing this
issue, the researchers created a structure that imitated a virus’ phospholipid coating to avoid
detection by the immune system, as seen in figure 6. To do this, they strictly controlled the
density of the attached lipid conjugates. When inserted into mice, the nanoparticles with the
phospholipid coating were able to last in the mice’s bloodstream for hours while the uncoated
nanoparticles were rapidly broken down. This designed strategy provided a “platform for the
engineering of sophisticated, translation-ready DNA nanodevices” (Perrault, S. D., & Shih, W.
M. (2014, April 2)).
Figure 6. DNA Nanostructure Mimicking the Structure of a Virus
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A BRIEF OVERVIEW OF DNA ORIGAMI AND ITS APPLICATION
Conclusion
DNA Origami is still a new, progressing concept but has already proven to be a very
promising technology. The combination of chemistry, biology and computer science has led to a
new advancement that can ultimately save millions of lives. Through further research it seems
probable that DNA origami can be used to target specific cells, diagnose particular issues
without affecting unrelated cells, and to act as a miniature computer that is viable in the human
body.
Works Cited
Amir, Y., Ben-Ishay, E., Levner, D., Ittah, S., Abu-Horowitz, A., & Bachelet, I. (2014).
Universal computing by DNA origami robots in a living animal. Nature Nanotech Nature
Nanotechnology, 9(5), 353-357. doi:10.1038/nnano.2014.58
DNA 'origami' could help build faster, cheaper computer chips - American Chemical Society.
(2016, March 13). Retrieved September 26, 2016, from
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A BRIEF OVERVIEW OF DNA ORIGAMI AND ITS APPLICATION
https://www.acs.org/content/acs/en/pressroom/newsreleases/2016/march/dna-
origami.html
DNA Nanorobot [Video file]. (2012). In Vimeo.
Garde, D. (2012, May 15). DNA origami could allow for 'autonomous' delivery. Retrieved
September 26, 2016, from http://www.fiercepharma.com/r-d/dna-origami-could-allow-
for-autonomous-delivery
Jiang, Q., Song, C., Nangreave, J., Liu, X., Lin, L., Qiu, D., . . . Ding, B. (2012). DNA Origami
as a Carrier for Circumvention of Drug Resistance. J. Am. Chem. Soc. Journal of the
American Chemical Society, 134(32), 13396-13403. doi:10.1021/ja304263n
Kean, S. (2016, September). Fun With DNA. Retrieved from
http://www.theatlantic.com/magazine/archive/2016/09/fun-with-dna/492743/
Lin, C., Liu, Y., Rinker, S., & Yan, H. (2006). DNA Tile Based Self-Assembly: Building
Complex Nanoarchitectures. ChemPhysChem, 7(8), 1641-1647.
doi:10.1002/cphc.200600260
Perrault, S. D., & Shih, W. M. (2014, April 2). System Maintenance: From Monday, September
26, 7pm to 11pm EDT. Retrieved September 26, 2016, from
http://pubs.acs.org/doi/full/10.1021/nn5011914
Rothemund, P. W. (2006). Folding DNA to create nanoscale shapes and patterns. Nature,
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Rothemund, P. (2016). DNA Origami: Folded DNA as a Building Material for Molecular
Devices - P. Rothemund - 5/25/16. Retrieved September 26, 2016, from
https://www.youtube.com/watch?v=yPkQsrQwpj8
Said, H., Schüller, V. J., Eber, F. J., Wege, C., Liedl, T., & Richert, C. (2013). M1.3 – a small
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scaffold for DNA origami . Nanoscale, 5(1), 284-290. doi:10.1039/c2nr32393a
Seeman, N., Zhang, Y., Du, S. & Chen, J. (1995). Construction of DNA Polyhedra and
Knots Through Symmetry Minimization. Supramolecular Stereochemistry, 27-32.
doi:10.1007/978-94-011-0353-4_5
Spickernell, S. (2014, April 8). DNA nanobots deliver drugs in living cockroaches. Retrieved
September 26, 2016, from https://www.newscientist.com/article/mg22229643-100-dna-
nanobots-deliver-drugs-in-living-cockroaches/
Zadegan, R. M., & Norton, M. L. (2012). Structural DNA Nanotechnology: From Design to
Applications. International Journal of Molecular Sciences, 13(12), 7149-7162.
doi:10.3390/ijms13067149
Zadegan, R. M., Jepsen, M. D., Thomsen, K. E., Okholm, A. H., Schaffert, D. H., Andersen, E.
S., . . . Kjems, J. (2012). Construction of a 4 Zeptoliters Switchable 3D DNA Box
Origami. ACS Nano, 6(11), 10050-10053. doi:10.1021/nn303767b
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