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

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,

Assembly of Graphs Whose Edges are Helix Axes: Prototyping a Calculation Phiset Sa-Ardyen Natasha 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,

Add junction molecules for the vertices and the duplex molecules for the edges. Let them hybridize and then be ligated. Treat all partially formed 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,

Components of a Graph Nodes Edges P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126,

Design of Oligonucleotides for a Monochromatic Prototype Experiment Edges e 1,e 2,e 3,e 8 are 4 helical turns, e 3,e 4,e 7, are 6 helical turns, e 6 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,

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

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

1084 Nucleotides Vertices and Edges P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126,

Schematic of the Graph P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126,

Topoisomerase I Characterization of Cyclic DNA Molecules P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126,

Single-Restriction Analysis P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126,

Double Restriction Strategy P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126,

Round the Clock Mapping -- 1st Set P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126,

Round the Clock Mapping -- 2nd Set P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126,

Round the Clock Mapping -- 3rd Set 2% > P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126,

Round the Clock Mapping -- 4th Set 2% > P. Sa-Ardyen, N. Jonoska & Seeman, N.C. (2004),J. Am. Chem.Soc., 126,

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 Office Nanoscience Technologies, Inc. WEB PAGE