The goal of this research is to determine how local regions in DNA undergo conformational transitions during specific interactions with proteins. Fluorescence and absorption spectroscopy will detect both local and global conformational changes. The method measures DNA which may be a minor component and senses conformational changes in both DNA and protein induced by complex formation. Dr. Norlund aims to determine: 1. Thermodynamics of DNA structural motions and binding in the Eco RI-DNA complex. 2. Time-dependent conformation in the recognition sequence duringcleavage. 3. The binding constant of Eco RI to DNA using a direct fluorometric method. 4. Contributions of ribose, base stacking and local charge to fluorescence changes. 5. Whether kinks exist in the Eco RI recognition sequence before binding? 6. Whether Eco RI interaction with GAA bases are stronger than with TTC. 7. Whether melting "bubbles" form around less stable bases as suggested? 8. Whether partially-stacked bases are first recognized by the Eco RI Endonuclease. 9. Amplitudes and rates of DNA base transient excursions. 10. Whether distribution models explain lifetimes better than discrete exponentials.
