1. 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. 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. 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 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. 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 don’t. Lesli Mark ‡, Kyoung Nan Kim †, Marya Lieberman † ‡ Saint Joseph’s High School, South Bend, IN 46617, † Department of Chemistry and Biochemistry, Notre Dame, IN,46556 References 1.Rothemund, P. W. K. Nature, 2006, 440, 297 – 302 2.http://www.physorg.com/news119196747.html. Accessed July 20thhttp://www.physorg.com/news119196747.html 3.Yonggang Ke; Stuart Lindsay; Yung Chang; Yan Liu; Hao Yan SCIENCE 2008 319 180 4.http://www.andrew.cmu.edu/user/jamess3/JWSfac.htm. Accessed July 23rd.http://www.andrew.cmu.edu/user/jamess3/JWSfac.htm 5.http://nano.mtu.edu/afm.htm. Accessed July 23rd.http://nano.mtu.edu/afm.htm 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 Positioning and Orientation of DNA Origami a. b. c. Paul Rothemund 1 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 Yan 3, 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) 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 a. b.b. 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. a. b. Figure 3. The molecular structure of the self-assembled monolayers (SAMs) in TAE/Mg2+ pH 8; (a) APTES, (b) TMAC 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. Results 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 6. Paul Rothemund’s 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. a. b. 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. b. a. b. c. d. 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.’ Flat DNA Rolled DNA a. b. 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. 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. a. b. a. b. 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. 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. A B B A a. b. Index Pattern