DNAScaffolded SelfAssembling NanoCircuitry

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DNA-Scaffolded Self-Assembling Nano-Circuitry

• An Ongoing Research Project
• with Dr. Soha Hassoun
• Presentation by Brandon Lucia and Laura Smith

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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

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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

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...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.ed
u/dwyer/pubs/DAC43.pdf
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...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

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...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

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...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_pa
per_IP7D228dwyer29_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
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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

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More About Motifs

• Triangles
• Crossover Molecules
• Double
• Triple
• Paranemic
• Six-helix Hexagonal Bundles

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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

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Benefits of Double Crossover Molecules

• Building Blocks for Nanostructures
• Circuits
• Nanorobotics
• Can also be used in other motifs
• Self-assembly

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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
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Benefits of Triangular Arrays

• Nanoscale
• Withstands High Temperature
• Self-assembly
• Furthur rigidity with double crossover molecules
• Reduced cyclical assembly

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Hexagons

• 6 DNA double helixes
• 2 Crossover sites
• Correct spacing gives hexagonal form
• 1D and 2D hexagonal arrays
• Either blunt or sticky ends

Six-Helix Bundle Motif Schematics
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
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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

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Future Goals

• Non-equilateral triangles
• Triangles for 3D assembly
• Sophisticated structures
• Best structure to use
• More complicated motifs