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:
NSF-ITR: EIA : Structural DNA Nanotechnology Nadrian C. Seeman, Subcontractor Department of Chemistry New York University New York, NY 10003, USA February 17, 2003
Reciprocal Exchange: A Theoretical Tool To Generate New DNA Motifs
Reciprocal Exchange in a Double Helical Context
Biological Reciprocal Exchange: The Holliday Junction
Seeman, N.C. (1982), J. Theor.Biol. 99, Design of Immobile Branched Junctions: Minimize Sequence Symmetry
Mao, C., LaBean, T.H., Reif, J.H. & Seeman, N.C. (2000), Nature 407, A Cumulative XOR Calculation: Extracting the Answer
A Cumulative XOR Calculation: Data Mao, C., LaBean, T.H., Reif, J.H. & Seeman, N.C. (2000), Nature 407,
Natasha Jonoska Phiset Sa-Ardyen N-Colorability of Graphs
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.
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
Fred Mathieu Chengde Mao Six-Helix Bundle
Six-Helix DNA Bundle Fred Mathieu Shiping Liao Chengde Mao
DNA Nanomechanical Devices
B-Z Device Chengde Mao
Right-Handed and Left-Handed DNA
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 +++
Mao, C., Sun, W., Shen, Z. & Seeman, N.C. (1999), Nature 397,
Sequence-Dependent Device Hao Yan
Derivation of PX DNA Seeman, N.C. (2001) NanoLetters 1,
The PX-JX 2 System is Robust Yan, H., Zhang, X., Shen, Z. & Seeman, N.C. (2002), Nature 415,
System to Test the PX-JX 2 Device
AFM Evidence for Operation of the PX-JX 2 Device Yan, H., Zhang, X., Shen, Z. & Seeman, N.C. (2002), Nature 415,
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, (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-JX 2 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,
Cassette to Insert the PX-JX 2 Device ~Perpendicularly Into a TX Lattice PX Conformation JX 2 Conformation
Molecular Models of the 2 states of the Sequence-Driven DNA Devices
Application of the PX-JX 2 Device in a 1D Molecular Pegboard
Towards 2D Circuits Alessandra Carbone (IHES)
Circuits and triangular patterns
2 layers assembly
Tiles inputs outputs operation TX Molecule
Molecular Programming: programmed board 4 different states
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-JX 2 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-JX 2 device into a TX array.