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Mao, C., LaBean, T.H., Reif, J.H. &
Seeman, N.C. (2000), Nature 407, 493-496.
A Cumulative XOR Calculation: Assembly
1
0
X3
X4
1
X1
X2
0
C2
C1
Y11
1
Y2
Y30
0
Y4
0
Y41
1
0
1
C1
C2
1
1
X41
X1
X2
X3
Y1
Y2
Y3
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C 1 X 1
X 2
Y 1
C 2
Y 2
Mao, C., LaBean, T.H., Reif, J.H. & Seeman, N.C. (2000), Nature 407, 493-496.
A Cumulative XOR Calculation:Extracting the Answer
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A Cumulative XOR Calculation: Data
2,0001,500
800600500
400
300
200
100
X2 = 1
Y1 = 1
Y2 = 0
Y3 = 1
Y4 = 1
X3 = 1X4 = 0
X1 = 1C2
M 1 0
Calculation 1
/01
C2,0001,500800600500
400
300
200
100
X2 = 0
Y1 = 1
Y2 = 1
Y3 = 0
X3 = 1X4 = 0
X1 = 1 C2
MC 1 0
Calculation 2
/01
Y4 = 0
Mao, C., LaBean, T.H., Reif, J.H. & Seeman, N.C. (2000), Nature 407, 493-496.
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Assembly of Graphs Whose Edges are Helix Axes:
Prototyping a Calculation
Phiset Sa-ArdyenNatasha Jonoska (U. South Florida)
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The Vertex 3-Colorability Problem
Given a graph, color the vertices with three colors such that adjacent vertices are colored distinctly.
P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .
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Add junction molecules for the vertices and the duplex molecules for the edges. Let them hybridize and then be ligated. Treat all partiallyformed molecules with exonuclease and check if there is a circular molecule in the tube.
A DNA Solution to the Problem.
P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .
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Components of a Graph
Nodes
Edges
P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .
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Design of Oligonucleotides for a Monochromatic Prototype Experiment
Edges e1,e2,e3,e8 are 4 helical turns, e3,e4,e7, are 6 helical turns,e6 is 8 helical turns. No sequence of 6 nucleotides is repeated
P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .
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Junctions Used
P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .
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Edges Used
P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .
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1084 Nucleotides
Vertices and Edges
P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .
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Schematic of the Graph
P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .
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Topoisomerase I Characterization of Cyclic DNA Molecules
P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .
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Single-Restriction Analysis
P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .
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Double Restriction Strategy
P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .
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Round the Clock Mapping -- 1st Set
P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .
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Round the Clock Mapping -- 2nd Set
P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .
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Round the Clock Mapping -- 3rd Set
2%------------------------->
P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .
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Round the Clock Mapping -- 4th Set
2%------------------------->
P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .
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Summary of Results• Polyhedral Catenanes, Knots and Borromean Rings can be Assembled from Branched DNA by Ligation.
• 2D Lattices with Tunable Features have been Made from Branched DNA Components; Progress towards 3D has been made.
• Algorithmic Assemblies have been Prototyped; a 3-Colorability Problem has been Prototyped.
• Heterologous Species have been Included in DNA Nanoconstructs.
• Nanomechanical Devices have been Assembled from Branched DNA, including a Walker and a Translation Device. A Machine has been Incorporated into a 2D Lattice.
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SUPPORT
National Institute of General Medical Sciences Office of Naval Research
National Science Foundation DARPA/AFOSR
Army Research OfficeNanoscience Technologies, Inc.
WEB PAGEHTTP://SEEMANLAB4.CHEM.NYU.EDU