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Iterative Optimization of DNA Duplexes for Crystallization of SeqA-DNA Complexes
Published on: November 1, 2012
Comparative studies of high resolution Z-DNA crystal structures. Part 1: Common hydration patterns of alternating
R V Gessner1, G J Quigley, M Egli
1Institute for Clinical Chemistry and Biochemistry, Rudolf Virchow University Hospital, Berlin, Germany.
Journal of Molecular Biology
|March 4, 1994
Summary
Water molecules form distinct patterns around Z-DNA, acting as integral parts of its structure. Ions and polycations can displace some water, but many remain ordered, influencing DNA conformation.
Area of Science:
- Structural Biology
- Biophysics
- Crystallography
Background:
- The left-handed Z-DNA conformation presents a unique structural motif compared to the canonical B-DNA.
- Understanding the hydration patterns of Z-DNA is crucial for elucidating its biological roles and interactions.
Purpose of the Study:
- To analyze the detailed water structure in three crystal forms of the Z-DNA hexamer [d(CGCGCG)]2.
- To identify common hydration motifs and their relationship with DNA bases and phosphate backbone.
Main Methods:
- X-ray crystallography was used to determine the structures of three Z-DNA crystal forms.
- Analysis of water molecule positions and interactions within the first hydration shells.
Main Results:
- Identified conserved water-bridging motifs between guanine O-6 and cytosine N-4 groups, and along the minor groove connecting cytosine O-2 groups.
- Observed water molecules bridging guanine N-2 nitrogens to phosphate oxygens across the minor groove.
- Found less ordered water structure between phosphate groups, correlated with interphosphate distances.
- Noted displacement of water by ions (Na+, Mg2+) and spermine, but many water molecules are integral to the DNA structure.
Conclusions:
- Numerous water molecules in Z-DNA crystals are integral components of the DNA structure, exhibiting ordered arrangements.
- The hydration patterns are largely independent of local crystallographic variations, suggesting intrinsic structural roles.
- Ions and polycations compete with water for binding sites, highlighting the dynamic nature of DNA hydration.
