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Figure 4.
Figure 4. Hydration of the G-quartet linked G[4]T[4]G[4] DNA
dimer. Electron density maps and schematic representations are
shown side-by-side for water molecules bound in the four
grooves. The electron density map is colored gray for the DNA
grooves and blue for the water molecules. In the schematic
phosphorous atoms are colored yellow, non-bridging phosphate
oxygen atoms are red, N2 (and N3 if shown) atoms are green, the
C8 atom is gray, water molecules are cyan for 1–2 σ peaks in
the S.A. omit electron density maps and dark blue for>2 σ
peaks. The deoxyribose group is a pentagon and the bases are
represented as rectangles. The position in the 5′ → 3′
sequence and the syn/anti conformation about the N-glycosyl bond
of each base is indicated. From top to bottom the grooves are
the (a) wide groove (10 Å across), (b) intermediate I (4.6
Å across), (c) narrow (3.0 Å across), and (d)
intermediate II (4.6 Å across). The two intermediate
grooves and associated hydration patterns are pseudo 2-fold
symmetric, so each DNA-water interaction is corroborated by two
independent observations. In solution, the wide and narrow
grooves are each pseudo 2-fold symmetric, but water interactions
are not exactly repeated in the top and bottom halves of these
two grooves presumably because of protein and lattice
interactions.
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