There is yet another barrier to elongating RNA polymerases, both bacterial and eukaryotic, one that also applies to DNA polymerases, as discussed in Chapter 5 (see Figure 5–20). To describe this issue in more detail, we need first to consider a subtle property inherent in the DNA double helix called DNA supercoiling. DNA supercoiling is the name given to a conformation that DNA adopts in response to superhelical tension; alternatively, creating loops or coils in a double-helical DNA molecule can create such tension. Figure 6–19 illustrates why. There are approximately 10 nucleotide pairs for every helical turn in a DNA double helix. If we imagine a helix whose two ends are fixed with respect to each other (as they are in a DNA circle, such as a bacterial chromosome, or in a tightly clamped loop, as is thought to exist in eukaryotic chromosomes), one large DNA supercoil will form to compensate for each 10 nucleotide pairs that are opened (unwound). The formation of this supercoil is energetically favorable because it restores a normal helical twist to the base-paired regions that remain, which would otherwise need to be overwound because of the fixed ends.
RNA polymerase creates superhelical tension as it moves along a stretch of DNA that is anchored at its ends (see Figure 6–19C). As long as the polymerase is not free to rotate rapidly (and such rotation is unlikely given the size of RNA polymerases and their attached transcripts), a moving polymerase generates positive superhelical tension in the DNA in front of it and negative helical tension behind it. For eukaryotes, this situation is thought to provide a bonus: although the positive superhelical tension ahead of the polymerase makes the DNA helix
DNA with free end DNA with fxed ends
Figure 6–19 Superhelical tension in DNA causes DNA supercoiling. (A) For a DNA molecule with one free end (or a nick in one strand that serves as a swivel), the DNA double helix rotates by one turn for every 10 nucleotide pairs opened.
(B) If rotation is prevented, superhelical tension is introduced into the DNA by helix opening. In the example shown, the DNA helix contains 10 helical turns, one of which is opened. One way of accommodating the tension created would be to increase the helical twist from 10 to 11 nucleotide pairs per turn in the double helix that remains. The DNA helix, however, resists such a deformation in a springlike fashion, preferring to relieve the superhelical tension by bending into supercoiled loops. As a result, one DNA supercoil forms in the DNA double helix for every 10 nucleotide pairs opened. The supercoil formed in this case is a positive supercoil. (C) Supercoiling of DNA is induced by a protein tracking through the DNA double helix. The two ends of the DNA shown here are unable to rotate freely relative to each other, and the protein molecule is assumed also to be prevented from rotating freely as it moves. Under these conditions, the movement of the protein causes an excess of helical turns to accumulate in the DNA helix ahead of the protein and a deficit of helical turns to arise in the DNA behind the protein, as shown.
more difficult to open, the tension should facilitate the partial unwrapping of the DNA in nucleosomes, inasmuch as the release of DNA from the histone core helps to relax this tension.