It is a strange model and embodies several unusual features. However, since DNA is an unusual substance, we are not hesitant in being bold.

James D. Watson

The quote above is taken from a letter to a friend written by the codiscoverer of the structure of DNA, James D. Watson, a month before their discovery was made public.1 Watson got it right. DNA is strange, it is unusual, and harnessing its power has required and will require truly bold acts by scientific thinkers in every discipline. Yet, that’s where the fun is, and that’s where the promise of self-assembly truly comes alive. In this chapter we examine DNA based self-assembly. We’ll look at the

progress that’s been made, highlight the pitfalls and problems, and see some of the tremendous opportunity for nanoscale engineering that is made possible by DNA. We begin in Section 8.2 with a brief review of DNA’s structural and chemical properties. We’ll review the important concept of base pairing, sometimes called Watson-Crick base pairing, that is responsible for DNA’s ability to self-replicate and its usefulness as a self-assembling structural material. In Section 8.3, we’ll examine some of the early successes in using DNA as a self-assembling construction material. We’ll learn about sticky ends and branched junctions, two forms of DNA that make construction possible. We’ll see how by using sticky ends and branched junctions various groups have succeeded in self-assembling three dimensional nanoscale polyhedra from DNA. We’ll also see some of the problems they encountered along the way, and learn how many of these obstacles are being overcome. We’ll see how the common problem of rigidity is overcome through the use of the DNA double crossover molecule (DX). The DX molecule will play a central role in Section 8.4 where we examine DNA tiles. We’ll see how these tile systems are similar to many of the systems of Chapter 6 and we’ll see why DNA tiles succeed where macroscale tiles often fail. This section and Section 8.5 will also provide us with examples of programmable self-assembly. We’ll see how

changing the sequence of base pairs on sticky ends, or changing a family of tile types amounts to programmable control over self-assembled structures. We’ll also see how structures formed from tiles can be used as templates for functional nanodevices. In Section 8.6 we’ll see how the promise of DNA tiling has been vastly extended through the method known as DNA Origami. In this technique, arbitrary two dimensional shapes can be self-assembled from a long single strand of DNA. In turn, these complex shapes can be used as tiles in self-assembled DNA tile structures. In Section 8.7, we’ll see how DNA can be used directly as a template for the assembly of nanostructures. We’ll examine a DNA template design for a nanoscale transistor, a key component of digital electronics, and one that has already been built using DNA based self-assembly. Finally in Section 8.8, we’ll examine DNA based self-assembly in the context of what we’ve learned in the previous seven chapters. While DNA is strange, and it is unusual, we’ll see that DNA based self-assembly presents us with the same obstacles and challenges we’ve encountered before.