Formation of Nanostructures by DNA-Programmed Assembly and Conjugate Coupling

The fundamental idea behind our research is to use Nature’s strategy for programmed self-assembly at the nanoscale by employing short synthetic DNA sequences as an encoding tool for materials and molecules. The unique specificity of DNA interactions, our ability to code specific DNA sequences and to chemically functionalize DNA, makes it the ideal material for controlling self-assembly of components attached to DNA sequences. We have developed some new approaches in this area such as the use of DNA for self-assembly and covalent coupling of organic modules. Various custom designed molecular modules that contain DNA chains for recognition, a carbon backbone, and functional chemical groups to bridge the organic modules have been prepared. Such conjugates have been applied for the DNA-programmed formation of macromolecular networks.

Adding Functionality to DNA Arrays. The Development of Semisynthetic DNA–Protein Conjugates

The use of semisynthetic DNA-protein conjugates allows one to combine the unique properties of DNA nanostructures with the almost unlimited variety of functional protein components. Proteins have been tailored by billions of years of evolution to specifically perform highly complex tasks, such as catalytic turnover, energy conversion, or translocation of other components. Taking advantage of the extraordinary specificity of Watson-Crick base pairing, semisynthetic proteins conjugated with single-stranded DNA oligomers offer the possibility to functionalize DNA arrays with protein content. In this lecture I will illustrate examples of the current state-of-the-art of the chemistry of DNA-protein hybrids and their applications in DNA-based nanotechnology. Perspectives arising from this approach will be discussed, which include the fabrication of nanoscaled elements for sensing, catalysis, and transduction of biological recognition events.

Toward Self-Replicating Colloids Using Sticky DNA

We describe ongoing efforts to develop colloidal particles with information encoded in their shape and interactions, information that can be used to direct their self-assembly.

We will describe two of our strategies:

1. making colloids with directional interactions and
2. coding information via ssDNA functionalized colloidal surfaces to direct colloidal self-assembly.

DNA computation

Andrew D. Ellington. Zack Both Simpson, Michael Wittig

Ever since Adleman's seminal demonstration, computational scientists and biologists have been fascinated by the use of DNA as a computational device. The primary driver for considering the use of DNA is the possibility of massive parallelism. However, offset against this is the fact that DNA machines are inherently slow, cumbersome, and error-prone relative to silicon machines. From this vantage, it seems unlikely that DNA will ever be able to remotely challenge silicon, at least in the sense of solving mathematically difficult problems or executing complex algorithms.

In more recent years, DNA computation has addressed more modest mathematical or algorithmic goals, and has rightly focused on 'talking to itself,' and interfacing with biology. The work of pioneers like Milan Stojanovic and Eric Winfree has again been seminal in identifying and directing these applications. Our own contribution has been to consider how nucleic acid machines might be adapted to function in primitive signal transduction operations that could be adapted to synthetic biological circuits.

Into the future, the promise of DNA computation can best be realized not only by a self-conversation, but by building a conceptual universe parallel to both electronic computation and molecular biology where DNA serves not so much as an information storage or processing device, but as a material. In this regard, we have become interested in the nascent field of amorphous computation, and adapting DNA machines to serve as part of amorphous computers whose output is matter rather than information.