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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. Outline. Introduction Bottom- Up fabrication Self-assembling DNA structures

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Bottom up microfabrication using dna l.jpg
Bottom-Up Microfabrication Using DNA

Presentation Given By:

Ben Burns


Janeczka Oates

EE 410/510- Microfabrication and Semiconductor Processes

University of Alabama in Huntsville

Outline l.jpg

  • 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

Self assembly l.jpg


  • 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

What is deoxyribonucleic acid dna l.jpg
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


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



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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 (<80 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....

Dna used to assemble swnt fet l.jpg
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

Slide14 l.jpg

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): <2 x 10-6 Torr, 4nm @ 0.5 Às-1

  • Si etch: ICP-RIE: SF6+C4F8, 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)

Conclusion l.jpg

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


Poor side walls:

Instead of

References l.jpg

J F Allemand et al. “pH-dependent specific binding and combing of DNA.” Biophys J. 1997 October; 73(4): 2064–2070.

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]