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NSF-ITR: EIA-0086015: Structural DNA Nanotechnology

NSF-ITR: EIA-0086015: Structural DNA Nanotechnology. Nadrian C. Seeman, Subcontractor Department of Chemistry New York University New York, NY 10003, USA ned.seeman@nyu.edu February 17, 2003. Reciprocal Exchange: A Theoretical Tool To Generate New DNA Motifs. Reciprocal Exchange in a

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NSF-ITR: EIA-0086015: Structural DNA Nanotechnology

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

  2. Reciprocal Exchange: A Theoretical Tool To Generate New DNA Motifs

  3. Reciprocal Exchange in a Double Helical Context

  4. Biological Reciprocal Exchange: The Holliday Junction

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

  6. Sticky-Ended Cohesion: Affinity

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

  8. 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.

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

  10. 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.

  11. A Method to Establish DNA Motif Flexibility

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

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

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

  15. ConstructionofCrystallineArrays

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

  17. 2D DX Arrays Erik Winfree (Caltech) Furong Liu Lisa Wenzler

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

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

  20. 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.

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

  22. 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.

  23. Holliday Junction Parallelogram Arrays Chengde Mao

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

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

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

  27. Triple Crossover Molecules

  28. 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, 1848-1860.

  29. 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, 1848-1860.

  30. ProgressTowardThree-DimensionalArrays Furong Liu Jens Birktoft Yariv Pinto Hao Yan Tong Wang Bob Sweet Pam Constantinou Chengde Mao Phil Lukeman Jens Kopatsch Bill Sherman Mike Becker

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

  32. 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

  33. AlgorithmicAssembly Chengde Mao Thom LaBean John Reif

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

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

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

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

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

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

  40. 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.

  41. 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

  42. Six-Helix Bundle Fred Mathieu Chengde Mao

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

  44. DNANanomechanicalDevices

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