| Deoxyribonucleic acid is a molecule that exists on the margin of two worlds: one that obeys the regulations of the classical mechanics and one that is governed by the laws of quantum physics. As such, DNA has to find a way to satisfy both, which at times means “bending” rules.; In this thesis emphasis is on the characterization of structural and hydrodynamic properties of DNA and how its geometry accommodates deviations from its chemically native structure. Various damages and sequence specific features such as urea base, mismatches and dA-tracts were examined to elucidate how these unusual building blocks affect DNA structure and motion. Methods employed included NMR solution structure determination, molecular simulations, diffusion coefficient measurements, enzymatic assays, chromatographic procedures, and chemical modifications.; A shape function method for monitoring the flexibility and curvature of DNA has been developed that is based on the measurements of diffusion coefficients. Furthermore, an attempt to assess the effects of such structural elements on the biology of DNA has been made in the context of replication and cleavage of RNA-DNA hybrids by RNase H.; Results of these experiments showed that structure of DNA containing urea residue is largely B-DNA, with limited and localized structural distortion, but perturbed electrostatics around the damaged base, which was reflected in increased flexibility of DNA containing this particular residue. It was found that DNA containing dA tract possesses a curvature that is a function of temperature and is highly sensitive to the concentration of magnesium cations.; DNA is functionally a very active molecule. We have shown that the same notion applies when it comes to looking at DNA in a structural sense. Hence, we have to leave the notion of DNA as a rigid, rod-like molecule behind, and accept the new reality in which the structure of DNA is reflected in its function and activity. |
