NSFITR EIA0086015 Structural DNA Nanotechnology Nadrian C Seeman

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NSF-ITR: EIA-0086015: Structural DNA Nanotechnology Nadrian C. Seeman, Subcontractor Department of Chemistry New York

NSF-ITR: EIA-0086015: Structural DNA Nanotechnology Nadrian C. Seeman, Subcontractor Department of Chemistry New York University New York, NY 10003, USA ned. [email protected] edu February 17, 2003

Reciprocal Exchange: A Theoretical Tool To Generate New DNA Motifs

Reciprocal Exchange: A Theoretical Tool To Generate New DNA Motifs

Reciprocal Exchange in a Double Helical Context

Reciprocal Exchange in a Double Helical Context

Biological Reciprocal Exchange: The Holliday Junction

Biological Reciprocal Exchange: The Holliday Junction

Design of Immobile Branched Junctions: Minimize Sequence Symmetry Seeman, N. C. (1982), J. Theor.

Design of Immobile Branched Junctions: Minimize Sequence Symmetry Seeman, N. C. (1982), J. Theor. Biol. 99, 237 -247.

Sticky-Ended Cohesion: Affinity

Sticky-Ended Cohesion: Affinity

Sticky-Ended Cohesion: Structure Qiu, H. , Dewan, J. C. & Seeman, N. C. (1997)

Sticky-Ended Cohesion: Structure Qiu, H. , Dewan, J. C. & Seeman, N. C. (1997) J. Mol. Biol. 267, 881 -898.

The Central Concept: Combine Branched DNA with Sticky Ends to Make Objects, Lattices and

The Central Concept: Combine Branched DNA with Sticky Ends to Make Objects, Lattices and Devices Seeman, N. C. (1982), J. Theor. Biol. 99, 237 -247.

A Method for Organizing Nano-Electronic Components Robinson, B. H. & Seeman, N. C. (1987),

A Method for Organizing Nano-Electronic Components Robinson, B. H. & Seeman, N. C. (1987), Protein Eng. 1, 295 -300. .

A Suggestion for a Molecular Memory Device Organized by DNA (Shown in Stereo) Robinson,

A Suggestion for a Molecular Memory Device Organized by DNA (Shown in Stereo) Robinson, B. H. & Seeman, N. C. (1987), Protein Eng. 1, 295 -300.

A Method to Establish DNA Motif Flexibility

A Method to Establish DNA Motif Flexibility

Geometrical Constructions (Regular Graphs) Cube: Junghuei Chen Truncated Octahedron: Yuwen Zhang

Geometrical Constructions (Regular Graphs) Cube: Junghuei Chen Truncated Octahedron: Yuwen Zhang

Cube . . Chen, J. & Seeman. N. C. (1991), Nature 350, 631 -633.

Cube . . Chen, J. & Seeman. N. C. (1991), Nature 350, 631 -633. .

Truncated Octahedron Zhang, Y. & Seeman, N. C. (1994), J. Am. Chem. Soc. 116,

Truncated Octahedron Zhang, Y. & Seeman, N. C. (1994), J. Am. Chem. Soc. 116, 1661 -1669.

Construction of Crystalline Arrays

Construction of Crystalline Arrays

Derivation of DX and TX Molecules Seeman, N. C. (2001) Nano. Letters 1, 22

Derivation of DX and TX Molecules Seeman, N. C. (2001) Nano. Letters 1, 22 -26.

2 D DX Arrays Erik Winfree (Caltech) Furong Liu Lisa Wenzler

2 D DX Arrays Erik Winfree (Caltech) Furong Liu Lisa Wenzler

Derivation of DX+J Molecules Seeman, N. C. (2001) Nano. Letters 1, 22 -26.

Derivation of DX+J Molecules Seeman, N. C. (2001) Nano. Letters 1, 22 -26.

Schematic of a Lattice Containing 1 DX Tile and 1 DX+J Tile

Schematic of a Lattice Containing 1 DX Tile and 1 DX+J Tile

AFM of a Lattice Containing 1 DX Tile and 1 DX+J Tile Winfree, E.

AFM of a Lattice Containing 1 DX Tile and 1 DX+J Tile Winfree, E. , Liu, F. , Wenzler, L. A. & Seeman, N. C. (1998), Nature 394, 539 -544.

Schematic of a Lattice Containing 3 DX Tiles and 1 DX+J Tile

Schematic of a Lattice Containing 3 DX Tiles and 1 DX+J Tile

AFM of a Lattice Containing 3 DX Tiles and 1 DX+J Tile Winfree, E.

AFM of a Lattice Containing 3 DX Tiles and 1 DX+J Tile Winfree, E. , Liu, F. , Wenzler, L. A. & Seeman, N. C. (1998), Nature 394, 539 -544.

Holliday Junction Parallelogram Arrays Chengde Mao

Holliday Junction Parallelogram Arrays Chengde Mao

Holliday Junction Parallelogram Arrays Mao, C. , Sun, W & Seeman, N. C. (1999),

Holliday Junction Parallelogram Arrays Mao, C. , Sun, W & Seeman, N. C. (1999), J. Am. Chem. Soc. 121, 5437 -5443.

Holliday Junction Parallelogram Arrays Mao, C. , Sun, W & Seeman, N. C. (1999),

Holliday Junction Parallelogram Arrays Mao, C. , Sun, W & Seeman, N. C. (1999), J. Am. Chem. Soc. 121, 5437 -5443.

Triple Crossover Molecules Furong Liu, Jens Kopatsch, Hao Yan Thom La. Bean, John Reif

Triple Crossover Molecules Furong Liu, Jens Kopatsch, Hao Yan Thom La. Bean, John Reif

Triple Crossover Molecules

Triple Crossover Molecules

TX+J Array La. Bean, T. H. , Yan, H. , Kopatsch, J. , Liu,

TX+J Array La. Bean, T. H. , Yan, H. , Kopatsch, J. , Liu, F. , Winfree, E. , Reif, J. H. & Seeman, N. C (2000), J. Am. Chem. Soc. 122, 1848 -1860.

TX Array With Rotated Components La. Bean, T. H. , Yan, H. , Kopatsch,

TX Array With Rotated Components La. Bean, T. H. , Yan, H. , Kopatsch, J. , Liu, F. , Winfree, E. , Reif, J. H. & Seeman, N. C (2000), J. Am. Chem. Soc. 122, 1848 -1860.

Progress Toward Three-Dimensional Arrays Furong Liu Jens Birktoft Yariv Pinto Hao Yan Tong Wang

Progress Toward Three-Dimensional Arrays Furong Liu Jens Birktoft Yariv Pinto Hao Yan Tong Wang Bob Sweet Pam Constantinou Chengde Mao Phil Lukeman Jens Kopatsch Bill Sherman Mike Becker

A 3 D TX Lattice Furong Liu Jens Birktoft Yariv Pinto Hao Yan Bob

A 3 D TX Lattice Furong Liu Jens Birktoft Yariv Pinto Hao Yan Bob Sweet Pam Constantinou Phil Lukeman Chengde Mao Bill Sherman Mike Becker

A 3 D Trigonal DX Lattice Chengde Mao Jens Birktoft Yariv Pinto Hao Yan

A 3 D Trigonal DX Lattice Chengde Mao Jens Birktoft Yariv Pinto Hao Yan Bob Sweet Pam Constantinou Phil Lukeman Furong Liu Bill Sherman Mike Becker

Algorithmic Assembly Chengde Mao Thom La. Bean John Reif

Algorithmic Assembly Chengde Mao Thom La. Bean John Reif

A Cumulative XOR Calculation: Tiles Mao, C. , La. Bean, T. H. , Reif,

A Cumulative XOR Calculation: Tiles Mao, C. , La. Bean, T. H. , Reif, J. H. & Seeman, N. C. (2000), Nature 407, 493 -496.

A Cumulative XOR Calculation: System Mao, C. , La. Bean, T. H. , Reif,

A Cumulative XOR Calculation: System Mao, C. , La. Bean, T. H. , Reif, J. H. & Seeman, N. C. (2000), Nature 407, 493 -496.

A Cumulative XOR Calculation: Assembly Mao, C. , La. Bean, T. H. , Reif,

A Cumulative XOR Calculation: Assembly Mao, C. , La. Bean, T. H. , Reif, J. H. & Seeman, N. C. (2000), Nature 407, 493 -496.

A Cumulative XOR Calculation: Extracting the Answer Mao, C. , La. Bean, T. H.

A Cumulative XOR Calculation: Extracting the Answer Mao, C. , La. Bean, T. H. , Reif, J. H. & Seeman, N. C. (2000), Nature 407, 493 -496.

A Cumulative XOR Calculation: Data Mao, C. , La. Bean, T. H. , Reif,

A Cumulative XOR Calculation: Data Mao, C. , La. Bean, T. H. , Reif, J. H. & Seeman, N. C. (2000), Nature 407, 493 -496.

N-Colorability of Graphs Natasha Jonoska Phiset Sa-Ardyen

N-Colorability of Graphs Natasha Jonoska Phiset Sa-Ardyen

A 3 -Colorable Graph and its Prototype for Computation • • A graph is

A 3 -Colorable Graph and its Prototype for Computation • • A graph is 3 -colorable if it is possible to assign one color to each vertex such that no two adjacent vertices are colored with the same color. In this example, one 2 -armed branched molecule, four 3 -armed branched molecules and one 4 -armed branched molecule are needed. (b) The same graph was chosen for the construction. Since the vertex V 5 in (a) has degree 2, for the experiment a double helical DNA is used to represent the vertex V 5 and the edges connecting V 5 with V 1 and V 4. The target graph to be made consists of 5 vertices and 8 edges. (c) The target graph in DNA representation.

Results • An irregular DNA graph whose edges correspond to DNA helix axes has

Results • An irregular DNA graph whose edges correspond to DNA helix axes has been constructed and isolated based on its closed cyclic character. • The molecule may contain multiple topoisomers, although this has no impact on the characterization of the product. • The graph assembles with the correct edges between vertices, as demonstrated by restriction analysis

Six-Helix Bundle Fred Mathieu Chengde Mao

Six-Helix Bundle Fred Mathieu Chengde Mao

Six-Helix DNA Bundle <--------7. 3 Microns--------> Fred Mathieu Shiping Liao Chengde Mao

Six-Helix DNA Bundle <--------7. 3 Microns--------> Fred Mathieu Shiping Liao Chengde Mao

DNA Nanomechanical Devices

DNA Nanomechanical Devices

B-Z Device Chengde Mao

B-Z Device Chengde Mao

Right-Handed and Left-Handed DNA

Right-Handed and Left-Handed DNA

A Device Based on the B<-->Z Transition - Co(NH 3)6+++ + Co(NH 3)6+++ Mao,

A Device Based on the B<-->Z Transition - Co(NH 3)6+++ + Co(NH 3)6+++ Mao, C. , Sun, W. , Shen, Z. & Seeman, N. C. (1999), Nature 397, 144 -146.

Mao, C. , Sun, W. , Shen, Z. & Seeman, N. C. (1999), Nature

Mao, C. , Sun, W. , Shen, Z. & Seeman, N. C. (1999), Nature 397, 144 -146.

Sequence-Dependent Device Hao Yan

Sequence-Dependent Device Hao Yan

Derivation of PX DNA Seeman, N. C. (2001) Nano. Letters 1, 22 -26.

Derivation of PX DNA Seeman, N. C. (2001) Nano. Letters 1, 22 -26.

PX DNA Seeman, N. C. (2001) Nano. Letters 1, 22 -26.

PX DNA Seeman, N. C. (2001) Nano. Letters 1, 22 -26.

Yan, H. , Zhang, X. , Shen, Z. & Seeman, N. C. (2002), Nature

Yan, H. , Zhang, X. , Shen, Z. & Seeman, N. C. (2002), Nature 415, 62 -65. .

Switchable Versions of PX and JX 2

Switchable Versions of PX and JX 2

Machine Cycle of the PX-JX 2 Device

Machine Cycle of the PX-JX 2 Device

The PX-JX 2 System is Robust Yan, H. , Zhang, X. , Shen, Z.

The PX-JX 2 System is Robust Yan, H. , Zhang, X. , Shen, Z. & Seeman, N. C. (2002), Nature 415, 62 -65.

System to Test the PX-JX 2 Device

System to Test the PX-JX 2 Device

AFM Evidence for Operation of the PX-JX 2 Device Yan, H. , Zhang, X.

AFM Evidence for Operation of the PX-JX 2 Device Yan, H. , Zhang, X. , Shen, Z. & Seeman, N. C. (2002), Nature 415, 62 -65.

New Cohesive Motifs

New Cohesive Motifs

Paranemic Cohesion Xiaoping Zhang

Paranemic Cohesion Xiaoping Zhang

Paranemic Cohesion with the PX Motif Left: Ubiquitous Reciprocal Exchange Creates a PX Molecule.

Paranemic Cohesion with the PX Motif Left: Ubiquitous Reciprocal Exchange Creates a PX Molecule. Center Right: The Strand Connectivity of a PX Molecule. Far Right: The Blue and Red Dumbbell Molecules are Paranemic.

PX Cohesion of DNA Triangles: Theory

PX Cohesion of DNA Triangles: Theory

PX Cohesion of DNA Triangles: Experiment Zhang, X. Yan, H. , Shen, Z. &

PX Cohesion of DNA Triangles: Experiment Zhang, X. Yan, H. , Shen, Z. & Seeman, N. C. (2002) J Am. Chem. Soc. 124, 12940 -12941 (2002)

Edge-Sharing Hao Yan

Edge-Sharing Hao Yan

One-Dimensional Arrays of Edge-Sharing Triangles (Short Direction) Yan, H. & Seeman, N. C. (2002)

One-Dimensional Arrays of Edge-Sharing Triangles (Short Direction) Yan, H. & Seeman, N. C. (2002) J. Supramol. Chem. , in press.

One-Dimensional Arrays of Edge-Sharing Triangles (Long Direction) Yan, H. & Seeman, N. C. (2002)

One-Dimensional Arrays of Edge-Sharing Triangles (Long Direction) Yan, H. & Seeman, N. C. (2002) J. Supramol. Chem. , in press.

One-Dimensional Arrays of Double Edge-Sharing Triangles Yan, H. & Seeman, N. C. (2002) J.

One-Dimensional Arrays of Double Edge-Sharing Triangles Yan, H. & Seeman, N. C. (2002) J. Supramol. Chem. , in press.

A Cassette for the Insertion of a PX-JX 2 Device into a 2 D

A Cassette for the Insertion of a PX-JX 2 Device into a 2 D TX Array Baoquan Ding

TX Array With Rotated Components La. Bean, T. H. , Yan, H. , Kopatsch,

TX Array With Rotated Components La. Bean, T. H. , Yan, H. , Kopatsch, J. , Liu, F. , Winfree, E. , Reif, J. H. & Seeman, N. C (2000), J. Am. Chem. Soc. 122, 1848 -1860.

Cassette to Insert the PX-JX 2 Device ~Perpendicularly Into a TX Lattice PX Conformation

Cassette to Insert the PX-JX 2 Device ~Perpendicularly Into a TX Lattice PX Conformation JX 2 Conformation

Molecular Models of the 2 states of the Sequence-Driven DNA Devices

Molecular Models of the 2 states of the Sequence-Driven DNA Devices

Application of the PX-JX 2 Device in a 1 D Molecular Pegboard

Application of the PX-JX 2 Device in a 1 D Molecular Pegboard

Towards 2 D Circuits Alessandra Carbone (IHES)

Towards 2 D Circuits Alessandra Carbone (IHES)

Circuits and triangular patterns

Circuits and triangular patterns

2 layers assembly

2 layers assembly

Tiles inputs operation TX Molecule outputs

Tiles inputs operation TX Molecule outputs

Molecular Programming: programmed board 4 different states

Molecular Programming: programmed board 4 different states

Control Region & Sticky Ends on the Same Strand

Control Region & Sticky Ends on the Same Strand

Mix & Split Synthesis -- Central

Mix & Split Synthesis -- Central

Mix & Split Synthesis -- Ends

Mix & Split Synthesis -- Ends

Triple Crossover Molecules

Triple Crossover Molecules

An Algorithmic Arrangement Based on Mix & Split Synthesis

An Algorithmic Arrangement Based on Mix & Split Synthesis

Summary of Results (1) • Reciprocal exchange generates new DNA motifs, and sequence-symmetry minimization

Summary of Results (1) • Reciprocal exchange generates new DNA motifs, and sequence-symmetry minimization provides an effective way to generate sequences for them. • Sticky ends, PX cohesion and edge-sharing are can hold DNA motifs together in a sequence-specific fashion.

Summary of Results (2) • 2 D lattices with tunable features have been built

Summary of Results (2) • 2 D lattices with tunable features have been built from DX, TX and DNA parallelogram motifs. Preliminary evidence for 3 D assembly has been obtained. • DNA nanomechanical devices have been produced using both the B-Z transition and PX-JX 2 conversion through sequence control.

Summary of Results (3) • An algorithmic 4 -bit cumulative XOR calculation has been

Summary of Results (3) • An algorithmic 4 -bit cumulative XOR calculation has been performed. • An irregular graph has been synthesized in solution, establishing the principle of using this type of assembly for calculations. • New motifs include a 6 -helix bundle and a cassette for inserting a PX-JX 2 device into a TX array.