COMP 146 |
| DNA-protein interactions depend on various specific aspects of both the nucleic acid and the protein. Among them, the flexibility of DNA and its effect on binding affinities are crucial in understanding the mechanisms involved in nucleic acid-protein interactions. Here, the elastic rod theory is used together with normal mode and Langevin mode analysis in implicit solvent to characterize the flexibility and other properties of nucleic acids. The - bending, twisting, stretching - rigidities extracted from these all-atom simulations are in good agreement with experiments. In this study we were especially interested in - salt concentration and sequence - effects on the overall flexibility of linear fragments and minicircles of DNA. The well-known CTG and CGG trinucleotide repeats, responsible for several degenerative disorders are found to be more flexible than random DNA; in agreement with several recent studies, while poly(dA).poly(dT) is the stiffest sequence we have encountered. With these results in hand we extended our analysis to the study of the core-histone binding within the nucleosome assembly. |
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Protein-Nucleic Acid Interactions: Experimental and Modeling Analysis
8:30 AM-12:15 PM, Monday, August 20, 2007 BCEC -- 156B, Oral
Division of Computers in Chemistry |