Laser temperature jump study of solvent effects of poly(adenylic acid) stacking.

The dynamics of the single-stranded, helix--coil transition of poly(adenylic acid) have been investigated by using the Raman laser temperature jump technique. The driving forces of this conformational transition have been probed by varying the cosolvent in mixed aqueous solutions. The rate of helix formation correlates well with the inverse of the solution viscosity. This correlation and the low activation barrier of approximately 4 kcal/mol for this process indicate a rotational diffusion controlled reaction. The rate of coil formation has a much higher activation barrier, presumably due to the strength of base stacking in the helix. This unstacking rate is virtually unaffected by alcohol cosolvents. A significant increase in this rate occurs when polar cosolvents such as urea, formamide, or acetonitrile are added. Absorbance changes with temperature suggest that urea specifically solvates the adenine base. The polar cosolvents appear to break up the stacked, helical conformation by interacting with the bases.