Opening and Closing DNA: Theories on the Nucleosome

Abstract

DNA—the carrier of the genetic information—is at the base of many central life processes [1]: replication, transcription, and repair of genetic material depend on the unique properties ofDNA, especially the base pairing.One has, however, to appreciate the fact that themolecular machinery of eucaryotes (plants and animals) does not deal with naked DNA but with chromatin, a DNA–protein complex in which DNA is wrapped and folded in a hierarchical fashion [2]. On the lowest level DNA is wrapped nearly twice aroundanoctamerofhistoneproteins.Ashort stretchof the “linkerDNA” connects to the next such protein spool. The resulting string of so-called nucleosomes folds into higher order structures, the details ofwhich are still under debate (see Figure 7.1). The structure of the nucleosome core particle (NCP), the particle that is left when the linker DNA is digested away, is known in exquisite detail from X-ray crystallographyat 2.8 A ! resolution [3] andmore recently at 1.9A ! [4].Theoctamer is composedof two molecules each of the four core histone proteins H2A, H2B, H3, and H4. At physiological conditions the stable oligomeric aggregates of the core histones are the H3–H4 tetramer (an aggregate of two H3 and two H4 proteins) and the H2A–H2B dimer; the octamer is then only stable if it is associated with DNA [5]. The two dimers and the tetramer are put together in such a way that the resulting octamer forms a cylinderwith about a 65A ! diameter and about a 60A ! height.With grooves, ridges, and binding sites the octamer defines thewrapping path of the DNA, a left-handed helical ramp of 1 and 3/4 turns, a 147 base-pairs (bp) length, and a roughly 28A ! pitch. This aggregate has a twofold axis of symmetry (the dyad axis) that is perpendicular to the superhelix axis. A schematic view of the NCP is given in Figure 7.2.