The free solution mobility of DNA

Abstract

The free solution mobility of DNA has been measured by capillary electrophoresis in the two buffers most commonly used for DNA gel electrophoresis, Tris‐borate‐EDTA (TBE) and Tris‐acetate‐EDTA (TAE). The capillaries were coated with polymers of either of two novel acrylamide monomers, N‐acryloylaminoethoxyethanol or N‐acryloylaminopropanol, both of which are stable at basic pH and effectively eliminate the electroendosmotic mobility due to the capillary walls. The free solution mobility of DNA in TAE buffer was found to be (3.75 ± 0.04) × 10⁻⁴ cm² V⁻¹ s⁻¹ at 25°C, independent of DNA concentration, sample size, electric field strength, and capillary coating, and in good agreement with other values in the literature. The free solution mobility was independent of DNA molecular weight from ∼ 400 base pairs to 48.5 kilobase pairs, but decreased monotonically with decreasing molecular weight for smaller fragments. Surprisingly, the free solution mobility of DNA in TBE buffer was found to be (4.5 ± 0.1) × 10⁻⁴ cm² V⁻¹ s⁻¹, about 20% larger than observed in TAE buffer, presumably because of the formation of nonspecific borate‐deoxyribose complexes. © 1997 John Wiley & Sons, Inc. Biopoly 42: 687–703, 1997