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Albany 2001

category image Biomolecular
Stereodynamics
SUNY at Albany
June 19-23, 2001

Studies on the mechanism of migration of DNA through polyacrylamide gels

We have studied the electrophoretic migration of linear random-sequence B-DNA molecules through polyacrylamide gels, as a function of temperature, and of MPD and MgCl2 concentration. We observe a significant effect of MPD on the migration of generic DNA through polyacrylamide gels. The effect is chain-length dependent, especially at lower MPD concentration. When both MPD and MgCl2 are present in the gels, certain MgCl2 concentrations can cancel the effect of MPD on the electrophoretic mobility of ÔgenericÕ B-DNA sequences. The effects of temperature are dissimilar to the effects of MPD on B-DNA. This means that these environmental effects are not unique to A-tract regions, or A-tract-containing molecules. Thus, the difference between solution and crystalline studies regarding DNA bending cannot be traced to unique effects of these environmental factors exclusively on A-tract regions.

To distinguish between the effects of environmental factors on the structure of the DNA double helix, versus the effects on the gel matrix itself, and hence on the interaction of the DNA with the gel matrix, we have developed a methodology that is capable of quantitatively describing the electrophoretic mobility of oligomeric B-DNA through polyacrylamide gels in the presence of varying concentration of organic solvents such as MPD. Our analysis is based on a generalisation of OgstronÕs pore distribution model that takes into account polyelectrolyte effects such as counterion condensation, coulombic end effects, salt concentration, the non-ideality of the buffer as well as the screening of the hydrodynamic interactions.

Tali E. Haran*, Ilana Cohen*, and Udayan Mohanty#

* Department of Biology, Technion, Technion City, Haifa, 32000 Israel, e-mail: bitali@techunix.technion.ac.il, Fax no.: 972-4-8225153.
# Department of Chemistry, Boston College, Chestnut Hill, MA 02467 USA, e-mail: mohanty@bc.edu, Fax no.: 617-552-2705.