Helix axis

The sugar-phosphate backbone is represented by connected circles in color and the base pairs as blue planks. Four base pairs are shown from the top of the helix to highlight how the grooves are formed due to the asymmetric connections. The position of the helix axis is marked by a cross. 

FIGURE 6.8 The arrangement of N—H and C=0 groups (each with an individnal dipole moment) along the helix axis creates a large net dipole for the helix. Numbers indicate fractional charges on respective atoms. 

An alternative form of the right-handed double helix is A-DNA. A-DNA molecules differ in a number of ways from B-DNA. The pitch, or distance required to complete one helical turn, is different. In B-DNA, it is 3.4 nm, whereas in A-DNA it is 2.46 nm. One turn in A-DNA requires 11 bp to complete. Depending on local sequence, 10 to 10.6 bp define one helical turn in B-form DNA. In A-DNA, the base pairs are no longer nearly perpendicular to the helix axis but instead are tilted 19° with respect to this axis. Successive base pairs occur every 0.23 nm along the axis, as opposed to 0.332 nm in B-DNA. The B-form of DNA is thus longer and thinner than the short, squat A-form, which has its base pairs displaced around, rather than centered on, the helix axis. Figure 12.13 shows the relevant structural characteristics of the A- and B-forms of DNA. (Z-DNA, another form of DNA to be discussed shortly, is also depicted in Figure 12.13.) A comparison of the structural properties of A-, B-, and Z-DNA is summarized in Table 12.1. 

Helix axis location Major groove Through base pairs Minor groove... 

Figure 12.16), can insert between the stacked base pairs of DNA. The bases are forced apart to accommodate these so-called intercalating agents, causing an unwinding of the helix to a more ladderlike structure. The deoxyribose-phosphate backbone is almost fully extended as successive base pairs are displaced 0.7 nm from one another, and the rotational angle about the helix axis between adjacent base pairs is reduced from 36° to 10°. 

Fig. 1. — Schematic drawing of a hypothetical polysaccharide chain whose helix axis is along the c-edge of the unit cell.

Fig. 9. — Antiparallel packing arrangement of the 3-fold helices of (1— 4)-(3-D-xylan (7). (a) Stereo view of two unit cells roughly normal to the helix axis and along the short diagonal of the ab-plane. The two helices, distinguished by filled and open bonds, are connected via water (crossed circles) bridges. Cellulose type 3-0H-0-5 hydrogen bonds stabilize each helix, (b) A view of the unit cell projected along the r-axis highlights that the closeness of the water molecules to the helix axis enables them to link adjacent helices.

Fic. 10.—Parallel packing arrangement of 6-fold, A-amylose (8) molecules, (a) A stereo side view of less than 2 turns of a pair of double helices 10.62 A (=al2) apart. The two strands in each helix are distinguished by open and filled bonds, and the helix axis is also drawn, for convenience. Note that atom 0-6 mediates both intra- and inter-double helix hydrogen bonds. 

Fig. 21.—Structure of the 6-fold anhydrous curdlan III (19) helix, (a) Stereo view of a full turn of the parallel triple helix. The three strands are distinguished by thin bonds, open bonds, and filled bonds, respectively. In addition to intrachain hydrogen bonds, the triplex shows a triad of 2-OH - 0-2 interchain hydrogen bonds around the helix axis (vertical line) at intervals of 2.94 A. (b) A c-axis projection of the unit cell contents illustrates how the 6-0H - 0-4 hydrogen bonds between triple helices stabilize the crystalline lattice.

Fig. 24.—(a) Stereo view of slightly over a turn of the 3-fold double helix of i-carrageenan (23). The two chains are distinguished by open and filled bonds for clarity. The vertical line is the helix axis. Six interchain hydrogen bonds per turn among the galactose residues stabilize the double helix. The sulfate groups lined up near the periphery are crucial for intermolecular interactions. 

Fig. 38.—Stereo view of three turns of the 2-fold galactomannan (45) helix containing galactose side-chains on alternate mannose residues. In this conformation, the side chains are turned up toward the non-reducing end, and the backbone is stabilized by intrachain hydrogen bonds. The helix axis is represented by the vertical line.

The E. coli M41 mutant CPS (46) has a complex chemical sequence. Its repeating unit is an anionic hexamer a tetrasaccharide -A-B-C-D- in the main chain and a disaccharide -F-E- side chain, E attached to C (Table II). Polycrystalline and oriented fibers of the sodium salt of 46 have produced good diffraction data, with reflections up to 3 A resolution. Careful X-ray analysis60 has shown that the polymer forms a left-handed, smooth and sinuous, 2-fold helix of pitch 30.4 A. As shown in Fig. 39a, the main chain is fairly close to the helix axis. A notable observation is that side chain E-F, turned up toward the non-re-... 

Fig. 39.—fa) Stereo view of two turns of the left-handed. 2-fold helix of E. coli capsular polysaccharide (46) stabilized by hydrogen bonds involving both main and side chains. The vertical line represents the helix axis. 

Here, ry is the separation between the molecules resolved along the helix axis and is the angle between an appropriate molecular axis in the two chiral molecules. For this system the C axis closest to the symmetry axes of the constituent Gay-Berne molecules is used. In the chiral nematic phase G2(r ) is periodic with a periodicity equal to half the pitch of the helix. For this system, like that with a point chiral centre, the pitch of the helix is approximately twice the dimensions of the simulation box. This clearly shows the influence of the periodic boundary conditions on the structure of the phase formed [74]. As we would expect simulations using the atropisomer with the opposite helicity simply reverses the sense of the helix. 

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