Iodo-CCGG: A Single Crystal Structure of A-DNA

Iodo-CCGG was synthesized by the triester method and crystallized in space group P43212. Electron density maps were phased using the anomalous scattering from the iodines and refined with the Jack-Levitt constrained refinement program. The final crystallographic R factor was 16.5% for 2 σ data and 19.9% for all data. Solution of the structure revealed the first fragment of A-DNA to be seen in a single crystal. The helix has a 2.2Å rise per residue, 10.6 base pairs per turn, and an average propeller twist of 17°. A total of 86 water molecules were located in the crystal. Of these, 47 were within 3.5Å of the ICCGG molecule. A second layer of hydration is formed by water molecules which are within 3.5Å of two or more first layer water molecules. The hydration sites on ICCGG are ordered based on the relative strengths of DNA to water bonds. as judged by their bond lengths. ICCGG packs together with the bottom of one helix in the minor groove of another. The packing scheme indicates that the minor groove of A-DNA is a relatively hydrophobic site. This fact may be important in the recognition of A-DNA by proteins and drugs. A list of refined coordinates of ICCGG is given in the appendix.