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

Citation

Conner, Benjamin Norman (1982) Iodo-CCGG: A Single Crystal Structure of A-DNA. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/3t68-dc11. https://resolver.caltech.edu/CaltechTHESIS:05142018-150830492

Abstract

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.

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