Packing DNA into Cells
The DNA of the E. coli chromosome has a molecular weight of about 2 × 109and thus is about 3 × 106base pairs long. Since the distancebetween base pairs in DNA is about 3.4 Å, the length of the chromosome is 107 Å or 0.1 cm. This is very long compared to the 104 Å length of a bacterial cell, and the DNA must therefore wind back and forth many times within the cell. Observation by light microscopy of living bacterial cells and by electron microscopy of fixed and sectioned cells show, that often the DNA is confined to a portion of the interior of the cell with dimensions less than 0.25 µ.
To gain some idea of the relevant dimensions, let us estimate the number of times that the DNA of a bacterium winds back and forth within a volume we shall approximate as a cube 0.25 µ on a side. This will provide an idea of the average distance separating the DNA duplexes and will also give some idea of the proportion of the DNA that lies on
Figure 1.6 Calculation of the num-ber of times the E. coli chromosome winds back and forth if it is confined within a cube of edge 0.25 µ. Each of the n layers of DNA possesses n seg-ments of length 0.25 µ.
the surface of the chromosomal mass. The number of times, N, that the DNA must wind back and forth will then be related to the length of the DNA and the volume in which it is contained. If we approximate the path of the DNA as consisting of n layers, each layer consisting of n segments of length 0.25 µ (Fig. 1.6), the total number of segments is n2. Therefore, 2,500n2 Å = 107 Å and n = 60. The spacing between adjacent segments of the DNA is 2,500 Å/60 = 40 Å.
The close spacing between DNA duplexes raises the interesting prob-lem of accessibility of the DNA. RNA polymerase has a diameter of about 100 Å and it may not fit between the duplexes. Therefore, quite possibly only DNA on the surface of the nuclear mass is accessible for transcrip-tion. On the other hand, transcription of the lactose and arabinose operons can be induced within as short a time as two seconds after adding inducers. Consequently either the nuclear mass is in such rapid motion that any portion of the DNA finds its way to the surface at least once every several seconds, or the RNA polymerase molecules do penetrate to the interior of the nuclear mass and are able to begin transcription of any gene at any time. Possibly, start points of the arabinose and lactose operons always reside on the surface of the DNA.
Compaction of the DNA generates even greater problems in eu-karyotic cells. Not only do they contain up to 1,000 times the amount of the DNA found in bacteria, but the presence of the histones on the DNA appears to hinder access of RNA polymerase and other enzymes to the DNA. In part, this problem is solved by regulatory proteins binding to regulatory regions before nucleosomes can form in these positions. Apparently, upon activation of a gene additional regulatory proteins bind, displacing more histones, and transcription begins. The DNA of many eukaryotic cells is specially contracted before cell division, and at this time it actually does become inaccessible to RNA polymerase. At all times, however, accessibility of the DNA to RNA polymerase must be hindered.
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