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![[Figure 3]](cb5136fig3mag.jpg)
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Figure 3
The hydration patterns of selected sequences of highly populated NtC classes. Water probability densities are displayed as a mesh and HSs as small balls. Base-related water density and HSs are displayed in blue and those for the backbone in yellow. These and other hydration patterns can be visualized using WatNA. (a) Typical hydration of bases in the BB00 class shown for the CG sequence. Pyrimidines have one HS in each groove; purines have two in the major groove and one in the minor groove. (b) HSs of the phosphate charged O atoms OP1 and OP2 in all 16 dinucleotide sequences of BB00, the NtC class best representing the BI form. Spheres in different shades of yellow represent HSs in different sequences; water densities are only displayed in matching colors for four of the sequences for clarity. The alignment shows three HSs for both OP1 and OP2 atoms. The most prominent HS in all sequences is the HS hydrating the OP2 atom. Waters constituting this HS are stabilized by van der Waals contact with the pyrimidine C6 or purine C8 base atom (base and sugar atoms are not shown for clarity). (c) Both NtC classes representing the BI form, BB00 and BB01, have similar structures and their hydration is also very similar. Data are for the AC sequence. (d) The BII form, NtC class BB07, has a unique HS in the minor groove. The HS is stabilized by contacts to N3(R)/O2(Y) of the first base and deoxyribose O4′ atoms of both sugar rings. The BII hydration is shown here for the CA sequence. (e) The hydration of the A form represented here by NtC class AA00 in the CG sequence. The most prominent difference relative to the hydration pattern of the BI form is the phosphate hydration, with two large water densities connected to the phosphate OP2 atom. One of these densities overlaps with the base hydration and water would fluctuate between the positions of the HSs highlighted by red arrows. (f) Hydration of the NtC class BBS1 occurring in the GG sequence, mostly in quadruplex structures. (g) The hydration pattern of the CG step of the Z form that is described by NtC class ZZ1S. (h) The hydration pattern of the GC step of the Z form, described by NtC class ZZS1. The hydration pattern of the left-handed DNA is very different from that in both right-handed forms: water densities are mostly located between the base planes rather than in the planes, and base and phosphate hydration merge in the minor rather than the major groove. |
![[Figure 3]](cb5136fig3.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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