Self Assembly : Nature’s Way To Do It Arbel Artzy Schnirman Biology Seminar 2008 Part 1

Self Assembly Self-Assembly (SA) is the spontaneous organization of molecules or objects into well-defined aggregates via noncovalent interactions (or forces) Building Blocks: molecules and objects with coded information for self-assembly Processing: mix, shake, and form product

Attractive Features of Self- Assembly Understanding life Self-assembly proceeds spontaneously The self-assembled structure is often at or close to thermodynamic equilibrium Self-assembly tends to reject defects, and also has self-healing capability Self-assembly is one of the few practical strategies for making ensembles of nanostructures

The development of self-assembly as a useful approach to the synthesis and manufacturing of complex systems and materials has been identified as a "grand challenge" in the 2003 U.S. National Academies report "Beyond the Molecular Frontier". Science magazine included (7/1/05) "How far can we push chemical self-assembly" in the top-25 list of "big questions" facing science

Principles of Molecular Self- Assembly PNAS April 16, 2002 vol. 99 no –4774

Present Application SCIENCE VOL MARCH 2002

Future Applications Crystallization at All Scales Robotics and Manufacturing Nanoscience and Technology Microelectronics “We understand very little about how dissipation of energy leads to the emergence of ordered structures from disordered components in these systems. But we know that they are vitally important in the cell. That knowledge, by itself, makes it worthwhile to study them” SCIENCE VOL MARCH 2002

Inspiration byNature Inspiration by Nature NATURE VOL JANUARY 2001 René Binet’s entrance to the World Exposition in Paris, 1900, inspired by Haeckel’s drawings of radiolarians

Why DNA? "The nucleic-acid 'system' that operates in terrestrial life is optimized (through evolution) chemistry incarnate. Why not use it... to allow human beings to sculpt something new, perhaps beautiful, perhaps useful, certainly unnatural." Roald Hoffmann, writing in American Scientist, 1994 Roald Hoffmann, writing in American Scientist, 1994 Diameter of about 2 nanometres Short structural repeat (helical pitch) of about 3.4–3.6 nm Stiffness with a persistence length of around 50 nm Programmable molecular recognition-Sticky-ended

One Dimension One Dimension Higher Dimension Higher Dimension

Construction of a DNA Truncated Octahedron J. Am. Chem. SOC. 1994,116,

5-TTGTTCCAGATCTAAATACCTGAACCTTAAGTGTGGTATTTAGATCTGGAACTT-3 5-ACACCAAGGTTCACCGACCAGCGCCTGCTCATTTTTATGAGCAGGCGCTGGTCGGACACTTAGGCTAC-3 J. Am. Chem. SOC. 1994,116,

5-TTGTTCCAGATCTAAATACCTGAACCT-3 5-ACACCAAGGTTCACCGACCAGCGCCTGCTCATT-3 5-TTTATGAGCAGGCGCTGGTCGGACACTTAGGCTAC-3 5-TAAGTGTGGTATTTAGATCTGGAACTT-3 J. Am. Chem. SOC. 1994,116,

5-TTGTTCCAGATCTAAATACC 5-ACACCAAGGTTCACCGACCAGCGCCTGCTCATT-3 5-TTTATGAGCAGGCGCTGGTCGGACACTTAGGCTAC-3 GGTATTTAGATCTGGAACTT-3 5-TAAGTGT TGAACCT-3 J. Am. Chem. SOC. 1994,116,

5-ACACCAAGGTTCA CCGACCAGCGCCTGCTCATT-3 5-TTTATGAGCAGGCGCTGGTCGG ACACTTAGGCTAC-3 5-TTGTTCCAGATCTAAATACC GGTATTTAGATCTGGAACTT-3 5-TAAGTGT TGAACCT-3 J. Am. Chem. SOC. 1994,116,

TGAACCT-3 5-TTGTTCCAGATCTAAATACC GGTATTTAGATCTGGAACTT-3 5-ACACCAAGGTTCA CCGACCAGCGCCTGCTCATT-3 5-TTTATGAGCAGGCGCTGGTCGG 5-TAAGTGT ACACTTAGGCTAC-3 J. Am. Chem. SOC. 1994,116,

16 Yield: 10% J. Am. Chem. SOC. 1994,116,

Yield: 1% J. Am. Chem. SOC. 1994,116,

Yield: 30% J. Am. Chem. SOC. 1994,116,

2

2 Each of the 7 links yield: 50% Total yield: < 1% J. Am. Chem. SOC. 1994,116,

Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra NATURE| Vol March 2008

Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra NATURE| Vol March 2008

Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra NATURE| Vol March 2008

Origami First step Origami First step NATURE Vol March 2006

Origami Second step

NATURE Vol March 2006 Origami third step

NATURE Vol March 2006 Origami Fourth step Origami Fourth step

NATURE Vol March 2006 Origami Fifth step Origami Fifth step

NATURE Vol March 2006 Examples

NATURE Vol March 2006 Examples

Self-assembly is one of the few practical strategies for making ensembles of nanostructures Summary DNA will be a key player in bottom-up nanotechnology nanotechnology

1.Ball, P. (2001) Nature 409, He, Y., Ye, T., Su, M., Zhang, C., Ribbe, A. E., Jiang, W. & Mao, C. (2008) Nature 452, Kamien, R. D. (2003) Science 299, Rothemund, P. W. K. (2006) Nature 440, Seeman, N. C. (2003) Nature 421, Whitesides, G. M. & Grzybowski, B. (2002) Science 295, Zhang, Y. & Seeman, N. C. (1994) J. Am. Chem. Soc. 116,