DNA-Scaffolded Self-Assembling Nano-Circuitry

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

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

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