Positioning and Orientation of DNA Origami
Lesli
‡Saint
Kyoung Nan
Joseph’s High School, South Bend, IN 46617,
Introduction and Overview
b.
†Department
Marya
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
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).
†
Lieberman
of Chemistry and Biochemistry, Notre Dame, IN,46556
Results
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 DNA—extended 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.
c.
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)
†
Kim ,
Introduction and Overview
(Continued)
DNA origami is a self-assembling system, an ideal anchor for nanoelectronic 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.
a.
‡
Mark ,
a.
Discussion and Conclusion
6.47 nm
b.
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 don’t.
5.93 nm
b.
a.
1.0µm
Rolled DNA
Flat DNA
Figure 9. (a) Paul Rothemund’s 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.
280nm
0.00 nm
0.00 nm
b.
a.
Figure 6. Paul Rothemund’s DNA origami on APTES substrate. The DNA is pistacking to form long chains. (a) The origami are aggregating. (b) The width of
the chain is about 60 nm.
Figure 10. (a) Hao Yan’s DNA origami on mica are flat and don’t aggregate. (b)
The same origami on APTES are folded but still don’t aggregate.
Index Pattern
a.
8.16 nm
b.
4.67 nm
a.
b.
A
A
b.
a.
99nm
200nm
B
B
0.00 nm
0.00 nm
Figure 7. Hao Yan’s 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.
a.
Figure 2. (a) An image of Paul Rothemund’s DNA origami on mica (1 µm scale
bar). (b) An image of Hao Yan’s DNA origami with thymidine bumpers on mica
(230 nm scale bar). 1,2
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.
6.41 nm
b.
2.75 nm
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 (A:A, B:B). (Figure modified from reference 3).
In preparation for imaging DNA origami with sticky ends and index
patterns, I conducted control experiments in which I imaged Paul
Rothemund’s DNA origami and Hao Yan’s DNA origami on APTES
and TMAC substrates. This experiment shows how the DNA
origami binds on the substrates.
1.0µm
c.
5.77 nm
0.00 nm
d.
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.
References
220nm
0.00 nm
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
Rothemund’s origami, the offset appears to be either 0 nm or about 30 nm. The
pi-stacking in Paul Rothemund’s origami can allow different amounts of overlap,
but the sticky ends in my origami only allow the origami to stick in certain ways.
8.40 nm
1.
2.
3.
4.
a.
a.
b.
5.
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.
b.
1.0µm
470nm
0.00 nm
Figure 3. The molecular structure of the self-assembled monolayers (SAMs) in
TAE/Mg2+ pH 8; (a) APTES, (b) TMAC
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
0.00 nm
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.’
Acknowledgments
Thanks 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.