Dyad axis

FefNOafa 9H2O, which are connected by a screw dyad axis parallel to the [010] direction. The crystal field axes Z[ and Zj form the angles 61 and O2 with the applied magnetic field. (Reprinted with permission from [41] copyright 1978 by Elsevier)... 

Fig. 5. Three views of the NCP from Harp et al. [31]. (a) Ventral surface view, (b) Side view, (c) View down the molecular pseudo-dyad axis. The histones are represented by Ca ribbon models of the secondary structure elements, and the DNA model indicates the base pairing between complementary strands. The DNA is positioned asymmetrically by one-half base pair on the NCP. This results in a two sides arbitrarily referred to a dorsal and ventral (the surface shown here). The ventral surface of the NCP is best recognized by the extended N-terminal H3 tail protruding to the right. In these images, the pseudo-dyad axis is represented by vertical bars for both the ventral and side view. The pseudo-dyad axis passes through the center of the dyad view orthogonal to the plane of the page, (d) Color code for histone chains in the figures in this chapter. Note the change in hue denoting the two sides of the histone octamer.

Fig. 12. Asymmetry of the DNA phosphodiester backbone trace as seen in the Oak Ridge NCP structural model (PDB access code lEQZ). No attempt has been made to regularize the geometry of the DNA positions of phosphates are based solely on the experimental electron density. Here the two DNA gyres are overlaid, with the 72 bp ventral gyre in red and the 73 bp dorsal gyre in blue. The minor groove positions facing the histone core are numbered sequentially from the dyad axis. The most pronounced asymmetry is seen in position 2 (10 o clock).

When TLS refinement is applied to the tetramer subunit, the resulting libration is less easy to interpret, and much less correlated with an intranucleosomal element. The center of motion for the tetramer shifts away from the dyad axis... 

Fig. 17. Composite structural motions of subunits can be described with translation, libration, and screw-axis (TLS) analysis of the NCP. Analysis of the histone subunits are shown here, (a) Composite motion of histones H2A (blue) and H2B (blue) considered as individual elements and combined as H2A H2B dimer (red). Note for the individual histones that the axis of motion is parallel with the medial a-helix of the histone. The origin of the TLS axes are within the structural positions of the histone. The composite motion for the H2A H2B dimer is dominated by the motion of H2A, as is seen in the similarity of orientation and position of the two axes, (b) The orientation and motion of the two H2A H2B dimers appear symmetric across the dyad axis of the NCP. (c) H3 H4 composite motions when considered as dimers (blue) and as the tetramer (red). Interpretation is more complex because of the asymmetric magnitude of motion for the two dimers, and the different position in the axis of primary motion for the tetramer. These motions are most likely the consequence of packing interactions, described in greater detail in the text.

Fig. 18. TLS analysis of the palindromic DNA on the NCP. (a) Composite motions of the DNA gyres looking at the ventral surface with the DNA colored by atom type. The two gyres reflect the structural asymmetry of the NCP with non-coincident axes of motion and different orientations for the primary axis of motion. The ventral gyre TLS axes more closely resemble the composite motions of the individual H3 H4 dimers (Fig. 17c), the dorsal TLS axes resemble the composite motion of the tetramer. (b) The composite motions of the DNA gyres are shown in a view down the dyad axis. The DNA is shown in a surface representation colored by atom type. Note that axes of motion appear parallel and in plane with the pitch of the DNA. In this view the ventral surface is on the bottom of the image.

The second major area of interaction is near the dyad axis. Hydroxyl radical footprinting revealed protection at 65 and 75 bp from the DNA ends [40]. On the... 

HMGN proteins are small, ubiquitous, chromatin architectural elements that bind to the 147 bp nucleosome core via their highly conserved nucleosome binding domain. They bind as homodimers, interacting near base 25 of the nucleosome DNA, and near the dyad axis. When incorporated into minichromosomes, HMGN proteins decrease chromatin folding in a manner that is dependent on their C-terminal domain, with a concomitant increase in transcription. 

Figure 8. Zero node operations, (a) Strand switch to remove nodes in knots and catenanes. On the left is a 5-noded knot (50, with its polarity indicated by arrowheads. Passing to the middle, one strand switch has been performed, converting the knot to a catenane, drawn with lines of two different thicknesses. On the right, another strand switch has been performed, making a new 3-noded knot, (b) A strand switch in a DNA context. Backbones are indicated by thick arrows, held together by three base pairs on each side. The helix axis is horizontal, and the dyad axis is vertical. The strand switch reconnects the strands, but maintains polarity. The reaction symbol replaces the right directional in (a), (c) View down the dyad axis. The view in (b) has been rotated 90° about the horizontal axis. The hairpin nature of the product is clear here. It should be clear that the leftward reaction shown here is identical to the ligation shown in the last step of Figure 6.

The Holliday junction is a well-known intermediate in recombination, but it is not the only one. Another species is the DNA double-crossover molecule, termed DX. The DX molecule consists of two four-arm branched junctions that have been joined at two adjacent arms, to create a molecule containing two helical domains joined by two crossover points (Fu and Seeman 1993). There are five different motifs of the DX molecule these are illustrated in Figure 14, with a modification of one of them. The names of the DX molecules all begin with D, for double crossover . Those in the top row have P for their second letter, indicating that their helix axes are parallel hence, there is a dyad axis, vertical in the plane of the page and parallel to the helix axes, relating each helical domain of the DP molecules to the other domain. 

Those molecules in the bottom row have A for the second letter of their names, indicating that their helix axes are antiparallel. The terms parallel and antiparallel are derived from recombination chemistry, which assumes that the two domains contain homologous sequences in that case, parallel and antiparallel describe their relative orientations. There is a dyad axis perpendicular to the page relating the... 

Figure 14. Motifs of double crossover molecules. The top row contains the three parallel isomers of double crossover (DX) molecules, DPE, DPOW and DPON P in their name indicates their parallel structure. Arrowheads indicate 3 ends of strands. Strands drawn with the same thickness are related by the vertical dyad axis indicated in the plane of the paper. DPE contains crossovers separated by an even number (two) of half-turns of DNA, DPOx by an odd number in DPOW, the extra half turn is a major groove spacing, in DPON, it is a minor groove spacing. The middle row illustrates two other DX isomers, DAE, and DAO. The symmetry axis of DAE is normal to the page (and broken by the nick in the central strand) the symmetry axis of DAO is horizontal within the page in DAO, strands of opposite thickness are related by symmetry. DAE+J, in the second row, is a DAE molecule, in which an extra junction replaces the nick shown in DAE.

A) Top view, 422 symmetry d = dyad axis of symmetry, t = octomer bond. 

B) Side view, 422 symmetry T = tetrad axis of symmetry. (C) Dimer structure. (D) 222 symmetry, X = overall dyad axis of symmetry. The preferred structure is 422. (From Green 1964 Timasheff and Townsend 1964. Reprinted with permission of AVI Publishing Co., Westport, Conn.)... 

Monoclinic crystals have a single twofold or dyad axis (see Fig. 7-11). The unit cell might contain two molecules related one to another by the dyad or one dimeric molecule with the dyad located as in Fig. 7-11C. Orthorhombic crystals have three mutually perpendicular twofold axes and the unit cell is a rectangular solid. 

---