1. DNA-Scaffolded Self-Assembling Nano-Circuitry An Ongoing Research Project with Dr. Soha Hassoun Presentation by Brandon Lucia and Laura Smith

2. DNA-Scaffolded... DNA is special type of molecule  Made of a sugar backbone stuck together with nucleotide pairs A(denine), T(hymine), C(ytosine), and G(uanine)  Very interesting chemically but we don't really have much concern w/ that...  Very interesting Structurally Due to its unique shape and structural bonding characteristics

3. DNA-Scaffolded... We can make very tiny lattices out of DNA  In fact, we can make DNA make lattices out of itself, but I'll get to that later These lattices are made up of DNA structural “motifs”  A motif is a building block made out of DNA  Motifs have different shapes We use small motifs to build large motifs We use large motifs to build useful structures

4. ...Self-Assembling... DNA motifs know how to bond w/ one another  Chemistry! We know how we want them to bond We can program the DNA to bond into regular patterns  and take pictures of them Image courtesy Dwyer et al. http://www.ece.duke.edu/~dwyer/pu bs/DAC43.pdf

5. ...Self-Assembling... Sequence Selection  This is a really hard problem Motifs have a dangling single-helix “sticky-end”  this is what bonds to make bigger structures  need to ensure that this won't get stuck to the wrong thing  some metrics exist that rate the tendency to interfere between sequences, and the stability of sequences In one approach, controlled by thermodynamics  Certain sequences bond at higher temps than others gradually lower the temp, and they'll gradually bond in order

6. ...Nano-Circuitry So we can make little DNA Triscuits...what now?  Functionalization We need to attach metal / semiconductors to these structures somehow First, how to attach them at all?  Chemically bond Single Strand DNA (ssDNA) to particles, let that bond to a “sticky-end”

7. ...Nano-Circuitry Two Approaches:  1)Attach metal etc. after structure is built  2)Let structural self- assembly and functionalization occur simultaneously People are showing promising results from both methods Protein particles attached to structural DNA lattices Image courtesy Dwyer et al. http://www.ece.duke.edu/~dwyer/pubs/ICCAD05_p aper_IP7D2%28dwyer%29_rev0.pdf Gold nanowires on DNA substrate Image courtesy Pinto et al. Sequence-Encoded Self-Assembly of Multiple-Nanocomponent Arrays by 2D DNA Scaffolding. Nano-Device Letters, Vol. 5 No. 12 pp.2399- 2402 Oct. 11 2005

8. Further Work This has been a brief overview Lots of other work to be done  Architectures  Device Design  Fault Tolerance  Nano-Micro Interface concerns  How to use such such massive arrays of such tiny devices efficiently / usefully  DNA motif development, selection, analysis Which work best? Why?  Design Automation Issues in all of these areas

9. More About Motifs Triangles Crossover Molecules  Double  Triple  Paranemic Six-helix Hexagonal Bundles

10. Crossover Molecules Double crossover –Distance between crossovers must be in halfturns Triple crossover –Allows space for gaps in molecular arrays –Can incorporate well-structured out-of-plane components in 2D arrays. Paranemic crossover –Form crossovers at every point possible

11. Benefits of Double Crossover Molecules Building Blocks for Nanostructures  Circuits  Nanorobotics Can also be used in other motifs Self-assembly

12. Triangles, Tensegrity, and DNA Construction of DNA triangles –Tensegrity Rigid double helix Flexible single strand Creates stable rigid structure –Each side double helix –1D or 2D arrays DNA Triange Design Image courtesy of Tensegrity: Construction of Rigid DNA Triangles with Flexible Four-Arm DNA Junctions. Liu, D., Wang, M., Deng, Z., Walulu, R., and Mao, C. J. Am. Chem. Soc., 126, 8, 2324 - 2325, 2004, 10.1021/ja031754r

13. Benefits of Triangular Arrays Nanoscale Withstands High Temperature Self-assembly Furthur rigidity with double crossover molecules  Reduced cyclical assembly

14. Hexagons… 6 DNA double helixes 2 Crossover sites –Correct spacing gives hexagonal form –1D and 2D hexagonal arrays Either blunt or sticky ends Image courtesy of Six-Helix Bundles Designed from DNA Mathieu, F., Liao, S., Kopatsch, J., Wang, T., Mao, C., and Seeman, N.C. Nano Lett., 5, 4, 661 - 665, 2005, 10.1021/nl050084f Six-Helix Bundle Motif Schematics Two-dimensional Arrays of Six-helix Bundles

15. Benefits of Hexagonal Arrays Good for surfaces with designed curvature Characteristics of a potential strut Ability for either inner or outer uncharged surface  Inner especially useful for circuits Nanotubes Opens door for other curved structures  Investigate angles

16. Future Goals Non-equilateral triangles Triangles for 3D assembly Sophisticated structures Best structure to use More complicated motifs