1. NSF-ITR: EIA-0086015: Structural DNA Nanotechnology
Nadrian C. Seeman, Subcontractor
Department of Chemistry
New York University
New York, NY 10003, USA
February 17, 2003

3. A Theoretical Tool To Generate
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. Design of Immobile Branched Junctions: Minimize Sequence Symmetry
Seeman, N.C. (1982), J. Theor.Biol. 99,

7. Sticky-Ended Cohesion: Affinity

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

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

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

12. 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, B.H. & Seeman, N.C. (1987), Protein Eng. 1,

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

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

18. Construction of Crystalline Arrays

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

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

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

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

24. 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,

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

26. 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,

27. Holliday Junction Parallelogram Arrays
Chengde Mao

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

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

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

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

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

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

46. A 3-Colorable Graph and its Prototype for Computation
This is slide #3
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. Six-Helix Bundle
Fred Mathieu
Chengde Mao

49. <----------------7.3 Microns---------------->
Six-Helix DNA Bundle
Fred Mathieu
Shiping Liao
Chengde Mao
< Microns >

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
- Co(NH 3)6+++
+ Co(NH 3)6+++
Mao, C., Sun, W., Shen, Z. & Seeman,N.C. (1999), Nature 397,

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

55. Sequence-Dependent Device Hao Yan

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

57. Seeman, N.C. (2001) NanoLetters 1, 22-26.
PX DNA
Seeman, N.C. (2001) NanoLetters 1,

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

59. Switchable Versions of PX and JX2

60. Machine Cycle of the PX-JX2 Device

61. The PX-JX2 System is Robust
Yan, H., Zhang, X., Shen, Z. & Seeman, N.C. (2002), Nature 415,

62. System to Test the PX-JX2 Device

63. AFM Evidence for Operation
of the PX-JX2 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-JX2 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-JX2 Device ~Perpendicularly Into a TX Lattice
PX Conformation
JX2 Conformation

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

77. Application of the PX-JX2 Device in a 1D Molecular Pegboard

78. Alessandra Carbone (IHES)
Towards 2D Circuits
Alessandra Carbone (IHES)

79. Circuits and triangular patterns
We need to show that the shapes is one/unique and that we such a general hape we can implement any arbitrary function. I shall show it to youon this simpleexample. The generalisation goes the same way.
How to programme molecules to do what we want them to do? As a toy model, we consider boolean circuits and we show that we can induce molecules to compute aboolean function, i.e. a function that computes on 0/1 values. This is clearly just an example. You can make molecules to do similar operations and drive them to follow specific pathways in the assembly.
What we have shown is that one can generalise these ideas of molecular programming to compute any arbitrary boolean function and also to guide the construction of arbitrary 3D structures. A boolean circuit is always representable with a triangle of logical gates. The computation is realised afterwards by an assembly of other tiles over this plateform. In the first row, we have the input and the result is obtained on the tip of the triangle.
The representation of the circuit on a plane resolves the ambiguities in the assembly.

80. 2 layers assembly

81. Tiles TX Molecule inputs operation outputs
We need 13 different tiles to realise all boolean functions.
The molecule has 4 strands that form 3 helices each.
On the bottom we see the schematisation of a tile and its realisation with DNA. The codes….
The size of a tile is 15-20nm x 7nm
operation
TX Molecule
outputs

82. Molecular Programming: programmed board
4 different states
L’idee mathematique derriere mon travail en colaboration avec Seeman est de s’apercevoir qu’on peut concevoir des reseaux programmables bidimensionnelles pour en suite construire des objets tridimensionnels.
Dans la pratiques, ces reseaux 2D sont similaires aux reseaux ABCD precedent mais les molecules intercales C et D sont des plots moleculaires programmables a 4 etats differents, construit avec une paire de molecules programmables vues precedemment.
On peut faire un reseau aussi grand qu’on veut ou bien lui donner une forme triangulaire par exemple.

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-JX2 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-JX2 device into a TX array.