Quasi-stacked conformations

The emergent molecular view can be summed up as follows the adducts of less potent (+) syn- and (-) a t/-BaPDE s predominantly exist in quasi-intercalative conformations with relatively intact base stacking. On the other hand, (+) a //-BaPDE adducts exist in a locally disordered and flexible DNA structure, are labile and spend at least part of the time outside the DNA helix in the minor groove where it may get protonated more readily. 

The crystal structures of (EDT-TTFBr2)2MX4 and (EDO-TTFBr2)2MX4 are quite similar, although the space group symmetry is different in these two systems. However, this difference comes only from the conformation of terminal six-membered rings of the donor molecules, which plays no important role in the physical properties of the present salts. The donor molecules are stacked in a head-to-tail manner to form quasi-one-dimensional columns as shown in Fig. 6a. 

In homo-DNA (h-DNA) and pyranosyl-RNA (p-RNA), the hexitol ring is frozen in a single y-endo- ke eonformation, as opposed to the multiple conformations accessible to the furanose of DNA and RNA. The h-DNA duplexes have a quasi-linear orientation as opposed to the superhelical structure of DNA duplexes, and the distance between the base stacking planes is larger relative to that of DNA. The h-DNA duplexes also have different pairing stability, e.g., the pairing priorities of A-A exceeds that of A-T. In contrast to h-DNA, p-RNA, which is also quasi-linear, does not show altered pairing priorities. 

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