CRYSTAL-STRUCTURE OF THE B-DNA HEXAMER D(CTCGAG) - MODEL FOR AN A-TO-B TRANSITION

The crystal structure of the B-DNA hexamer d(CTCGAG) has been solved a t 1.9 Angstrom resolution by iterative single isomorphous replacement, using the brominated derivative d(CG(5Br)CGAG), and refined to an R-f actor of 18.6% for 120 nonhydrogen nucleic acid atoms and 32 water mol ecules, Although the central four base pairs form a typical B-form hel ix, several parameters suggest a transition to an A-like conformation at the termini, Based on this observation, a B-to-A transition was mod eled, maintaining efficient base stacking across the junction. The wid e minor groove (similar to 6.9 Angstrom) is reminiscent of that in the side-by-side double drug DNA complexes and hosts a double spine of hy dration. The global helix axes of the pseudo-continuous helices are at an acute angle of 60 degrees. The pseudocontinuous stacking is reinfo rced by the minor groove water structure extending between the two dup lexes. The crossover point of two pairs of stacked duplexes is at the stacking junction, unlike that observed in the B-DNA decamers and dode camers. This arrangement may have implications for the structure of a four-way DNA junction. The duplexes are arranged around a large (simil ar to 20 Angstrom diameter) channel centered on a 6(2) screw axis.