Bottom-Up Microfabrication Using DNA

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Bottom-Up Microfabrication Using DNA
Presentation Given By Ben Burns Janeczka
Oates EE 410/510-
Microfabrication and Semiconductor Processes
University of Alabama in Huntsville
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Outline

• Introduction
• Bottom- Up fabrication
• Self-assembling DNA structures
• DNA tiles
• Single Walled carbon Nano-Tube Field Effect
  Transistor (SWNT FET)
• DNA shadow lithography
• Conclusion
• Issues

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Bottom-Up Fabrication

• Starts with small-scale components and design
  larger structures

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Self-Assembly
DIY

• Self Assembly
• Is a Bottom-up rather than a Top-Down process as
  used in manufacturing or lithography
• Involves self-ordering substructures into
  superstructures
• Living organisms are best example
• Life (DNA) is a good basis for artificial
  bottom-up design

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What is Deoxyribonucleic Acid (DNA)?

• DNA is the genetic blueprint for all living
  organisms
• Composed of four nucleic acids adenine(A),
  guanine (G), cystosine (C), and thymine (T).
• Well understood assembly
• -Watson-Crick pairing
• Easy to make
• -Just order from company!
• Small Size

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Bottom-Up Fabrication

• DNA self-assembly is a bottom-up fabrication
  technique that can be used to achieve molecular
  scale resolution.
• Speed of DNA self-assembly reactions
• Between a few seconds to many minutes.
• Far slower per assembly than silicon technology.
• Concurrent DNA self-assembly
• Concurrent assemblies execute computations
  independently.
• Massively parallel
• Use
• DNA tilings and/or assembling structures bound to
  DNA

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DNA Tiling

• Like a puzzle
• Artificial ssDNA assembles to form a tile
• Sticky ends match to form lattice

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DX and TX Tiles

• Double crossover two strands of DNA fused
• Triple crossover three strands
• Lots of other ways to make tiles

DX
TX
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DNA Tiling

• AFM image of TX array

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DNA Tiling

• E) AFM image of the letters D, N, and A
  displayed on self-assembled 4 x 4 nano-arrays
  (lt80 nm / side)

• TEM image of 6nm gold particles labeled with
  15-mer oligo paired with matching strand on
  assembled DX lattice

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DNA Tiling

• Can be used for computation....

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DNA used to assemble SWNT FET
Assembly of a DNA-templated FET and wires
contacting it. The following steps are (i)
RecA monomers polymerize on a ssDNA molecule to
form a nucleoprotein filament. (ii) Homologous
recombination reaction leads to binding of the
nucleoprotein filament at the desired address on
an aldehyde-derivatized scaffold dsDNA molecule.
(iii) The DNA-bound RecA is used to localize a
streptavidin-functionalized SWNT, utilizing a
primary antibody to RecA and a biotin-conjugated
secondary antibody. (iv) Incubation in an AgNO3
solution leads to the formation of silver
clusters on the segments that are unprotected by
RecA. (v) Electroless gold deposition, using the
silver clusters as nucleation centers, results in
the formation of two DNA-templated gold wires
contacting the SWNT bound at the gap
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SWNT FET AFM Image Results

• Localization of a SWNT at a specific address on
  the scaffold dsDNA molecule using RecA. (A) An
  AFM image of a 500-base-long ( 250 nm) RecA
  nucleoprotein filament (black arrow) localized at
  a homologous sequence on a DNA scaffold molecule.
  Bar, 200 nm. (B) An AFM image of a
  streptavidin-coated SWNT (white arrow) bound to a
  500-base-long nucleoprotein filament localized on
  a -DNA scaffold molecule. Bar, 300 nm. (C) A
  scanning conductance image of the same region as
  in (B). The conductive SWNT (white arrow) yields
  a considerable signal whereas the insulating DNA
  is hardly resolved. Bar, 300 nm

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SWNT FET SEM Image Results
A DNA-templated carbon nanotube FET and metallic
wires contacting it. SEM images of SWNTs
contacted by self-assembled DNA-templated gold
wires. (A) An individual SWNT. (B) A rope of
SWNTs. Bars, 100 nm
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DNA Shadow NanoLithography
When Top-Down meets Bottom-Up

• Combination of traditional microfabrication and
  DNA
• DNA bonds to substrate treated with specific
  silane, CDMOS (chlorodimethyloctadecylsilane)
• thermal deposition of Al (small grain size) lt2 x
  10-6 Torr, 4nm _at_ 0.5 Às-1
• Si etch ICP-RIE SF6C4F8, 2x10-7 Torr, 1-4 min

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DNA Combing

• Substrate is treated with CDMOS
• 30 min, 90 C
• DNA attaches
• Substrate then dried

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DNA Shadow NanoLithography Results
Transfer of linear DNA pattern to silicon
surfaces by DSN SEM micrographs of linear (E)
nanometer-scale trenches etched into silicon.
Scale bar on the inset is 50 nm, and the trenches
are 8 nm wide.

• width depends on angle of deposition (7-22nm)
• sidewall quality depends on width (40nm depth)

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Conclusion

• One problem for integrating DNA is its low
  melting point.
• depends on AT/GC bonds (more GC higher Tm)
  30-70 C
• DX, TX 60-80 C
• There is no method to implement a chain reaction
  of self-assembling design steps
• Lots of errors in tiling assembly
• 'D''N''A' tiles yield 30
• hard to check
• fewer steps, fewer errors
• 3D tiles hard to control shape
• DSN
• Poor side walls

Instead of
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References

• J F Allemand et al. pH-dependent specific
  binding and combing of DNA. Biophys J. 1997
  October 73(4) 20642070.
• Héctor A. Becerril and Adam T. Woolley. DNA
  Shadow Nanolithography. Small 3.9 (2007)
  1534-38
• Kurt V. Gothelf and Thomas H. LaBean.
  DNA-programmed assembly of nanostructures. Org.
  Biomol. Chem., 2005, 3, 4023 4037
• Kinneret Keren et al. DNA-templated carbon
  nanotube field-effect transistor. Science
  302.5649 (2003) p1380(3)
• T. Kusakabe et al. DNA mediated sequential
  self-assembly of nano/micro components. In MEMS
  2008. IEEE 21st International Conference on
  (2008) 1052-1055
• Thomas H. LaBean et al. "Construction, Analysis,
  Ligation, and Self-Assembly of DNA Triple
  Crossover Complexes." J. Am. Chem. Soc. 122.9
  (2000) 1848-60
• Park, Sung Ha et al. Finite-Size, Fully
  Addressable DNA Tile Lattices For7med by
  Hierarchical Assembly Procedures Angewandte
  Chemie 118.40 (2006) 749-753
• John H. Rief, Thomas H. LaBean, Nadrian C.
  Seeman. Challenges and Applications for
  Self-Assembled DNA Nanostructures Lecture Notes
  In Computer Science Vol. 2054 (2000) 173-198
• John H. Reif, Thom LaBean and Nadrian Seeman
  Challenges and Applications for Self-Assembled
  DNA Nanostructures (2001) online
  http//scai.snu.ac.kr/cec2001/selfassemble.talk.pd
  f

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Questions?