Figure 1. In vivo, fluorescently stained, E. coli. DAPI is added to a culture of exponentially growing cells in an amount determined experimentally for each strain and medium; being low enough not to inhibit growth. Viewed under near blue ultraviolet fluorescence and phase contrast. The latter is necessary for visualizing the bacterial ‘body’.

Figure 2. Serial, longitudinal sections of E. coli, prepared by cryofixation and freeze-substitution (CFS) for the electron microscope. Five of a series of 11 thin sections, taken from the middle part of the cell, are shown. The nonuniform distribution of ribosomes can be distinguished. The bacterial chromatin is in the ribosome-free spaces, as shown by immunostaining. Bar, 0.5 m. Reprinted from Bohrmann et al. (1991). Copyright © 1991 American Society for Microbiology.

Figure 3. Serial sections, of which five are shown in Figure 1, are schematically redrawn on coloured foils and, with the ribosome-free spaces carefully cut out, superimposed to form a package that is a reconstruction of the whole cell. A sharp photographic image of this reconstructed cell is given in (a). The out-of-focus pictures (b1) to (b4) are obtained with a pinhole camera; these prints, on hard-grade paper, differ from each other only by the exposure time. (c) A light microscope phase-contrast micrograph is shown. According to the concentration of the surrounding refracting material, phase-contrast images vary

Figure 4. Proposed compaction forms of DNA. The same length of DNA is shown in the form of the loose (a) and compacted (b) plectonemic supercoiling. In (c) and (d) it is in a solenoidal form. The compaction ratio of the length of the stretched DNA molecule to that of the supercoiled, compacted form is about 9 in (b) and (c), but only 3 in (a). By normalizing the dimensions of the figure such that two windings of (c) correspond to those of a eukaryotic nucleosome, the bending (curvature) is then 0.23 for these and 0.25 and 0.26 for (b) and (a), respectively. The loose plectonemic form and its derivatives have been and still are extensively studied by electron microscopy and sedimentation rates. In the absence of a sufficient amount of adequate basic proteins as partners, ‘naked’ DNA shows neither the compacted form (b) nor (c). It is likely, that, upon liberation out of the cell, a putative compact solenoidal supercoil (c) is very likely to transform into a branched form of extended plectonemic supercoil. As yet, solenoidal compaction has been observed only with eukaryotic nucleosomes, where the DNA is wound around a solid core of histones. For prokaryotes a hypothetical form of a fragile chromatin, form (d), had been proposed. For the purpose of comparison, in (e), the solenoidal supercoil of eukaryotic chromatin is given.

Figure 5. A schematic redrawing of the situation depicted by the micrographs of Kavenoff but with an intact cell at the same scale for comparison. In this picture, the rather understated linear extension of the expanded, ‘explosed’ cell is 40 times the diameter of the rod-like cell before burst. Only one completely relaxed loop is shown to symbolize the difficulties to preserve supercoiling encountered by those who repeated the experiments.