Date of Award
Doctor of Philosophy
Genetics, Development and Cell Biology
Bioinformatics and Computational Biology
Daniel F. Voytas
This dissertation seeks to improve C2H2 zinc finger protein (ZFP) engineering through computational and experimental studies. Engineered ZFPs that are able to bind any desired DNA sequence in a genome have great potential for basic biological research and biomedical applications. Current methods to engineer ZFPs are either unreliable, due to high failure rates, or inaccessible to some researchers, due to high demands of labor, time and expertise.
We created a web-accessible database that organizes zinc finger modules (ZFMs) and ZFPs from our lab, our collaborators' labs and the literature. This database helps researchers by providing information about the existence of ZFMs or ZFPs and their performance in DNA binding. We then described rules that govern the interaction of ZFPs and DNA by analyzing the finger sequences in the ZFM pools created by Oligomerized Pool ENgineering (OPEN), a recently developed, reliable, rapid and publicly available ZFP engineering method. These rules will be valuable in the improvement of the OPEN method and the understanding of the interaction between engineered ZFPs and DNA
Fu, Fengli, "Computational approaches to understand interactions between zinc finger proteins and DNA" (2010). Graduate Theses and Dissertations. 11553.