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

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

Reciprocal Exchange in a Double Helical Context

Biological Reciprocal Exchange: The Holliday Junction

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

Sticky-Ended Cohesion: Affinity

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

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, 237-247.

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, 295-300..

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, 295-300.

A Method to Establish DNA Motif Flexibility

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

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

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, 1661-1669.

Construction of Crystalline Arrays

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

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

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

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

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.

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

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.

Holliday Junction Parallelogram Arrays Chengde Mao

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

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

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

Triple Crossover Molecules

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.

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.

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

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

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

Algorithmic Assembly Chengde Mao Thom LaBean John Reif

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

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

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

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

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

N-Colorability of Graphs Natasha Jonoska Phiset Sa-Ardyen

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.

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

Six-Helix Bundle Fred Mathieu Chengde Mao

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

DNA Nanomechanical Devices

B-Z Device Chengde Mao

Right-Handed and Left-Handed DNA

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, 144-146.

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

Sequence-Dependent Device Hao Yan

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

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

Yan, H. , Zhang, X. , Shen, Z. & Seeman, N. C Yan, H., Zhang, X., Shen, Z. & Seeman, N.C. (2002), Nature 415, 62-65..

Switchable Versions of PX and JX2

Machine Cycle of the PX-JX2 Device

The PX-JX2 System is Robust Yan, H., Zhang, X., Shen, Z. & Seeman, N.C. (2002), Nature 415, 62-65.

System to Test the PX-JX2 Device

AFM Evidence for Operation of the PX-JX2 Device Yan, H., Zhang, X., Shen, Z. & Seeman, N.C. (2002), Nature 415, 62-65.

New Cohesive Motifs

Paranemic Cohesion Xiaoping Zhang

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.

PX Cohesion of DNA Triangles: Theory

PX Cohesion of DNA Triangles: Experiment Zhang, X. Yan, H.,Shen, Z. & Seeman, N.C. (2002) J Am. Chem. Soc.124, 12940-12941 (2002)

Edge-Sharing Hao Yan

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

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

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

A Cassette for the Insertion of a PX-JX2 Device into a 2D TX Array Baoquan Ding

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.

Cassette to Insert the PX-JX2 Device ~Perpendicularly Into a TX Lattice PX Conformation JX2 Conformation

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

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

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

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.

2 layers assembly

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

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.

Control Region & Sticky Ends on the Same Strand

Mix & Split Synthesis -- Central

Mix & Split Synthesis -- Ends

Triple Crossover Molecules

An Algorithmic Arrangement Based on Mix & Split Synthesis

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.

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.

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.