The aim of this research is to understand the physical properties which determine the interactions of nucleic acids with other molecules. The thermodynamics and conformation of DNA helices with an extra, unpaired, base will be studied using optical absorbance and 1H,31P and 15N nuclear magnetic resonance. Two-dimensional Correlated Spectroscopy, Nuclear Overhauser Effect Spectroscopy and Heteronuclear Correlated Spectroscopy will be used to characterize the helical perturbation. The mechanism for frameshift mutagenesis will be investigated via the binding of ethidium ion to the perturbed helix. The location and physical properties of the ethidium binding site will be determined using 2D NMR. The potential of 15N NMR as a probe for hydrogen bonding will be investigated using modified bases as model systems. Two-dimensional 1H-15N heteronuclear correlated spectroscopy will be used to obtain the 15N chemical shifts and coupling constants in natural abundance. Variations in the hydrogen bonding will then be studied for the perturbed oligonucleotide helices. The interaction between oligonucleotides and drugs which bind covalently or non-covalently in the groove of the DNA will also be investigated using the 15N measurements as a probe. This research will provide new insight into the conformation of DNA which is strained either by containing an unpaired base or interacting with a drug. These investigations will also provide a new probe that can be used to study the biologically important phenomenon of hydrogen bonding.
