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.
Gisselfält
K
K
Department of Physical Chemistry, Chalmers University of Technology, Goteborg, Sweden.
Akerman
B
B
Jonsson
M
M
D010582:Bacteriophage lambda / Q000235:genetics; D002942:Circular Dichroism; D002945:Cisplatin / Q000031:analogs & derivatives / Q000494:pharmacology; D004279:DNA, Viral / Q000737:chemistry* / Q000187:drug effects; D004587:Electrophoresis, Agar Gel; D017900:Myoviridae / Q000235:genetics; D009690:Nucleic Acid Conformation / Q000187:drug effects; D013329:Structure-Activity Relationship
D004279:DNA, Viral; C032799:chlorodiethylenetriamine platinum; C034697:transplatin; D002945:Cisplatin