Effects of different cations on the hydrodynamic radius of DNA.

The effects of different cations on the hydrodynamic radius (RH) of a 48-bp synthetic DNA are measured by time-resolved fluorescence polarization anisotropy of intercalated ethidium. Relative statistical errors in RH are only approximately 1%. With increasing cation concentration, Na+ causes a small decrease in RH, Cs+ causes a somewhat larger decrease by up to 0.5 A at 100 mM, and (CH3CH2)4N+ causes an increase in RH by approximately 0.5 A at 100 mM. The qualitatively different effects of these monovalent cations indicates that the changes in RH with cation concentration do not arise primarily from electrolyte friction. Divalent cations cause much larger increases in RH with increasing cation concentration. Mg2+ causes an increase in RH by up to 1.0 A at 24.4 mM, and Mn2+ causes an increase in RH by up to 1.6 A at 24.4 mM. These effects are independent of DNA concentration. There is some positive correlation between the order of effects of the different cations on RH and the order of their effects on interhelical hydration forces. It is suggested that these different ions affect RH either by altering the hydration layer or possibly by some effect on DNA structure, such as stabilizing bends.