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“Molecular Self-Assembly of 3D Nanostructures Using DNA Scaffolding” Gabriel Lavella EECS 235, Presentation #2. Background: Comparison of Bottom Up Techniques Capable of Producing Long Range Complex Structures. Eric Drexeler, Productive Nanosystems: A Technology Roadmap, 2007. - PowerPoint PPT Presentation
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EECS 235, Spring 2009
“Molecular Self-Assembly of 3D Nanostructures Using DNA Scaffolding”
Gabriel Lavella
EECS 235, Presentation #2
EECS 235, Spring 2009
Background: Comparison of Bottom Up Techniques Capable of Producing Long Range Complex Structures
Eric Drexeler, Productive Nanosystems: A Technology Roadmap, 2007
EECS 235, Spring 2009
Migrating from 2-D to 3-D DNA Nano-structuresProblems and Strategies
Problems
1.DNA is too flexible to generate mechanically stable long range structures in solution
2.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)
EECS 235, Spring 2009
Strategy 1: Circular DNA joined through covalent junctions
J. H. Chen,N. C. Seeman, Synthesis from DNA of a molecule with the connectivity of a cube, Nature 1991, 350, 631- 633
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%)
EECS 235, Spring 2009
Strategy 2: Trisoligonucleotide Vertices
M. Scheffler et al.Self-Assembly of Trisoligonucleotidyls:The Case for Nano-Acetylene and Nano Cyclobutadiene, Angew. Chem. Int. Ed. 1999, 38, 3311 – 3315
Synthesis of Trisoligonucleotide molecules
20 unique trisoligonucleotide molecules created to form individual vertices of dodecahedron structure
AFM images of resulting structure
EECS 235, Spring 2009
Strategy 3: Paranemic Cohesion using DNA Struts
M. Scheffler et al.Self-Assembly of Trisoligonucleotidyls:The Case for Nano-Acetylene and Nano Cyclobutadiene, Angew. Chem. Int. Ed. 1999, 38, 3311 – 3315
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
EECS 235, Spring 2009
Strategy 4: Heirarachical Assembly
R. P. Goodman et al, Blocks for Molecular Nanofabrication Rapid Chiral Assembly of Rigid DNA Building Science 2005, 310, 1661 – 1665
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%
EECS 235, Spring 2009
Strategy 4: Heirarachical Assembly
R. P. Goodman et al, Blocks for Molecular Nanofabrication Rapid Chiral Assembly of Rigid DNA Building Science 2005, 310, 1661 – 1665
AFM images of resultant tetrahedral structures
Compressive forces before buckling
EECS 235, Spring 2009
References
1. J. H. Chen,N. C. Seeman, Synthesis from DNA of a molecule with the connectivity of a cube, Nature 1991, 350, 631- 633
2. M. Scheffler et al.Self-Assembly of Trisoligonucleotidyls:The Case for Nano-Acetylene and Nano-Cyclobutadiene, Angew. Chem. Int. Ed. 1999, 38, 3311 – 3315
3. R. P. Goodman et al, Blocks for Molecular Nanofabrication Rapid Chiral Assembly of Rigid DNA Building Science 2005, 310, 1661 – 1665
4. 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
5. Friedrich C. Simmel, Three-Dimensional Nanoconstruction with DNA. Angew. Chem. Int. Ed 2008, 47, 5884-5887