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EECS 235, Spring 2009 “Molecular Self-Assembly of 3D Nanostructures Using DNA Scaffolding” Gabriel Lavella EECS 235, Presentation #2

“Molecular Self-Assembly of 3D Nanostructures Using DNA Scaffolding” Gabriel Lavella

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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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Page 1: “Molecular Self-Assembly of 3D Nanostructures Using DNA Scaffolding” Gabriel  Lavella

EECS 235, Spring 2009

“Molecular Self-Assembly of 3D Nanostructures Using DNA Scaffolding”

Gabriel Lavella

EECS 235, Presentation #2

Page 2: “Molecular Self-Assembly of 3D Nanostructures Using DNA Scaffolding” Gabriel  Lavella

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

Page 3: “Molecular Self-Assembly of 3D Nanostructures Using DNA Scaffolding” Gabriel  Lavella

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)

Page 4: “Molecular Self-Assembly of 3D Nanostructures Using DNA Scaffolding” Gabriel  Lavella

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%)

Page 5: “Molecular Self-Assembly of 3D Nanostructures Using DNA Scaffolding” Gabriel  Lavella

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

Page 6: “Molecular Self-Assembly of 3D Nanostructures Using DNA Scaffolding” Gabriel  Lavella

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

Page 7: “Molecular Self-Assembly of 3D Nanostructures Using DNA Scaffolding” Gabriel  Lavella

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%

Page 8: “Molecular Self-Assembly of 3D Nanostructures Using DNA Scaffolding” Gabriel  Lavella

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

Page 9: “Molecular Self-Assembly of 3D Nanostructures Using DNA Scaffolding” Gabriel  Lavella

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