Zigzag strands

Figure 19. Topological structure of 2D antiparallel DX arrays. The four arrays are built from DAO or DAE molecules crossings are separated by an even (E) or odd (O) number of double helical half-turns. Strand polarities are shown by the arrowheads on their 3 ends. Strands are drawn with different thicknesses for clarity. Both DAO lattices contain vertical zigzag strands, only. DAE-E consists of molecular chain mail, and DAE-O produces reporter strands in both the horizontal direction (straight) and the vertical direction (zigzag).

In these connections, it is useful to consider the behavior of the chemical shift of the CH2 carbons of paraffins and polyethylene in the crystalline and noncrystalline components. It is known that the CH2 carbons in paraffinic chains appear at lower frequency by 4-6 ppm if a carbon atom three bonds away is in a gaMc/ie-conformation rather than in a frans-confor-mation (y-effect) [7]. In fact, cyclic paraffins which crystallize in a conformations are characterized by two parallel all-fran5-planar zigzag strands connected by two GGTGG loops, it is found that the CH2 carbons with a y-effect resonates at a lower frequency by about 6.5 ppm as compared with those with no y-effect [8, 9]. Furthermore, it is found that the CH2 carbons of cyclic paraffins, and n-paraffins in the noncrystalline state, appear at lower frequency by 2-3 ppm more than those in the crystalline state. In the crystalline state, the CH2 carbons assume the all-trans-zigzag conformation, which is fixed because motion is frozen, but in the noncrystalline state a rapid transition between the trans- and gawc/ie-conformations occurs [11]. Weeding et al. [12] obtained the same results on the noncrystalline state. 

The closest contact between the strands of the chain is AgT -Ag2 at a distance of 2.89 A, which is equal to the interatomic separation in silver metal. However, my interpretation of this contact is that it represents the onset of a repulsive interaction between the silver atoms. In this structure the linear geometry at silver indicates that its bonding is fulfilled by the two thiolates, and there is no requirement for secondary Ag S bonding. The slight bending of Agl and Ag2 outside their S - S lines, away from each other, is indicative of weak repulsion, not attraction, between them. It is believed that the two zigzag strands of the chain approach each other until limited by the internal repulsion between opposite silver atoms. A corollary of this interpretation is a strong... 

Figure 6 The double-stranded chain of AgSCMeEt, in which the zigzag strands of alternating Ag and S atoms are intertwined but not bonded note the small outward displacements of opposing Ag atoms on different strands, consistent with a weak repulsive interaction. Reproduced with permission from Inorg. Chem., 22, 3785 (1983)...

Domain 1 is at the N terminus, but spatially is the central of three domains. It is an antiparallel j3 barrel that is superficially reminiscent of the viral capsid fold, but actually has completely different topology (Fig. 7 see Color Insert). In the jelly roll, the /3 strands alternate between the two opposing sheets of the barrel. In E protein they zigzag up and down the same sheet, with the following exception. Strand B, which in chemical sequence falls between strands A and C of the outermost sheet, actually forms the end strand of the inner sheet. So, the strand order is ACDEF for the outer sheet, and BIHG for the inner. Strands F and G are hydrogen bonded, but there is no direct continuation of the sheets across the AB strand gap. 

Alexander Rich and his associates discovered a third type of DNA helix when they solved the structure of dCGCGCG. They found that this hexanucleotide forms a duplex of antiparallel strands held together by Watson-Crick base-pairing, as expected. What was surprising, however, was that this double helix was left-handed, in contrast with the right-handed screw sense of the A and B helices. Furthermore, the phosphates in the backbone zigzagged hence, they called this new form Z-DNA (Figure 27.10). 

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