Procedure for mapping the position of loop DNA sequences relative to the NM. A) Nucleoids prepared from freshly isolated primary rat hepatocytes were incubated with DNase I so as to progressively digest the loop DNA. Nucleoid samples with partially digested NM-bound DNA, as shown in the drawing and fluorescent micrographs (C) were used for PCR amplification of target sequences. The amplicons were run in agarose gels and scored as present (+) or absent (-) by an image analysis software as a function of nucleoid-sample digestion time (C) and the corresponding topological zones relative to the NM defined by the kinetics of nucleoid-DNA digestion. B) Drawing illustrating the local topology along a typical supercoiled DNA loop that correlates with both sensitivity to DNase I and distance relative to the NM thus defining topological zones relative to the NM.