Jodi Schneider: DNA Structure

REU Researcher: Jodi Schneider, St. John's College, MN
Mentor: Wilma Olson, Chemistry, Rutgers

The DNA base sequence, once thought to be interesting only as a carrier of the genetic blueprint, is now recognized as playing a structural role in modulating the biological activity of genes. Through subtle variations of bending and twisting at the level of neighboring base pairs, the chemical sequence not only generates a higher-order folding of the double helix itself but also produces structural motifs that facilitate the specific binding of proteins and other ligands. The consequent looping and twisting of the DNA assumes an important role in various biological processes.

Jodi worked with Prof. Wilma Olson (Chemistry, Rutgers) as part of the DIMACS special year in Molecular Biology. Her project involved finding the optimum shape of a closed circular DNA molecule given certain chemical and physical parameters. Olson and some of her students had been working with computer software to numerically compute such optimal shapes, but depending on the initial input shape (from which the final shape would be numerically computed) different "optimal" shapes could be realized. Schneider's specific task was to devise and then implement an algorithm which would help them find good starting shapes for the numerical algorithm input.

Schneider had much background work to do before being able to effectively work on this problem. She spent a few weeks learning about Euler symmetric parameters, the rudiments of linear algebra and Frenet-Seret differential geometry. She also tackled C programming. She said in her report "Learning how to program in C made me much more interested in programming and algorithm questions (because I now have more tools with which to think about them). At the same time, it made me sure that I don't want computing to be my primary work: you can waste days looking for silly errors. Interacting with other people with strong mathematical interests made my research experience even better. In particular, talking with others interested in or working in topology was very helpful to me. For instance, I was introduced to a graduate student who works on the question of unknotting number, relating her mathematics to DNA biology and chemistry."

Last modified Jan. 21, 1997.