INTRODUCTION: One of the goals of nanotechnology research is the creation of networks of electrically active species which function as integrated systems. The approach to assembly at the nanoscale which the Norton group is implementing is termed Directed Sequential Self-Assembly via DNA Nanostructures. Representations of structures targeted by the group are shown in the animation (see below). The building blocks (color coded violet and cyan) in the animation measure 4 nm by 16 nm. The attachment sites for surface self-assembly (color coded red and blue) are spaced 40 nm (red-blue dot separation) and 32 nm (red dot-red dot or line to line separation). Sequential assembly requires surface immobilization of a growth directing species. The immobilization strategy selected for this application employs the strong interaction between thiols and gold, and is described below. The semibiosynthetic nucleator, which is a one micron long strand of designer DNA is also defined below.

Below are listed 4 set of objectives which the group sought to achieve and the subsequent results. In addition, the challenges which objective presented are indicated.

Objectives: Design and synthesize generation 4 thiolated dendrimers monofunctionalized with one 20 mer DNA oligomer which can act as a primer in the Polymerase Chain Reaction (PCR). If the dendrimer diameter closely matches the diameter of the metallic dot, steric factors/competitive binding may limit occupation of the spot to one dendrimer

Results: A “trebler” chemistry is available which allows the production of short DNA molecules terminated with dendrimer like structures with a minimum of 3 thiols. This chemistry is compatible with commercial DNA synthesizers. These reactions, however, are particularly slow and produces low yields (3).

Challenges: Defining an efficient chemical route to large thiolated dendrimers compatible with PCR conditions and identifying suitable methods for characterization of these molecules.

Objectives: Design a repetitive Director (nucleation) Strand, synthesize using rolling circle synthesis (4), clone it into a plasmid, selectively amplify it using PCR, prepare single stranded DNA, attach one or both ends, align using flow, sequentially add building blocks to structure one step at a time.

Results:

Sequencing result. Each copy is depicted in a different color; the red color shows the EcoRI and XbaI restriction sites introduced into the DNA fragment.

Challenges: Cloning multiple tandem repeats and determining the sequence represents a significant challenge. A second challenge involves design of robust building blocks and experimentally identifying failure mechanisms during the sequential assembly process.

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