This project is focused on the conformational properties of a synthetic DNA poly(dA-dT), especially on its capability to isomerize into an unusual double helical form called X-DNA. (1) We propose to investigate, using conventional circular dichroism (CD), vacuum UV CD, and vacuum UV linear dichroism (LD) spectroscopy, how aliphatic substituents in place of the thymine methyl effect conformational properties of poly(dA-dT). (2) We propose to investigate, using conventional CD, vacuum UV CD, and vacuum UV LD spectroscopy, how partial replacement of adenine by amino 2adenine to various proportions affects conformational properties of poly(dA-dT). This collaborative effort will combine the expertise using various synthetic polynucleotides to investigate the conformational properties of DNA with making circular and linear dichroism measurements in the vacuum UV to determine conformation and base inclination. It is often difficult to keep these polymers in solution under the special conditions necessary to cause them to assume one of their forms, but we has been successful in working out conditions to keep them in solution, even at the high concentrations necessary for the short pathlengths used in vacuum UV work.
