STRUCTURE OF THE B-DNA DECAMER C-C-A-A-C-I-T-T-G-G IN 2 DIFFERENT SPACE-GROUPS - CONFORMATIONAL FLEXIBILITY OF B-DNA

For the first time, the same B-DNA oligomer has been crystallized and its structure solved in two different space groups. Crystallization of C-C-A-A-C-1-T-T-G-G with Ca2+ yields monoclinic space group C2 with a = 31.87 angstrom, b = 25.69 angstrom, c = 34.21 angstrom, beta = 114.1-degrees, and five base pairs per asymmetric unit. The 5026 2sigma data to 1.3 angstrom refine to R = 0.152 with 72 waters, one heptavalent hydrated calcium complex, and one cacodylate ion per asymmetric unit. In contrast, crystallization with Mg2+ yields trigonal space group P3(2)21 with a = b = 33.23 angstrom, c = 94.77 angstrom, gamma = 120-degrees, and 10 base pairs per asymmetric unit. The 1725 2sigma data to 2.2 angstrom refine to R = 0.164 with 36 water molecules and one octahedral magnesium complex per asymmetric unit. The monoclinic form is virtually isostructural with previously solved monoclinic decamers, including twist angles of ca. 50-degrees at C-A and T-G steps. In contrast, the trigonal structure has quite different local helix parameters, with twist angles of ca. 36-degrees at the corresponding steps. These local parameter differences can only be attributed to crystal packing, suggesting that certain sequences of B-DNA are more flexible and influenced by their surroundings than had previously been thought. Such deformability may be important for interaction of B-DNA with control proteins, where both static structure and dynamic deformability comprise components of the recognition process. The crossing of two helices at an angle of 120-degrees in the trigonal cell is a model for an antiparallel, uncrossed Holliday junction, as has been noted earlier by Timsit and Moras [Timsit, Y., & Moras, D. (1991) J. Mol. Biol. 221, 919-940] from a rhombohedral DNA dodecamer structure analysis.