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The precise placement of molecular and nanoparticle species at predetermined locations on a substrate surface remains a
current challenge. Some barriers are particularly relevant to soft matter such as biomolecules. The advent of DNA
Origami, invented by Rothemund, provides partial solutions to some challenges while raising new challenges. In this
paper, two particular levels of molecular placement will be discussed, associating large DNA based molecular
nanostructures with traditional lithographic nanostructures and the association of molecular scale species with particular
locations within large Origami structures. Typical plasmid based DNA Origami nanostructures are approximately 100
nm in diameter. This size scale closely matches that of gold nanoscale structures which are readily produced using ebeam
and other lithographic techniques. The strategy for associating large DNA based nanostructures with these
lithographic structures employs the placement of thiol terminated DNA molecules within the molecular assembly,
positioned to allow tethering of the biomolecular nanostructure to the substrate through gold-thiol bonds. Although a
number of soft chemistry mechanisms can be employed to associate DNA molecules with substrates, the use of the
origami constructs as substrates suggests that single stranded DNA provides the optimum attachment strategy. A solid
state asymmetric PCR process for ssDNA fabrication is therefore described and demonstrated. Structures generated with
the three tiered attachment strategy described here are amenable to characterization and assembly verification using
AFM and NSOM. While a complete convergence of top down and bottom up approaches cannot be claimed, it is clear
that the practice and methods of molecular lithography are rapidly advancing.
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