Toward molecular programming with DNA

ABSTRACT

Biological organisms are beautiful examples of programming. The program and data are stored in biological molecules such as DNA, RNA, and proteins; the algorithms are carried out by molecular and biochemical processes; and the end result is the creation and function of an organism. If we understood how to program molecular systems, what could we create? Lifelike technologies whose basic operations are chemical reactions? The fields of chemistry, physics, biology, and computer science are converging as we begin to synthesize molecules, molecular machines, and molecular systems of ever increasing complexity, leading to subdisciplines such as DNA nanotechnology, DNA computing, and synthetic biology. Having demonstrated simple devices and systems -- self-assembled structures, molecular motors, chemical logic gates -- researchers are now turning to the question of how to create large-scale integrated systems. To do so, we must learn how to manage complexity: how to efficiently specify the structure and behavior of intricate molecular systems, how to compile such specifications down to the design of molecules to be synthesized in the lab, and how to ensure that such systems function robustly. These issues will be illustrated for chemical logic circuits based on cascades of DNA hybridization reactions.

Bio

Erik Winfree is an Associate Professor in Computer Science, Computation & Neural Systems, and Bioengineering at Caltech. Winfree is the recipient of the Feynman Prize for Nanotechnology (2006), the NSF PECASE/CAREER Award (2001), the ONR Young Investigators Award (2001), a MacArthur Fellowship (2000), and MIT Technology Review's first TR100 list of "top young innovators" (1999). Prior to joining the faculty at Caltech in 2000, Winfree was a Lewis Thomas Postdoctoral Fellow in Molecular Biology at Princeton, and a Visiting Scientist at the MIT AI Lab. Winfree received a B.S. in Mathematics w/ Computer Science from the University of Chicago in 1991, and a Ph.D. in Computation & Neural Systems from Caltech in 1998. His website is http://dna.caltech.edu/~winfree/.

INDEX TERMS

Primary Classification:
  B. Hardware
  B.0 GENERAL

General Terms:
Algorithms, Design, Languages, Reliability, Theory

Keywords:
DNA, molecular programming