Effects of local changes in the helix flexibility on electrophoretic migration of DNA in agarose gel

We present a study of how kinks, flexible bends, and flexible joints in the DNA helix, induced by binding cis-diamminedichloroplatinum(II) (cis-DDP), transdiamminedichloroplatinum(II) (trans-DDP), and chlorodiethylenetriammineplatinum(II) (dien-Pt) to the DNA, affect the electrophoretic migration of DNA in agarose gels. For long DNA the conformation oscillates between extended and compact states during the migration, as for native DNA. The presence of flexible joints decreases both the length of time and the step length of the cycles, but in a compensatory manner so that there is no net effect on the mobility. This demonstrates that in some cases mobility alone cannot detect pertubations in the DNA helix. Kinks and flexible bends reduce the mobility because they both lead to longer time periods of the cycles. With kinks the reduction is strongest at low fields because at high fields the kinks are straightened out; the steps thus become even longer than for native DNA. The results suggest that a combination of mobility and orientation measurements on reptating DNA can be used for distinguishing different kinds of structural alterations in the DNA.