Date

2015

Document Type

Thesis

Degree

Master of Science

Department

Computer Science

First Adviser

Chen, Brian

Abstract

Electrostatic focusing has been shown to be a major component in DNA to protein interfaces. Since ribonucleic acid molecules are notoriously less consistent and uniform in structure than their DNA cousins, electrostatic focusing has not yet been evaluated between RNA and protein. This is the first survey of its kind showing the occurrence of focusing with specific amino acids and RNA secondary structures. With unique volumetric tools we quantify the electrostatic focusing phenomena in RNA and look at its impact on the electrostatic component of protein affinity. With those same tools we uncover which amino acids interact with focusing regions and how much they interface with those regions. We also demonstrate what types of secondary structures in RNA are commonly associated with electrostatic focusing.

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