Properties of supercoiled DNA in gel electrophoresis. The V-like dependence of mobility on topological constraint. DNA-matrix interactions |
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| Authors: | Y Zivanovic I Goulet A Prunell |
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| Affiliation: | 1. Clinic of Hematology and Clinical Immunology, Clinical Centre Niš, Niš, Serbia;2. Faculty of Medicine, University of Niš, Niš, Serbia;3. Mechanical Engineering Faculty, University of Niš, Niš, Serbia;1. Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Institute of Epidemiology, Greifswald – Insel Riems, Germany;2. Institute of Veterinary Pathology at the Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, Munich, Germany;3. Institute for Infectious Diseases and Zoonoses, Ludwig-Maximilians-Universität München, Munich, Germany;4. Clinic for Ruminants with Ambulatory and Herd Health Services at the Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, Oberschleißheim, Germany;5. Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, Ozzano Emilia, Bologna, Italy;1. Department of Molecular and Cell Biology, University of California, Berkeley, United States;2. Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States;3. Howard Hughes Medical Institute, UC Berkeley, Berkeley, United States;1. University of Tampere, School of Medicine, Tampere, Finland;2. Department of Anesthesia, Tampere University Hospital, Tampere, Finland;3. Cancer Center, Helsinki University Central Hospital, Helsinki, Finland;4. Science Center, Pirkanmaa Hospital District and School of Health Sciences, University of Tampere, Tampere, Finland;5. Department of Oncology, Tampere University Hospital, Tampere, Finland;6. Department of Pathology, Tampere University Hospital, Fimlab Laboratories, Tampere, Finland |
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| Abstract: | The dependence of the electrophoretic mobility of small DNA rings on topological constraint was investigated in acrylamide or agarose gels as a function of DNA size (from approximately 350 to 1400 base-pairs), gel concentration and nucleotide sequence. Under appropriate adjustment between the size of the DNA and the gel concentration, this dependence was found to be V-shaped in a limited interval around constraint O, the minimum mobility at the apex of the V being obtained for relaxed DNA. Analysis of the DNA size dependence of the V suggests that it is the result of a modulated compaction of the DNA rings by the gel matrix. Compaction appears to be maximum upon relaxation, and to decrease with increase in supercoiling. Consistent with this interpretation, gels were found to oppose structural departures from the B helix, such as Z transition and cruciform extrusion, which tend to relax the DNA molecule and make it more expanded. In contrast, when DNA size or gel concentration are large enough relative to one another, U shapes are observed instead of Vs, as a consequence of an increase in the mobility of the rings closer to relaxation. The relevance of these results to the situation of superhelical DNA in vivo is discussed. Application of the V to the measurement of the DNA helical twist is mentioned. |
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