The prospects of programming molecular systems to perform complex autonomous tasks has motivated research into the design of synthetic biochemical circuits. Of particular interest to us are cell-free nucleic acid systems that exploit non-covalent hybridization and strand displacement reactions to create cascades that implement digital and analog circuits. To date, circuits involving at most tens of gates have been demonstrated experimentally. Here, we propose a DNA catalytic gate architecture that we believe is suitable for practical synthesis of large-scale circuits involving possibly thousands of gates. We will review the current status of experimental implementations, suggest their future prospects, and discuss progress on developing a compiler that converts VHDL programs to sequences for DNA molecules.

Lulu Qian is a postdoctoral researcher working with Erik Winfree and Jehoshua Bruck at Caltech. She received a B.S. in Biomedical Engineering from Southeast University of China in 2002, and a Ph.D. in Biochemistry and Molecular Biology from Shanghai Jiao Tong University in 2007. Her current research in bionanotechnology concerns programming DNA circuits and DNA self- assembly. Significant past accomplishments include the design and synthesis of a DNA nanostructure in the shape of a 150 nm China map that folds from a single long strand and over 200 short strands. This was the first independent implementation of Rothemund's scaffolded DNA origami technique. Other work includes DNA computation as well as the genetics of schizophrenia.