Paradox lost: nucleosome structure and dynamics by the DNA minicircle approach

Publisher Summary This chapter focuses on the problem linking number paradox, which, because its solution was believed to reside in an overtwisting of nucleosomal DNA, was an incentive to early chromatin studies that aimed at measuring the local helical periodicity of nucleosomal DNA in situ . In addition to DNase and chemical cleavages, the distribution of specific di- and tri-nucleotides reflects the local helical periodicity. The DNA minicircle approach discussed in the chapter found the solution to the paradox to lie neither in nucleosomal DNA structure nor in nucleosome relative arrangement but in the ability of nucleosome immediate entry–exit DNA to cross positively, a counter-intuitive notion in view of the DNA left-handed wrapping around the histones. In the presence of linker histones, all nucleosomes, regardless of their sequence, can cross positively but lose access to the open conformation.