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1
Positioning and Orientation of DNA Origami
Lesli Mark, Kyoung Nan Kim, Marya
Lieberman Saint Josephs High School, South
Bend, IN 46617, Department of Chemistry and
Biochemistry, Notre Dame, IN,46556
Introduction and Overview DNA origami is a
self-assembling system, an ideal anchor for
nano-electronic devices. The scaffold of the DNA
is a single strand of DNA from m13mp18 viral DNA.
In order to hold the DNA in its rectangular 100
nm by 70 nm shape, hundreds of helper strands are
used. Helper strands are short single strands of
DNA which bind at specific parts of the DNA
resulting in the origami.
Results
Introduction and Overview (Continued)In order
for the DNA to be used as an anchor in electronic
logic chips, I had to control the position and
orientation of the DNA origami. Sticky ends and
index patterns may be the key to controlling the
origami. Sticky ends are single strands of
DNAextended helper strands. A portion of the
sticky end pairs up with a complementary section
of the origami, the remainder extends out from
the scaffold. In my DNA origami solution, there
are four types of sticky ends A, B, A?, and B?.
The sequences were designed so A pairs up only
with A? and B pairs up only with B ?. Index
patterns are hairpin/dumbbell loops. The index
attaches to a specific area of the origami, on
every origami. The loop acts as a bump on the
DNA origami, so I can tell what the orientation
is.
Discussion and Conclusion The three types of DNA
origami used in this project have different
structures when they attach to surfaces.
Sometimes the origami are flat like a piece of
paper and other times they are rolled like a
cardboard tube. Sometimes the short ends of the
origami stick together and sometimes they dont.
a.
b.
b.
a.
a.
b.
c.
Rolled DNA
Flat DNA
Figure 9. (a) Paul Rothemunds DNA origami on
mica are flat and the short ends stick together.
(b) The same origami on APTES are rolled up but
the short ends still stick together.
b.
a.
Figure 1. (a) The m13mp18 single stranded DNA
with more than 250 helper strands. (b) The helper
strands lining up with their corresponding bases
on the m13mp18 DNA. (c) The DNA origami after all
of the helper strands attaches to the m13mp18. 1
Figure 6. Paul Rothemunds DNA origami on APTES
substrate. The DNA is pi-stacking to form long
chains. (a) The origami are aggregating. (b) The
width of the chain is about 60 nm.
Figure 10. (a) Hao Yans DNA origami on mica are
flat and dont aggregate. (b) The same origami on
APTES are folded but still dont aggregate.
Paul Rothemund1 had imaged his DNA origami using
an Atomic Force Microscope. On mica, the origami
line up due to ?-stacking at the helix ends (see
figure 2a). Hao Yan3, a professor at Arizona
State University, developed DNA origami with
poly-thymidines that act as bumpers, preventing
the stacking of DNA origami. These origami do
not line up (see figure 2b)
Index Pattern
a.
b.
a.
b.
A?
A
b.
a.
Figure 11. (a) A cartoon of DNA origami with
sticky ends and index pattern. (b) My DNA origami
on mica are flat and the short ends stick
together. Unlike Paul Rothemunds origami, the
offset appears to be either 0 nm or about 30 nm.
The pi-stacking in Paul Rothemunds origami can
allow different amounts of overlap, but the
sticky ends in my origami only allow the origami
to stick in certain ways.
B
B?
Figure 7. Hao Yans DNA origami on APTES
substrate. (a) This image suggests that the
suspected DNA origami is rolling or folding on
itself. (b) Outlined is suspected origami that
is 80 nm long, 68 nm wide, and 2.1 nm tall.
My summer project will continue. The other
origami did stick to silicon, but on the APTES
surface they rolled up or folded up. I intend to
image my sample on APTES, TMAC and an APTES/TMAC
mixture other students in the group observed
origami binding flat to specific APTES/TMAC
mixtures. I also intend to reduce the
concentration of the free complements to the
sticky ends in order to prevent the offset
structure.
b.
a.
Figure 2. (a) An image of Paul Rothemunds DNA
origami on mica (1 µm scale bar). (b) An image of
Hao Yans DNA origami with thymidine bumpers on
mica (230 nm scale bar). 1,2
Figure 4. A DNA origami design. The green
strands are helper strands the red is the
m13mp18 DNA the dark blue strands are the index
patterns. The sticky ends are labeled (AA?,
BB?). (Figure modified from reference 3).

DNA origami could be useful to organize
nano-electronic logic chips. In order for this
to work, the DNA must be integrated with silicon
circuits. Since both silicon and DNA origami are
negatively charged they repel one another.
Application of cationic compounds that stick to
the silicon surface, such as APTES
(aminopropyltriethoxysilane) or TMAC
(N-trimethoxysilylpropyl -N,N,N-trimethylammonium
chloride) would allow for the attachment of the
origami.

• References
• Rothemund, P. W. K. Nature, 2006, 440, 297 302
• http//www.physorg.com/news119196747.html.
  Accessed July 20th
• Yonggang Ke Stuart Lindsay Yung Chang Yan Liu
  Hao Yan SCIENCE 2008 319 180
• http//www.andrew.cmu.edu/user/jamess3/JWSfac.htm.
  Accessed July 23rd.
• http//nano.mtu.edu/afm.htm. Accessed July 23rd.

In preparation for imaging DNA origami with
sticky ends and index patterns, I conducted
control experiments in which I imaged Paul
Rothemunds DNA origami and Hao Yans DNA origami
on APTES and TMAC substrates. This experiment
shows how the DNA origami binds on the
substrates.
c.
d.
a.
b.
b.
a.
AcknowledgmentsThanks to Dr. Paul Rothemund for
developing the DNA origami. Thanks to the ND
Radiation Lab for the use of the AFM. Thanks to
Lieberman and Huber labs. Thanks to the Kaneb
Center for the summer grant. A special thanks to
Dr. Lieberman and Kyoung Nan Kim for developing
the project and including me in it.
Figure 8. My sample of DNA origami with sticky
ends on mica. Images a and b were acquired on
a different day than image c and d. (a) The
DNA origami are aligning. (b) A magnified portion
of image a. The short ends of the origami
stick together but some are offset. This could
be a result of origami that are flipped upside
down. (c) The DNA origami are aggregated. Perhaps
a solution to this is diluting the solution. (d)
A magnified area of image c.
Figure 5. Atomic Force Microscopes (AFM) use a
sharp probe to scan the surfaces of samples to
produce images of the surface topography. AFM
images are essential to this project, they help
determine how the DNA origami are positioned and
oriented. 4,5
Figure 3. The molecular structure of the
self-assembled monolayers (SAMs) in TAE/Mg2 pH
8 (a) APTES,  (b) TMAC