DNA DUPLEX STABILITY

The factors, including hydrogen bonding, p-p stacking, and solvation, which control the stability of duplex DNA are under investigation. State-of-the-art experimental techniques, including electrospray ionization, liquid chromatography mass spectrometry (LCMS) and Fourier transform mass spectrometry (FTMS), are used to explore the binding affinities of DNA double-stranded oligomers in the gas phase, in the absence of solvent.  Because solvation plays a role in stabilizing the double helix, from affecting base pairing to mediating binding events, the study of naked DNA to examine intrinsic behavior is of fundamental importance. Our overall goal is twofold: 1) to undertake the systematic examination of DNA base pairs, base-stacked dimers, and longer oligonucleotides in order to lend insight into the intrinsic stability and behavior in the absence of solvent; and 2) to establish a novel method for the rapid assay of gas-phase and solution-phase binding affinities using mass spectrometry. Since biological processes are regulated, fundamentally, through specific DNA-protein recognition, and DNA protein recognition is controlled by DNA conformation, the study of duplex DNA structure and stability is highly significant.