Publication Date

May 2013

Advisor(s)

Ishita Mukerji

Major

Chemistry

Language

English (United States)

Abstract

DNA four-way junctions (4WJ) are central intermediates in processes such as replication and recombination. This project studies how different conformations of the junction relate to function, and how proteins interact with the junction to enhance or repress function. Previously, we have examined the 4WJ structure in the presence of different ions, and used Förster Resonance Energy Transfer (FRET) to map the binding site of the protein HU onto the junction. These FRET measurements were used to build four different models for the binding of HU protein to the 4WJ. Further FRET measurements are needed to narrow the possible orientations for HU binding the junction. In addition, a new, migrating 4WJ has been created and characterized. This 4WJ has been analyzed by FRET in the presence of ions and proteins to compare to the characteristics of the immobile junction.

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