Genes VII

A general principle is evident in the organization of all cellular genetic material. It exists as a compact mass, occupying a limited volume; and its various activities, such as replication and transcription, must be accomplished within these confines. The organization of this material must accommodate transitions between inactive and active states.

The condensed state of nucleic acid results from its binding to basic proteins. The positive charges of these proteins neutralize the negative charges of the nucleic acid. The structure of the nucleoprotein complex is determined by the interactions of the proteins with the DNA (or RNA).

A common problem is presented by the packaging of DNA into phages and viruses, into bacterial cells and eukaryotic nuclei. The length of the DNA as an extended molecule would vastly exceed the dimensions of the compartment that contains it. The DNA (or in the case of some viruses, the RNA) must be compressed exceedingly tightly to fit into the space available. So in contrast with the customary picture of DNA as an extended double helix, structural deformation of DNA to bend or fold it into a more compact form is the rule rather than exception.

The magnitude of the discrepancy between the length of the nucleic acid and the size of its compartment is evident from the examples summarized in Figure 18.1. For bacteriophages and for eukaryotic viruses, whether rod-like or spherical, the nucleic acid genome, whether DNA or RNA, whether single-stranded or double-stranded, effectively fills the container.

For bacteria or for eukaryotic cell compartments, the discrepancy is hard to calculate exactly, because the DNA is contained in a compact area that occupies only part of the compartment. The genetic material is seen in the form of the nucleoid in bacteria and as the mass of chromatin in eukaryotic nuclei at interphase (between divisions).

The density of DNA in these compartments is high. In a bacterium it is ~10 mg/ml, in a eukaryotic nucleus it is ~100 mg/ml, and in the phage T4 head it is >500 mg/ml. Such a concentration in solution would be equivalent to a gel of great viscosity. We do not entirely understand the physiological implications, for example, what effect this has upon the ability of proteins to find their binding sites on DNA.

The packaging of chromatin is flexible; it changes during the eukaryotic cell cycle. At the time of division (mitosis or meiosis), the genetic material becomes even more tightly packaged, and individual chromosomes become recognizable.

The overall compression of the DNA can be described by the packing ratio, the length of the DNA divided by the length of the unit that contains it. For example, the smallest human chromosome contains ~4.6 10⁷ bp of DNA (~10 times the genome size of the bacterium E. coli). This is equivalent to 14,000 µm (= 1.4 cm) of extended DNA. At the most condensed moment of mitosis, the chromosome is ~2 µm long. So the packing ratio of DNA in the chromosome can be as great as 7000.

Packing ratios cannot be established with such certitude for the more amorphous overall structures of the bacterial nucleoid or eukaryotic chromatin. However, the usual reckoning is that mitotic chromosomes are likely to be 5 V10 more tightly packaged than interphase chromatin, which therefore has a typical packing ratio of 1000 V2000.

A major unanswered question concerns the specificity of packaging. Is the DNA folded into a particular pattern, or is it different in each individual copy of the genome? How does the pattern of packaging change when a segment of DNA is replicated or transcribed?