286367 Counterion Condensation and DNA Electrophoretic Mobility

Wednesday, October 31, 2012: 12:30 PM
406 (Convention Center )
Nancy C. Stellwagen and Earle Stellwagen, University of Iowa, Iowa City, IA

The electrophoretic properties of double-stranded DNA, a relatively rigid polyanion, in free solution are very unusual because the mobility does not reflect the sizable charge on the helix backbone.  Conventional wisdom posits that for each base pair added to a DNA chain, the increase in charge is offset by the increase in frictional factor so that the mobility remains constant.  However, if charged groups are added to a DNA molecule without increasing its length or changing the frictional factor, the mobility remains essentially constant.  This observation suggests that the counterion cloud surrounding dsDNA is modulated to maintain a constant net charge on the phosphate groups in the DNA backbone. 

We have also measured the mobility of a series of 26 base pair dsDNAs containing A-tract sequences that are expected to bend the helix.   Measurements were made at constant ionic strength in solutions containing various ratios of tetrabutylammonium and Li ions.   A control with no A-tracts was electrophoresed at the same time, to correct for changes in the EOF and viscosity as a function of the type of cation in the solution.  The bulky hydrophobic tetrabutylammonium cation preferentially increases the mobility of the A-tract DNAs, suggesting that this cation selectively attenuates the counterion cloud above A-tract sequences.  The attenuation increases with increasing A-tract length but is modulated by the base composition of the flanking sequences.   Systematically decreasing the tetrabutylammonium concentration and increasing the Li concentration decreases the mobility dsDNAs containing A-tracts.  This decrease occurs in two discrete steps; the first step involves the return of the normal counterion cloud and the second step involves the bending of the A-tract sequence.  Thus, electrophoretic measurements in the presence of variable concentrations of tetrabutylammonium cations provide a rapid and sensitive measure of A-tract length and apparent bend angle.

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