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Torsional tension in the DNA double helix can be detected in the rotation ofthe double helix (3). The first rough estimates ofthe number ofdomains per Escherichia coli chromosome were calculated from the number of nicks (introduced by DNase) required to relax the supercoiling (2, 3). These studies indicated that the isolated nucleoids had 12 to 80 domains per genome equivalent of E. coli DNA. Later studies using more accurate methods showed that there were about 100 domains per genome equivalent (4,5), but that chromosomes isolated. from exponentially growing cells (mean generation time, 30 min) contained more than one.genome equivalent of DNA (6, 7) so that there were, on average, about 280 domains per chromosome.By use of analogous procedures, nuclear structures containing condensed DNA were later isolated from Drosophila melanogaster (8), mammalian (9, 10), and yeast (11) cells, and it was found that this packaged DNA was also segregated into multiple domains of supercoiling. The possible significance of the domain substructure of chromosomes and chromatin was immediately appreciated. Separate.domains permit the maintenance of different degrees of DNA torsional tension in different parts of the same chromosome. Thus, it is possible to relax the torsional tension in parts of a.chromosome without affecting other parts and also possible, in principle,,.to regulate the torsional strain independently in different domains, of the same chromosome. The last consideration is especially important because there are suggestions that the DNA torsional tension strongly influences rates of DNA transcription (12-15), recombination (16-18), replication (14, 19-21), viral encapsidation (22), transposition (23), and changes in chromosome-condensation (22). Thus, there could be a structural basis in chromosomes and chromatin permitting regulation of these DNA-dependent processes in different domains. Indeed, there is evidence in eukaryotes that initiation of DNA replication is regulated in units comprising many tandem replicons (24-26) and it has been proposed that the units may be equivalent to. a domain (27,28).Evidence supporting the domain structure of chromosomes has come exclusively.from studies of isolated chromosomes or nuclear structures. The stability. of the isolated bacterial chromosomes and some of the eukarytotic structures is dependent on nascent RNA molecules and proteins bound to the isolated chromosomes (1)(2)(3)8). When these chromosomes are incubated with RNase or when isolation is attempted from cells treated with inhibitors of RNA synthesis, the DNA unfolds (1-3, 8, 29) and the constraints that define domains are lost (3, 30). Investigations of the RNA components of isolated nucleoids have not revealed a unique class of chromosome-stabilizing RNA; it appears that the DNA-bound RNA molecules that interact most strongly are comprised predominantly (ifnot exclusively) of nascent mRNA and rRNA species (31). Thus, it has often been considered that some ofthe stabilizing interactions in these isolated...

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The DNA of Escherichia coli has been isolated in a compact structure containing small amounts of protein and RNA and having a sedimentation coefficient of approximately 3200 S. The molecular weight of the DNA in the complex is very large (probably higher than 109); the protein is predominantly core RNA polymerase; the RNA is chiefly nascent messenger and ribosomal chains. Solutions containing the complex have low vicosities; this plus its sedimentation rate suggest that the DNA is in a tightly folded conformation. The DNA unfolds after exposure to RNase or heat; this indicates that an RNA component of the complex is involved in stabilizing the structure..The DNA in bacterial cells as seen under the electron microscope is confined in regions of the cell called "nuclear bodies," but no nuclear membrane is observed (see, for example, refs. 1 and 2). Yet these chromosome-like structures have defined boundaries, which reorganize during the nuclear segregation that accompanies cell division (3). This implies that DNA folding within the nuclear body is maintained-at least partly--by internal interactions between the elements or regions of the nuclear body. The tertiary conformation of DNA within this body is unknown; however, studies of the rates at which different operons can be transcribed and regulated suggest that a considerable portion (perhaps all) of the genome is available for free interaction with other macromolecules (for examples see refs. 4-7). The packaging of the DNA must also be compatible with the requirements of semiconservative DNA replication and the eventual segregation of daughter double-helices (8, 9). These considerations imply that the-, tertiary structure of DNA within the cell is organized; however, this structure and the interactions that stabilize it are still to be determined.We describe here the isolation from E. coli of a DNA complex in which the DNA genome remains folded into a structure which is compact and nearly homogeneous in sedimentation. The complex is approximately 80% DNA by weight; it includes a small amount of protein and also contains nascent RNA. At least some of the RNA of the complex is essential for stabilizing the packaged structure, since the DNA unfolds as a result of RNase treatment. MATERIALS AND METHODSThe E. coli strain D-10 (RNase I-, ref. 10) was used in these studies. The bacteria were grown into the log phase in M9 media supplemented with 0.2% casamino acids.Viscosities of solutions of the DNA complex were measured at 250C in a falling-ball viscometer.Proteins were obtained from a DNA complex that had been purified by a scaled-up modification of the procedure described in the legend to Fig. 1 When E. coli cells are gently opened in solutions of high ionic strength, DNA is released from the cells but the solution does not become viscous. A DNA complex, having a nearly homogeneous sedimentation profile, can be isolated from the bulk of the ultraviolet-absorbing material of the lysate ( Fig. 1; see also ref. 12). This complex contains: nearly all of the DN...