THE STRUCTURE OF AN A-DNA OCTAMER D(CTCCGGAG)2 AND COMPARISON TO RELATED DNA STRUCTURES
Bohdan Schneider1, Jiri Charvát2, Thierry Prange3, William B. T. Cruse3
1 J. Heyrovský Institute of
Physical Chemistry, Academy of Sciences of the Czech Republic,
CZ-18223 Prague, Czech Republic
2 Faculty of Mathematics and Physics,
Charles University, Ke Karlovu 5, CZ-12000 Prague, Czech Republic
3 LURE, Bât. 209d,
Université Paris-Sud 91405 ORSAY Cedex, France
The crystal structure of the self-complementary DNA octamer d(CTCCGGAG) was determined and compared to other A-DNA octamers available in the Nucleic Acid Database.
The structure, measured at 4 °C, was refined to an R factor of 17.9 % using 1416 reflections to a resolution of 1.96 A. The octamer crystallized in the tetragonal space group P43212 with the unit cell a = b = 41.70 A and c = 23.34 A. Two strands, related by a crystallographic dyad axis, form a right handed duplex in the A-DNA conformation: The mean helix rotation is 33, the average rise 3.0 A, and deoxyriboses are in the C3´-endo conformation. The duplexes pack in an arrangement similar to other A-DNA octamers crystallized in the P 43212 group.
The first hydration shell was determined for the four DNA
bases on the basis of crystallographic data from 34 A-DNA
structures. This average hydration was compared to hydration
patterns observed in the reported structure and to the average
hydration previously determined for bases in B-DNA and Z-DNA
crystal structures.