ABSTRACT
Some of the most interesting features of double-helical DNA occur at the mesoscopic level; that is, at chain lengths of a few hundred base pairs [Laughlin et al. 2000]. For example, DNA loops of this size bring proteins bound at separate, widely spaced sites on the double helix into close contact, in uencing not only the three-dimensional organization of the genome but also the activity of proteins that control, shuf e, and express the genetic message [Semsey, Virnik, and Adhya 2005]. The nucleosome, the protein-DNA assembly that constitutes the basic packaging unit in the nucleus, binds similarly sized pieces of DNA: a 147-bp fragment winds ∼ 1.6 superhelical turns around the
core of eight histone proteins in the best-resolved nucleosome core-particle structure [Richmond and Davey 2003].
