The goal of this research is to understand how the structure and dynamics of DNA contribute to their biological function. Correlations will be sought between base sequence and local variations in the structure and dynamics of DNA. The primary technique used in this investigation will be nuclear magnetic resonance spectroscopy (NMR). Two-dimensional NMR nuclear Overhauser effect experiments will yield proton-proton internuclear distances less than 4.5Angstrom which can be interpreted in terms of a detailed three-dimensional structure. Hydrogen exchange experiments of the amino and imino protons in deoxyribo-oligonucleotides will be used to monitor the kinetics and thermodynamics for opening of individual base pairs in the duplex. These measurements probe the dynamic behavior of DNA in solution. The exchangeable exocyclic amino protons of DNA base pairs represent extremely valuable probes of the major and minor grooves in DNA but to date these protons have seen only limited application in structural studies. One important aspect of this program will be developing methodology designed to make these amino protons routine probes of DNA structure and dynamics. The research outlined in this proposal represents a fundamental and necessary background on which to base future investigations of the three-dimensional structure of protein-DNA or drug-DNA complexes in solution.
| Heus, H A; Pardi, A (1991) Nuclear magnetic resonance studies of the hammerhead ribozyme domain. Secondary structure formation and magnesium ion dependence. J Mol Biol 217:113-24 |
| Metzler, W J; Wang, C; Kitchen, D B et al. (1990) Determining local conformational variations in DNA. Nuclear magnetic resonance structures of the DNA duplexes d(CGCCTAATCG) and d(CGTCACGCGC) generated using back-calculation of the nuclear Overhauser effect spectra, a distance geometry algorithm and cons J Mol Biol 214:711-36 |
| Heus, H A; Uhlenbeck, O C; Pardi, A (1990) Sequence-dependent structural variations of hammerhead RNA enzymes. Nucleic Acids Res 18:1103-8 |
