Bulged core

In dc magnetic applications, an air-gap is usually required somewhere along the magnetic path of the core. In ferrite cores, the gap is placed in the center-leg of the core. The flux leaves one end of the core and flows towards the opposing end. The flux, though, repels itself and causes the flux lines to bulge out away from the centerline of the core. The presence of an air-gap creates an area... 

The major alternative mechanism for nucleosome redistribution to the bulge propagation mechanism is twist diffusion. Supporting this, it is clear that the nucleosome core particle is capable of accommodating alterations to DNA twist of 1-2 bp per double helical turn without significant changes to the... 

Fig. 20 Micellar fibers of PMPSnPEOtn in mixtures of THF and water (25/75 by volume). TEM images (a) visualizing the poly silane core of miceUar fibers (unstained, bar represents 250 nm) (b) revealing the PEO shell using nranyl acetate staining, (c) showing an example of the bulges found for many of these fibers, (d) Schematic representation of the structure of the micellar fibers showing the PMPS core and the PEO shell. Reproduced with permission from [79], Sommerdijk et al. (2000) Macromolecules 33 8289. American Chemical Society...

Many ribozymes and proteins that catalyze phosphoryl-transfer reactions use a mechanism employing two metal ions, and early on group II introns were hypothesized to use a similar mechanism (17). However, evidence for the existence of two metal ions in the catalytic core was only found very recently (12, 13, 18). A direct Mg + coordination of the pro-Sv oxygen of the first nucleotide of the catalytic triad is evident based on phosphorothioate substitution experiments (18). Recently, an intact group II was successfully crystallized for the first time (12). This structure confirms the metal contact from the first nucleotide of the catalytic triad and shows additional contacts to this metal ion from the second nucleotide of the catalytic triad and from the first nucleotide upstream of the bulge (Fig. 4a). This nucleotide is additionally coordinated to the second Mg + ion in the core. The distance between the two Mg + ions in the crystal stmcture is 3.9 A, which is in agreement with the proposed two-metal-ion mechanism (17). 

TAR) RNA, 59-mer). The aptamer has a TAR-Uke motif in its randomized region, having two bulge units adjacent to one another in opposite orientations. The core element for binding to Tat is a four central base pair helix flanked by two residues on each side. 

Figure 13 Comparison between (a) continuous and (b) bulged G-tetracf cores...

The structure of the bulged G-tetrad core can be considered as an intermediate between the continuous and the interrupted cores mentioned above. Figure 14 shows different examples of interrupted G-tetrad cores. The relative sugar orientations between two residues across the break point can be (i) 5 -to-5 (Figure 14a and b) (ii) 3 -to-3 [Figure 14(c)] and (hi) 5 -to-3 [Figure 14(d)]. 

Figure 2. Oxygen ELF = 0.85 localization domains of oxygen atoms in (a) cristobalite, (b) stishovite and (c) fluorite-type prototype structure. The bond directions which are not indicated on the figure are along the lines joining the oxygen core domain (the small sphere at the center of the pictures) and the disynaptic domains. In cristobalite the disynaptic domains are the two discs on both side of the core. In stishovite the valence domain is not fully resolved in irreducible domains, the disynpatic attractors are located within the three bulges lying in the horizontal plane. In fluorite-type structure, the four disynaptic domains form a tetrahedron.

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