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NSF-ITR: EIA-0086015: Structural DNA Nanotechnology Nadrian C. Seeman, Subcontractor Department of Chemistry New York University New York, NY 10003, USA.

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Presentation on theme: "NSF-ITR: EIA-0086015: Structural DNA Nanotechnology Nadrian C. Seeman, Subcontractor Department of Chemistry New York University New York, NY 10003, USA."— Presentation transcript:

1 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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3 Reciprocal Exchange: A Theoretical Tool To Generate New DNA Motifs

4 Reciprocal Exchange in a Double Helical Context

5 Biological Reciprocal Exchange: The Holliday Junction

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

7 Sticky-Ended Cohesion: Affinity

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

9 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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11 Robinson, B.H. & Seeman, N.C. (1987), Protein Eng. 1, A Method for Organizing Nano-Electronic Components

12 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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14 A Method to Establish DNA Motif Flexibility

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

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

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

18 Construction of Crystalline Arrays

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

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

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

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

24 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

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

26 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

27 Chengde Mao Holliday Junction Parallelogram Arrays

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

29 Holliday Junction Parallelogram Arrays

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

31 Triple Crossover Molecules

32 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,

33 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,

34 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

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

36 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

37 Algorithmic Assembly Chengde Mao Thom LaBean John Reif

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

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

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

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

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

45 Natasha Jonoska Phiset Sa-Ardyen N-Colorability of Graphs

46 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.

47 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

48 Fred Mathieu Chengde Mao Six-Helix Bundle

49 Six-Helix DNA Bundle Fred Mathieu Shiping Liao Chengde Mao

50 DNA Nanomechanical Devices

51 B-Z Device Chengde Mao

52 Right-Handed and Left-Handed DNA

53 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 +++

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

55 Sequence-Dependent Device Hao Yan

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

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

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

59 Switchable Versions of PX and JX 2

60 Machine Cycle of the PX-JX 2 Device

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

62 System to Test the PX-JX 2 Device

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

64 New Cohesive Motifs

65 Paranemic Cohesion Xiaoping Zhang

66 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.

67 PX Cohesion of DNA Triangles: Theory

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

69 Edge-Sharing Hao Yan

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

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

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

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

74 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,

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

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

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

78 Towards 2D Circuits Alessandra Carbone (IHES)

79 Circuits and triangular patterns

80 2 layers assembly

81 Tiles inputs outputs operation TX Molecule

82 Molecular Programming: programmed board 4 different states

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85 Control Region & Sticky Ends on the Same Strand

86 Mix & Split Synthesis -- Central

87 Mix & Split Synthesis -- Ends

88 Triple Crossover Molecules

89 An Algorithmic Arrangement Based on Mix & Split Synthesis

90 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.

91 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.

92 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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