The overall aim of this research is to probe the conformation of polynucleotides and nucleic acids in solution, which may well be different from their conformation in crystals and fibers. Indeed, studies on the number of base pairs per turn for various DNAs indicate that this parameter is flexible, varying with sequence and certainly not the integral 10-fold repeat originally found for B-form fibers. Furthermore, a number of studies indicate that the base pairs make a fair inclination angle with the helix axis even under B-form solution conditions. Here we propose to resume our vacuum ultraviolet linear dichroism (LD) studies to determine the angle at which bases are inclined with respect to he helix axis for various base sequences and under various solution conditions. IN a flow LD experiment on helical nucleic acids with one type of basis, there are three unknowns: the inclination of the bases, the orientation of the axis around which the bases are inclined, and the coefficient for alignment of the polymer in the flow. If there is more than one kind of base in the nucleic acid, then each type of base may have a different inclination and axis. Our laboratory had developed a special flow linear dichroism instrument that will make measurements into the vacuum ultraviolet region so that the information content of the data is sufficient to solve for all of the unknowns. In previous work we determined inclination angles for some simple deoxypolynucleotides, and for DNA itself. We would now study simple ribopolynucleotides in aqueous solution, and simple deoxyribonucleotides under solution conditions that produce the A form. Furthermore, we propose to determine accurately the number of base pairs per turn for A-form DNA. We would then use the new base inclination and helix repeat data to calculate the corresponding vacuum ultraviolet CD spectra. These calculated spectra would be compared with CD spectra measured into the vacuum UV region on our special instrumentation. Furthermore, we would compare the interproton distances between the bases for these new helical repeats and base inclinations to the values obtained form NOESY data from modern 2D NMR work. Taken together, this work should be valuable for determining the true base orientation for polynucleotides and nucleic acids in solution.
