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Electrophoresis of Positioned Nucleosomes

Laboratoire Joliot-Curie et Laboratoire de Physique, Ecole Normale Supérieure de Lyon, Lyon, France

Correspondence: Address reprint requests to M. Castelnovo, Tel.: 33-472-728873; E-mail: martin.castelnovo{at}ens-lyon.fr.

We present in this article an original approach to compute the electrophoretic mobility of rigid nucleo-protein complexes like nucleosomes. This model allows us to address theoretically the influence of complex position along DNA, as well as wrapped length of DNA on the electrophoretic mobility of the complex. The predictions of the model are in qualitative agreement with experimental results on mononucleosomes assembled on short DNA fragments (<400 bp). Influences of additional experimental parameters like gel concentration, ionic strength, and effective charges are also discussed in the framework of the model, and are found to be qualitatively consistent with experiments when available. Based on the present model, we propose a simple semi-empirical formula describing positioning of nucleosomes as seen through electrophoresis.