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

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

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.

Assembly of Graphs Whose Edges are Helix Axes:

Prototyping a Calculation

Phiset Sa-ArdyenNatasha Jonoska (U. South Florida)

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 .

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 .

Components of a Graph

Nodes

Edges

P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .

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 .

Junctions Used

P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .

Edges Used

P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .

1084 Nucleotides

Vertices and Edges

P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .

Schematic of the Graph

P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .

Topoisomerase I Characterization of Cyclic DNA Molecules

P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .

Single-Restriction Analysis

P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .

Double Restriction Strategy

P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .

Round the Clock Mapping -- 1st Set

P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .

Round the Clock Mapping -- 2nd Set

P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .

Round the Clock Mapping -- 3rd Set

2%------------------------->

P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .

Round the Clock Mapping -- 4th Set

2%------------------------->

P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126, 6648-6657 .

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.

SUPPORT

National Institute of General Medical Sciences Office of Naval Research

National Science Foundation DARPA/AFOSR

Army Research OfficeNanoscience Technologies, Inc.

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