Dynamic Mobility of DNA

Abstract

The dynamic mobility (μ d ) of double-stranded DNA (at 1 MHz) has been measured for the first time, by measurements of the electrokinetic sonic amplitude (ESA) and the hydrated density. Calfthymus DNA (average size 3000 base pairs) and herring sperm DNA (300 bp) have been used as models for a flexible polymer and a semirigid rod, respectively. In both cases the ESA is proportional to the DNA concentration at least up to 1.5 mg/mL, allowing μ d of noninteracting DNA molecules to be determined from the slopes. For calf thymus DNA μ d is very similar to literature values on the steady-state mobility, available between 50 and 4 mM NaCl. Unexpectedly, the dynamic mobility at 1 mM NaCl is lower than that at 4 mM, and thermal melting experiments rule out denaturation as a cause for this nonmonotonic dependence of μ d on ionic strength. Using the free-draining approximation valid in steady-state electrophoresis of DNA, we evaluate the charge fraction α from the dynamic mobility. Above 4 mM NaCl α is essentially constant at 0.60 ± 0.05, indicating that DNA can be viewed as a constant-charge cylinder also in the dynamic mobility, but at 1 mM the charge fraction drops to 0.2. The herring sperm DNA has a considerably lower dynamic mobility than calf thymus DNA, which is confirmed by measurements of the ultrasonic vibration potential. Part of the lower dynamic mobility of the herring sperm DNA can be ascribed to partial denaturation. The fact that the charge fraction is smaller than that calculated from steady-state mobilities of completely denatured DNA indicates, however, that the smaller size also contributes to the low mobility of the herring sperm DNA.