Molecular Modeling for Distance Measurements

            Ryan Biczo, Chemistry            

Faculty Mentor: Dr. Donald Hirsh

              The main goal of this project is to create a model which can predict the structure of biological macromolecules which contain a metal ion and stable radical. The model is duplex DNA that contains a metal ion bound by EDTA to a thymidine base on one strand and a stable nitroxide radical on the other. One of my projects was to recreate this experimental model in a molecular modeling program called HyperChem in order to predict the distances between the metal ion and the nitroxide radical. I modeled four different DNA structures (each with the same base pair sequence but with different distances between the metal-EDTA complex and nitroxide radical). Different conformations of the thymidine-EDTA conjugate were tested in HyperChem to see which had the lowest energy. These different conformations also yielded metal ion-nitroxide radical distances. As illustrated in the figure, this affects the strength of the interaction k1d, between unpaired electrons on the metal ion and nitroxide radical.

              My other project was to recover the metal-EDTA DNA strand from previous experiments; this DNA required a custom synthesis and is very expensive. The goal was to find a method to separate the double helix DNA and collect the metal-EDTA DNA strand. High pressure liquid chromatography (HPLC) was performed at high temperature to denature the double helix, which is held together by hydrogen bonding, and separate each strand. A reverse phase column, which separates molecules based on their hydrophobicity was used and the gradient and pH were adjusted to give the best separation possible for the two DNA strands. Only the metal-EDTA strand had the resolution needed for collection, thus the other could not be recovered. After collection of the one strand it was checked for purity and then concentrated and stored for later use.

Personal Statement

              This summer I have learned much about instrumentation (HPLC, UV-Vis, and EPR), and about problem solving in the lab. Just listening to my peers projects proved to be an insight; helping me learn more about chemistry then I did before. Both the independence (from following set instructions) and teamwork (with peers and faculty if needed) seemed to balance out the learning experience and helped me grow as a researcher. There was always a positive learning environment and good times to be had.