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
Presentation Given By:
EE 410/510- Microfabrication and Semiconductor Processes
University of Alabama in Huntsville
Starts with small-scale components and design larger structures
*Life (DNA) is a good basis for artificial bottom-up design
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.
DNA tilings and/or assembling structures bound to DNA
Like a puzzle
Artificial ssDNA assembles to form a tile
Sticky ends match to form lattice
AFM image of TX array
Can be used for computation....
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
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
“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 “
* When Top-Down meets Bottom-Up
“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.”
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:
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] http://scai.snu.ac.kr/cec2001/selfassemble.talk.pdf