DNA-Scaffolded Self-Assembling Nano-Circuitry

An Ongoing Research Project with Dr. Soha Hassoun

Presentation by Brandon Lucia and Laura Smith

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

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

...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

...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

...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”

...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 latticesImage courtesy Dwyer et al.http://www.ece.duke.edu/~dwyer/pubs/ICCAD05_paper_IP7D2%28dwyer%29_rev0.pdf

Gold nanowires on DNA substrateImage courtesy Pinto et al.Sequence-Encoded Self-Assembly ofMultiple-Nanocomponent Arrays by 2DDNA Scaffolding. Nano-Device Letters, Vol. 5 No. 12 pp.2399-2402 Oct. 11 2005

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

More About Motifs

Triangles Crossover Molecules

Double Triple Paranemic

Six-helix Hexagonal Bundles

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

Benefits of Double Crossover Molecules

Building Blocks for Nanostructures Circuits Nanorobotics

Can also be used in other motifs Self-assembly

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 DesignImage 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

Benefits of Triangular Arrays

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

Reduced cyclical assembly

Hexagons…

• 6 DNA double helixes

• 2 Crossover sites– Correct spacing gives

hexagonal form– 1D and 2D hexagonal

arrays

• Either blunt or sticky ends

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

Six-Helix Bundle Motif Schematics

Two-dimensional Arrays of Six-helix Bundles

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

Future Goals

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