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Department of Chemistry
New York University
New York, NY 10003, USA
This is an abstract for a talk to be given at the Fifth Foresight Conference on Molecular Nanotechnology. The full paper is now available.In recent years, we have spent a great deal of effort to construct molecular building blocks from unusual DNA motifs. DNA is an extremely favorable construction medium: The sticky-ended association of DNA molecules occurs with high specificity, and it results in the formation of B-DNA, whose structure is well known. The use of stable branched DNA molecules permits one to make stick-figures. We have used this strategy to construct a covalently closed DNA molecule whose helix axes have the connectivity of a cube, and a second molecule, whose helix axes have the connectivity of a truncated octahedron .
In addition to branching topology, DNA also affords control of linking topology, because double helical half-turns of B-DNA or Z-DNA can be equated, respectively, with negative or positive crossings in topological objects. Consequently, we have been able to use DNA to make four topological species , [circle, trefoil knots of both signs and a figure-8 knot] from a single strand. By making RNA knots, we have discovered the existence of an RNA topoisomerase. It is possible that branched objects could be made by PCR or biological replication by transforming their catenated topologies to knotted topologies. DNA-based topological control has also led to the construction of Borromean Rings, which could be used in DNA-based computing applications.
The key feature previously lacking in DNA construction has been a rigid molecule. We have discovered that antiparallel DNA double crossover molecules can provide this capability. We have incorporated these components in DNA assemblies that make use of this rigidity to achieve control on the geometrical level, as well as on the topological level. Some of these involve double crossover molecules, and others involve double crossovers associated with geometrical figures, such as triangles and deltahedra.
This research has been supported by grants from the National Institute of General Medical Sciences and the Office of Naval Research.
Professor Nadrian C. Seeman, Department of Chemistry, New York University, New York, NY 10003, USA
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