DNA electrophoretic mobility and deformation in agarose gels

Abstract

Time-dependent electrophoretic mobility, μ, of large DNA fragments in agarose gels and the corresponding conformational changes under an applied electric field can be measured by means of movements of fluorescence pattern after photobleaching (MOFPAP) and transient electric birefringence (TEB), respectively. The short-time (≈ min) averaged electrophoretic mobility initially increased with increasing electric field-on time and finally reached a steady state value. The rate of increase in μ is closely related to the DNA size/gel pore size ratio. The change may also be correlated to the rate of deformation of DNA chains as observed by TEB. The field-free decay for large DNA fragments in agarose gels is very slow, lasting tens of seconds. Coupling of TEB and MOFPAP measurements together with fluorescence microscopy and dichroic measurements should permit us to provide a better description of the short-time averaged mechanisms responsible for polymer chain motions in pulsed field gel electrophoresis.