Student: Bryson W. Finklea
School: St. John's College
Research Area: DNA Packing
Project Name: Characterizing Intermolecular Contacts of DNA
Faculty Advisor: Wilma Olson, Department of Chemistry and Chemical Biology
Rutgers University
Additional Advisors: A. R. Srinivasan, Department of Chemistry and Chemical Biology
Rutgers University

The following are my introductory and final Powerpoint presentation slides for the summer (additional footnotes have been added):
First presentation Second presentation

Background for Project

DNA molecules are found in living cells in nature and also in various science and technology laboratories, including nanotechnology labs and crystallography labs. In each of these settings DNA packs together, whether it is one long fiber looping back beside itself or separate DNA molecules next to each other.

In nature, DNA must pack into cells because, for example, the human genome--the DNA information contained in every cell of our bodies--is 3 billion base pairs long, or about 2 meters.

In nanotechnology, the machines are built from DNA molecules because they are "nice" for their engineering purposes. The researchers in this field appreciate knowledge they receive from other DNA researchers, but for their work it is incidental that DNA is the blueprint of life.

The structure of DNA can be most closely studied in crystal form because of the rigidity and symmetry of the crystal. Crystals of DNA are grown in a lab under special conditions. The crystals look like small gems and are often microscopic. The primary method for studying DNA crystals has been to pass x-rays through them and study the resulting diffraction patterns.

Most of the molecules of DNA in the crystals formed to date are about 10 base pairs long. About 2,500 of these short strings of DNA (and of RNA, a related biological molecule) have been studied. The information found has been entered into the Nucleic Acid Database (NDB) based here at Rutgers University.

The information entered includes orthoginal coordinates of some of the atoms in the crystal, as well as equations, lengths, and angles that represent the particular type of symmetry found in the crystal.

This 3-D symmetry in a crystal has a 2-D analogue in wallpaper designs--looking at wallpaper can provide intuition about the molecular structure of crystals. In each design there is a smallest unit that is repeated in various ways either translated, reflected, rotated, inverted, or acted upon by certain combinations of these. There are examples of these on the web, such as the pictures and descriptions found at Wallpaper Groups constructed by David E. Joyce of Clark University.

The 3-D symmetry in crystals is described by the mathematics of space groups--a branch of math that was completely understood around 1900. This is unusual, since branches of math usually continue to grow and sprout new branches. There are 17 possible 2-D symmetry patterns and 230 possible 3-D symmetry patterns or space groups. Most molecular crystals fall into only a few of the possibilities.

Introduction to Project

My project this summer is to write a computer program that characterizes the intermolecular contacts between DNA molecules that are packed in crystals. From information already entered into the Nucleic Acid Database (NDB) (see above), I will reconstruct the location of the atoms in the crystals and calculate additional measurements for the entries. Two ideas we have for measurements or characterizations are the distance between closest atoms of two molecules and the angle between axes of two molecules. As we study our findings we may also wish to make additional characterizations.

Since my background is in pure mathematics, this REU is introducing me to both molecular biology and computer programming, as well as to the specific research project. The FORTRAN program I am using is based on a version previously prepared by Dr. A.R. Srinivasan.

Please see the links to my Powerpoint presentations for more details on the project and computer program.

Additional REU Activities

My advisor Dr. Olson and DIMACS have been kind enough to allow me to explore other avenues in mathematical biology this summer as well. In particular, I have attended a conference held by the Computational Neuroscience Society in Baltimore July 18-20, 2004. I have also done additional work to learn more about mathematical and computational neurscience, including inviting and arranging Eric Brown, a postdoc of Princeton and soon NYU, to give a seminar to the REU students here.

I also have been able to explore the role that a scientist can play in working for justice in the world. I have met with Dr. Joel Lebowitz of the mathematics department here at Rutgers and the co-chair of the Committee of Concerned Scientists, which works for human rights of scientists throughout the world.

Last updated on 7/29/04