NSF-ITR: EIA-0086015: Structural DNA Nanotechnology

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NSF-ITR EIA-0086015Structural DNA
Nanotechnology
Nadrian C. Seeman, Subcontractor Department of
Chemistry New York University New York, NY 10003,
USA ned.seeman_at_nyu.edu 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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Design of Immobile Branched Junctions Minimize
Sequence Symmetry
Seeman, N.C. (1982), J. Theor.Biol. 99, 237-247.
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Sticky-Ended Cohesion Affinity
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Sticky-Ended Cohesion Structure
Qiu, H., Dewan, J.C. Seeman, N.C. (1997) J.
Mol. Biol. 267, 881-898.
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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.
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A Method for Organizing Nano-Electronic Components
Robinson, B.H. Seeman, N.C. (1987), Protein
Eng. 1, 295-300..
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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)
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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,
631-633..
Cube..
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Zhang, Y. Seeman, N.C. (1994), J. Am. Chem.
Soc. 116, 1661-1669.
Truncated Octahedron
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ConstructionofCrystallineArrays
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Derivation of DX and TX Molecules
Seeman, N.C. (2001) NanoLetters 1, 22-26.
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2D DX Arrays
Erik Winfree (Caltech) Furong Liu Lisa Wenzler
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Derivation of DXJ Molecules
Seeman, N.C. (2001) NanoLetters 1, 22-26.
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Schematic of a Lattice Containing 1 DX Tile and 1
DXJ Tile
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AFM of a Lattice Containing 1 DX Tile and 1 DXJ
Tile
Winfree, E., Liu, F., Wenzler, L.A. Seeman,
N.C. (1998), Nature 394, 539-544.
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Schematic of a Lattice Containing 3 DX Tiles and
1 DXJ Tile
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AFM of a Lattice Containing 3 DX Tiles and 1 DXJ
Tile
Winfree, E., Liu, F., Wenzler, L.A. Seeman,
N.C. (1998), Nature 394, 539-544.
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Holliday Junction Parallelogram Arrays
Chengde Mao
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Holliday Junction Parallelogram Arrays
Mao, C., Sun, W Seeman, N.C. (1999), J. Am.
Chem. Soc. 121, 5437-5443.
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Holliday Junction Parallelogram Arrays
Mao, C., Sun, W Seeman, N.C. (1999), J. Am.
Chem. Soc. 121, 5437-5443.
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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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TXJ 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.
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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, 1848-1860.
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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
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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, 493-496.
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A Cumulative XOR Calculation System
Mao, C., LaBean, T.H., Reif, J.H. Seeman, N.C.
(2000), Nature 407, 493-496.
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A Cumulative XOR Calculation Assembly
Mao, C., LaBean, T.H., Reif, J.H. Seeman, N.C.
(2000), Nature 407, 493-496.
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A Cumulative XOR Calculation Extracting the
Answer
Mao, C., LaBean, T.H., Reif, J.H. Seeman, N.C.
(2000), Nature 407, 493-496.
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A Cumulative XOR Calculation Data
Mao, C., LaBean, T.H., Reif, J.H. Seeman, N.C.
(2000), Nature 407, 493-496.
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N-Colorability of Graphs
Natasha Jonoska Phiset Sa-Ardyen
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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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Six-Helix Bundle
Fred Mathieu Chengde Mao
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Six-Helix DNA Bundle
Fred Mathieu Shiping Liao Chengde Mao
lt----------------7.3 Microns----------------gt
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DNANanomechanicalDevices
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B-Z DeviceChengde Mao
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Right-Handed and Left-Handed DNA
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A Device Based on the Blt--gtZ Transition
Co(NH 3)6
- Co(NH 3)6
Mao, C., Sun, W., Shen, Z. Seeman,N.C. (1999),
Nature 397, 144-146.
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Mao, C., Sun, W., Shen, Z. Seeman, N.C. (1999),
Nature 397, 144-146.
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Sequence-Dependent DeviceHao Yan
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Derivation of PX DNA
Seeman, N.C. (2001) NanoLetters 1, 22-26.
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PX DNA
Seeman, N.C. (2001) NanoLetters 1, 22-26.
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Yan, H., Zhang, X., Shen, Z. Seeman, N.C.
(2002), Nature 415, 62-65..
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Switchable Versions of PX and JX2
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Machine Cycle of the PX-JX2 Device
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The PX-JX2 System is Robust
Yan, H., Zhang, X., Shen, Z. Seeman, N.C.
(2002), Nature 415, 62-65.
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System to Test the PX-JX2 Device
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AFM Evidence for Operation of the PX-JX2 Device
Yan, H., Zhang, X., Shen, Z. Seeman, N.C.
(2002), Nature 415, 62-65.
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NewCohesive 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, 12940-12941 (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 theInsertion of a PX-JX2 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, 1848-1860.
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Cassette to Insert the PX-JX2 DevicePerpendicula
rly Into a TX Lattice
PX Conformation
JX2 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-JX2 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
operation
TX Molecule
outputs
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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-JX2
  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-JX2 device into a TX
  array.

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