From Sequence to Function Through Secondary Structure Kinetics of RNA and DNA

Author: Meruelo, Alejandro Daniel

Year: 2006

Degree: Senior thesis (Major)

Advisor: Mabuchi, Hideo

Committee Member: None, None

Option: Physics

DOI: 10.7907/4bxt-wa89

Abstract

A number of efforts to determine function from sequence of RNA and DNA have been made with varying success. Here we study the determination of function from sequence of DNA and RNA through their secondary structure kinetics, specifically the series of transitions between secondary structures. This series of transitions or microscopic structure can be described by a system of ordinary differential equations that can be approximating using balanced truncation to determine the macroscopic structure. By doing so, we have been able to identify signature topological features of microscopic structure and mathematically characterize the corresponding classes of macroscopic structure. Thus we are now able to take large, complex systems, reduce them, and understand their behavior. In the future, we hope to be able to identify small microscopic changes that lead to large macroscopic changes and possibly phasetransition like conditions between secondary states. Ultimately, this may lead to the development of a secondary-structure kinetics theory describing how one or more strands of DNA pair with one another to form different secondary structures and its potential future experimental verification.

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