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The crystal structure of the DNA decamer C-G-A-T-C-G-A-T-C-G has been solved to
a resolution of 1.5 A, with a final R-factor of 16.1% for 5,107 two-sigma
reflections. Crystals are orthorhombic space group P2(1)2(1)2(1), with cell
dimensions a = 38.93 A, b = 39.63 A, c = 33.30 A, and 10 base pairs/asymmetric
unit. The final structure contains 404 DNA atoms, 142 water molecules treated as
oxygen atoms, and two Mg(H2O)6(2+) complexes. Decamers stack atop one another to
simulate continuous helical columns through the crystal, as with three
previously solved monoclinic decamers, but the lateral contacts between columns
are quite different in the orthorhombic and monoclinic cells. Narrow and wide
regions of the minor groove exhibit a single spine or two ribbons of hydration,
respectively, and the minor groove is widest when BII phosphate conformations
are opposed diagonally across the groove. Phosphate conformation, in turn,
appears to have a base sequence dependence. Twist, rise, cup, and roll are
linked as has been observed in the three monoclinic decamers and can be
characterized by high or low twist profiles. In all five known decamer crystal
structures and eight representative dodecamers, a high twist profile is observed
with G-C and G-A steps whereas all other R-R steps are low twist profiles (R =
purine). A-T and A-C steps are intermediate in character whereas C-A and C-G
exhibit behavior that is strongly influenced by the profiles of the preceding
and following steps. When sufficient data are in hand, sequence/structure
relationships for all helix parameters probably should be considered in a 4-base
pair context. At this stage of limited information the problem is compounded
because there are 136 unique 4-base steps x-A-B-y in a double helix as compared
with only 10 2-base steps A-B.
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