Publication Date

April 2019

Advisor(s)

Francis Starr

Major

Physics

Language

English (United States)

Abstract

Four-way Holliday junctions are cruciform-shaped DNA structures which play vital roles in biological processes. In this thesis, we validate the ability of an explicit ion coarse-grained model for DNA (3SPN.2) to accurately simulate Holliday junction dynamics above and below DNA junction melting temperatures. We analyze a variety of junction behaviors, including ion binding, junction conformations, junction melting, and branch migration, and compare our results with expected results from scientific literature. We discuss four different methods to determine the structure of the junction, evaluate the drawbacks and advantages of these different methods by comparing them with each other and with data from previous studies and show that results qualitatively reflect our expectations of DNA junction structure at equilibrium. Then we use one of these methods to show that DNA junction dynamics as produced by the 3SPN.2 explicit ion model demonstrate the expected trends from literature. Next, we investigate melting by observing the dissociation of individual bases during our simulations and provide quantitative predictions for the dynamics of junction melting. Our results show that melting initiates at specific locations on a per-strand basis. These simulations helped inspire fluorescence melting experiments which strategically place nucleotide base analogs at several locations along junction strands and validate the primary predictions of the modeling. We offer a comprehensive overview of DNA junction research made possible using the 3SPN.2 explicit ion model for DNA and conclude that this model is a useful tool for exploring Holliday junction structure and dynamics in the presence of ions.

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