Department of Biology, Beloit College, 700 College Street, Beloit, WI 53511

Email: jungck@beloit.edu
Web sites: http://bioquest.org, http://www.beloit.edu/~jungck

Co-author:
Srebrenka Robic

Molecular and Cell Biology, University of California Berkeley, 306 Stanley Hall,
Berkeley, CA 94720; robic@zebra.berkely.edu

Does DNA simply unzip in replication, recombination, and repair? Imagine the string in your junk drawer multiplied many times and you will have some idea of how tangled exceptionally long strings of DNA are in the cell. Such supercoiled DNA is demonstrably almost impossible to unknot simply by unraveling. Mathematicians pointed this out to biologists shortly after Watson, Crick, Wilkins, and Franklin solved the three dimensional geometry of DNA. Geometry and topology are quite different. Topology is geometry on rubberized graph paper or as DeWitt Summers has said: "Topology is geometry in California all twisted and bent out of shape." DNA topology is able to deal with writhing (bends extending over a long distance), twisting (local coiling), links (over and under crosses or the sum of negative and positive supercoils), and knots in DNA. Mathematicians predicted that enzymes (topoisomerases) must exist that catalyze the breaking and re-joining of DNA in order to unravel DNA and that these enzymes must have holes in them. What if replicated DNA strands were tied in a knot and a cell tries to divide? Might this be a problem in some diseases? How can knot theory help us understand DNA packing? How can we estimate the rates at which enzymes unknot DNA? My presentation will be filled with audience involvement with supercoiled zipper models of DNA unwinding, Velcro ribbon models and telephone cords & connector models to demonstrate the action of type I and II DNA topoisomerases, "Why Knots," the University of Minnesota Supercomputer movie "Not Knot," wire sculpture models by the artist Dennis Dreher (a student of "Bucky" Fuller) of polysomes folded into chromosomes (coiled-coiled-coiled-coils), macramé coils, Tensegritoy^® models of actin and microtubule networks inside of cells, and numerous slides. Come to understand why mathematical biologists help experimentalists through visualization made possible by theory, or, as goes Dolf Sielacher’s adage: "I wouldn’t have seen it, if I hadn’t believed it."