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Protein-DNA interactions are fundamental in biology, evolution, disease, and biotechnology. This dissertation describes the use of state-of-the-art molecular modeling algorithms and supercomputing to more fully understand the molecular details of protein-DNA interfaces, anal to redesign protein-DNA recognition in order to create cutting edge reagents for genomic medicine. Here I show that all-atom physical modeling protocols derived from "first principles" and knowledge-based biophysical properties can recapitulate many native properties of DNA-binding proteins and enzymes, and can be used to rationally design the cleavage specificity of a homing endonuclease at multiple and adjacent base pairs.
| Advisor: | Baker, David |
| Commitee: | |
| School: | University of Washington |
| School Location: | United States -- Washington |
| Source: | DAI-B 71/02, Dissertation Abstracts International |
| Source Type: | DISSERTATION |
| Subjects: | Systematic, Biochemistry |
| Keywords: | Gene therapy, Homing endonucleases, Protein-DNA interactions |
| Publication Number: | 3394201 |
| ISBN: | 9781109609967 |
