Avoiding acid fixation or squashing, the structure of Drosophila salivary gland polytene chromosomes has been examined in detail in nuclei, with special emphasis on the organization of the DNA in the chromosome bands. Cut serial sections, optical serial sections, scanning electron microscopy (SEM) on whole mounts, high-voltage electron microscopy (HVEM) on whole mounts, and pancreatic DNase I digestion monitored by fluorescent microscopy have been used to complement one another in this analysis. With all five of these techniques, stereo pairs were used to aid in the three-dimensional reconstruction of chromosomal structures. Evidence is presented that most, if not all, of the polytene chromosome bands are torus-shaped. The DNA of these bands is largely confined to the rim, with the interior essentially DNA-free. The chromatin in each polytene band is also seen to have an extremely regular and highly ordered substructure. This substructural organization is largely radially symmetric in the bands and generally parallel to the chromosome axis. In addition, each band appears to be a distinct architectural entity with regard to its exact structural features and dimensions. A model is presented that follows these organizational boundary conditions.

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