1. “Molecular Self-Assembly of 3D Nanostructures Using DNA Scaffolding”
Gabriel Lavella
EECS 235, Presentation #2

2. Background: Comparison of Bottom Up Techniques Capable of Producing Long Range Complex Structures
Eric Drexeler, Productive Nanosystems: A Technology Roadmap, 2007

3. Migrating from 2-D to 3-D DNA Nano-structures Problems and Strategies
DNA is too flexible to generate mechanically stable long range structures in solution
Large and defect free structures difficult to achieve because of poor hybridization of complementary sequences (discussed in prior presentation)
Strategies
1. Circular DNA joined through covalent junctions (N. C. Seeman, 1991)
2. Trisoligonucleotide vertices (G. Kiedrowski,1999)
3. Parameteric cohesion using DNA struts(G. F. Joyce, 2004)
4. Hierarchical assembly (R.P. Goodman, 2005)

4. Strategy 1: Circular DNA joined through covalent junctions
First demonstration of 3D DNA nanostructures
Process becomes very complicated for more complex structures
Ligation yields are approximately 10% and purification of intermediate structures is required after each ligation. (total yield 1%)
J. H. Chen,N. C. Seeman, Synthesis from DNA of a molecule with the connectivity of a cube, Nature 1991, 350,

5. Strategy 2: Trisoligonucleotide Vertices
Synthesis of Trisoligonucleotide molecules
20 unique trisoligonucleotide molecules created to form individual vertices of dodecahedron structure
AFM images of resulting structure
M. Scheffler et al.Self-Assembly of Trisoligonucleotidyls:The Case for Nano-Acetylene and Nano Cyclobutadiene, Angew. Chem. Int. Ed. 1999, 38, 3311 – 3315

6. Strategy 3: Paranemic Cohesion using DNA Struts
Similar to Rothenmund Origami Method
Single long (1669 nt) and 5 (40nt) staple strands hybridize to form an unfolded octohedron (shown in b)
Paranemic cohesion then facilitates intramolecular folding into an octohedron
Cryo-electron microscope images of resultant structures
M. Scheffler et al.Self-Assembly of Trisoligonucleotidyls:The Case for Nano-Acetylene and Nano Cyclobutadiene, Angew. Chem. Int. Ed. 1999, 38, 3311 – 3315

7. Strategy 4: Heirarachical Assembly
DNA hybridization temperature is dependent on strand length. Gradual cooling allows long strands to hybridize first.
Controlled assembly is achieved specifying the order in which strands assemble. This allows alignment of subsequent sequences and prevent nicks from occurring in the final structure.
Here the edges of strand 1 & 2, and 3 & 4 form first, other edges can then form cooperatively.
The process resulted in high yields of >95%
R. P. Goodman et al, Blocks for Molecular Nanofabrication Rapid Chiral Assembly of Rigid DNA Building Science 2005, 310, 1661 – 1665

8. Strategy 4: Heirarachical Assembly
AFM images of resultant tetrahedral structures
Compressive forces before buckling
R. P. Goodman et al, Blocks for Molecular Nanofabrication Rapid Chiral Assembly of Rigid DNA Building Science 2005, 310, 1661 – 1665

9. References
J. H. Chen,N. C. Seeman, Synthesis from DNA of a molecule with the connectivity of a cube, Nature 1991, 350,
M. Scheffler et al.Self-Assembly of Trisoligonucleotidyls:The Case for Nano-Acetylene and Nano-Cyclobutadiene, Angew. Chem. Int. Ed. 1999, 38, 3311 – 3315
R. P. Goodman et al, Blocks for Molecular Nanofabrication Rapid Chiral Assembly of Rigid DNA Building Science 2005, 310, 1661 – 1665
W. M. Shih, J. D. Quispe, G. F. Joyce, A 1.7-kilobase single-stranded DNA that folds into a nanoscale Octahedron, Nature 2004, 427, 618 – 621
Friedrich C. Simmel, Three-Dimensional Nanoconstruction with DNA. Angew. Chem. Int. Ed 2008, 47,