A complete understanding of the internal motions of the molecular and atomic components of biologically significant sequences of DNA is the long-term objective to which the proposed work would contribute. Such an knowledge would bear directly on the detailed understanding of the dynamics of protein-DNA interactions. The work proposed here would add to establishing a dynamics-function paradigm. Specifically, it is proposed to: (a) perform far-infrared measurements in order to determine how: sequence, length, and both physiological and genotoxic counterions affect the long wavelength vibrations of oligonucleotides, and (b) carry out a program to observe the effects of H-bond melting on biologically relevant low frequency vibrations of various oligonucleotides. Similar samples have been studied in the middle infrared and far-infrared measurements have been made on some random polynucleotide sequences. Resources for accomplishing these tasks are uniquely available for an undergraduate institution. Senior thesis students will make measurements with the on-campus research-level Fourier transform infrared spectrometer. They will also purify large quantities of oligonucleotides produced at a neighboring research laboratory.
