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NSF-ITR: EIA : Structural DNA Nanotechnology Nadrian C. Seeman, Subcontractor Department of Chemistry New York University New York, NY 10003, USA February 17, 2003

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Reciprocal Exchange: A Theoretical Tool To Generate New DNA Motifs

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Reciprocal Exchange in a Double Helical Context

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Biological Reciprocal Exchange: The Holliday Junction

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

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Sticky-Ended Cohesion: Affinity

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

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

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

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

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A Method to Establish DNA Motif Flexibility

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

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

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

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Construction of Crystalline Arrays

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Seeman, N.C. (2001) NanoLetters 1, Derivation of DX and TX Molecules

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

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Seeman, N.C. (2001) NanoLetters 1, Derivation of DX+J Molecules

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

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

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

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

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Chengde Mao Holliday Junction Parallelogram Arrays

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

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Holliday Junction Parallelogram Arrays

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Triple Crossover Molecules Furong Liu, Jens Kopatsch, Hao Yan Thom LaBean, John Reif

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Triple Crossover Molecules

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

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

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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

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

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

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Algorithmic Assembly Chengde Mao Thom LaBean John Reif

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A Cumulative XOR Calculation: Tiles Mao, C., LaBean, T.H., Reif, J.H. & Seeman, N.C. (2000), Nature 407,

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A Cumulative XOR Calculation: System Mao, C., LaBean, T.H., Reif, J.H. & Seeman, N.C. (2000), Nature 407,

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A Cumulative XOR Calculation: Assembly Mao, C., LaBean, T.H., Reif, J.H. & Seeman, N.C. (2000), Nature 407,

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

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A Cumulative XOR Calculation: Data Mao, C., LaBean, T.H., Reif, J.H. & Seeman, N.C. (2000), Nature 407,

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Natasha Jonoska Phiset Sa-Ardyen N-Colorability of Graphs

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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 V5 in (a) has degree 2, for the experiment a double helical DNA is used to represent the vertex V5 and the edges connecting V5 with V1 and V4. The target graph to be made consists of 5 vertices and 8 edges. (c) The target graph in DNA representation.

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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

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Fred Mathieu Chengde Mao Six-Helix Bundle

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Six-Helix DNA Bundle Fred Mathieu Shiping Liao Chengde Mao

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DNA Nanomechanical Devices

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B-Z Device Chengde Mao

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Right-Handed and Left-Handed DNA

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

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

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Sequence-Dependent Device Hao Yan

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Derivation of PX DNA Seeman, N.C. (2001) NanoLetters 1,

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PX DNA Seeman, N.C. (2001) NanoLetters 1,

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

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Switchable Versions of PX and JX 2

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Machine Cycle of the PX-JX 2 Device

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

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System to Test the PX-JX 2 Device

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

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New Cohesive Motifs

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Paranemic Cohesion Xiaoping Zhang

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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.

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PX Cohesion of DNA Triangles: Theory

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

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Edge-Sharing Hao Yan

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

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

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

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

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

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

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

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

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Towards 2D Circuits Alessandra Carbone (IHES)

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Circuits and triangular patterns

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2 layers assembly

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Tiles inputs outputs operation TX Molecule

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Molecular Programming: programmed board 4 different states

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Control Region & Sticky Ends on the Same Strand

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Mix & Split Synthesis -- Central

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Mix & Split Synthesis -- Ends

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Triple Crossover Molecules

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An Algorithmic Arrangement Based on Mix & Split Synthesis

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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.

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

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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.

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