The Use of Fenton chemistry to Identify Oxidative Damage Sites in RNA
Author: Sherrell Haney (chemistry)
Faculty mentor: Christine Chow
In organisms, cells are constantly undergoing oxidative damage. Much research is being done to understand the effects of oxidative damage to nucleic acids. Determining if specific nucleic acids are more susceptible to oxidative damage may lead to a better understanding of its downstream effects.
In order to simulate oxidative damage in vivo, we are using an in vitro system that applies Fenton chemistry to generate oxygen radicals. Our goal is to generate the radicals and use structural changes of DNA as an indicator of oxidative damage. By using agarose gel electrophoresis, we can study the DNA structure and identify whether it is supercoiled, nicked, or linear.
This observation serves as an indicator for oxidative damage of the nucleotide. By using tRNA as a competitor, we can determine the relative reactivity of RNA versus DNA. Furthermore, we are analyzing modified RNAs using computational approaches to determine sites most likely to be damaged by hydroxyl radicals generated in the Fenton reaction. The main tool being used is the PyMOL program.
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Sherrell Haney: The Use of Fenton chemistry to Identify Oxidative Damage Sites in RNA