DNA Computing:
The Origin of Biological
Information Processing
Professor Laura Landweber
Princeton University
Freshman Seminar
Spring, 1999
A changing view of biology has given rise to the new field of "DNA computers". This field seeks to use biological molecules such as DNA and RNA to solve basic mathematical problems. Fundamentally, many of these experiments recapitulate natural evolutionary processes that take place in biology, especially during the early evolution of life and the creation of genes. This seminar will explore both new uses of nucleic acids as the building blocks of life but also complex architectural structures and even biomolecular-computing "hardware". We will also examine the information processing in cells that have had billions of years to evolve and to perfect a "molecular computer". This seminar concludes by examining the "biological software" invented by nature. We ask whether we can tap into these processes and harness the parallel processing ability of DNA to tackle really hard problems? The ultimate challenge is to find the right questions and to identify the type of problem that molecules can solve in a tiny drop of solution.
Week Click on links to obtain selected readings for that week.
2/4 DNA Architecture
Principles of molecular biology
From Microsoft to "Bio-soft"
Arrival of "biological mathematics"
New York Times article on DNA computing from 4/11/95.
WIRED magazine article (text only) from August 1995.
Restriction enzymes
DNA Glossary
2/11 Fundamentals of Computing
Turing Machines, NP-Completeness, Universal Computers
read: Garey and Johnson chapters 1 and 2
optional link: History of Computing
2/18 The Traveling Salesman: A DNA Computer
Comic Version
Illustrated summary
On Constructing a Molecular Computer by Len Adleman
3/4 Evolution in a Test Tube I: The RNA World
RNA as an enzyme
Directed evolution in sequence space
3/11 DNA as Lego: Universal Computation by Self-Assembly of DNA
From cubes to Borromean rings and Sierpinski triangles (Erik Winfree)
3/25 Evolution in a Test Tube II: Solving hard problems
Amos et al. Error-resistant Implementation of DNA Computations
Satisfiability: Teaching RNA to play Chess and other DNA games
4/1 More Molecular Tinkertoys
Nanostructures and Semiconductors
Richard Feynman, There's Plenty of Room at the Bottom
Science Report on Nanotechnology
A DNA wire
Ned Seeman's lecture: "DNA Nanotechnology" 2 pm LTL 003
4/8 Building Genetic Codes
The origin of the natural genetic code
4/15 Development and Evolution
The Burgess Shale and the Cambrian Explosion
4/22 RNA Editing and Gene Scrambling
Molecular Evolution and Cellular Computation
Sigma Xi lecture: "The Origin of Life…" 5:30 pm Guyot 10
4/29 Genetic regulation and amorphous computing
Towards in vivo digital circuits