Technologies and approaches derived from physical chemistry will be used to study NHP6A, a non-specific DNA-binding protein. NHP6A, and its functionally-equivalent counterparts in bacteria (HU protein) and in mammals (HMG-1/2), are thought to facilitate the formation of nucleoprotein complexes by bending or wrapping DNA into a specific configuration. The proposed work will involve the creation of a fusion protein consisting of the sequence-specific Hin recombinase DNA-binding domain and NHP6A. The length of peptide linking the two proteins will be varied to bring NHP6A into its preferred minor groove binding site. Detailed quantitative studies of this fusion protein with DNA will involve electrophoretic mobility shift assays and chemical footprinting techniques. Atomic resolution structures of the fusion protein in its unbound and DNA-bound forms will complement these biophysical studies. The long range goal of these studies is to provide a framework for designing a DNA recognition molecule which covers a desired length of DNA. Additionally, these studies will help delineate the fundamental differences between specific and non-specific binding to DNA.
| Rodgers, Michael E; Schleif, Robert (2009) Solution structure of the DNA binding domain of AraC protein. Proteins 77:202-8 |
| Rodgers, Michael E; Holder, Nakisha D; Dirla, Stephanie et al. (2009) Functional modes of the regulatory arm of AraC. Proteins 74:81-91 |
| Dirla, Stephanie; Chien, John Yeh-Heng; Schleif, Robert (2009) Constitutive mutations in the Escherichia coli AraC protein. J Bacteriol 191:2668-74 |
| Frato, Katherine E; Schleif, Robert F (2009) A DNA-assisted binding assay for weak protein-protein interactions. J Mol Biol 394:805-14 |
