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Ordered water structure around a B-DNA dodecamer. A quantitative study.

M L Kopka, A V Fratini, H R Drew

    Journal of Molecular Biology
    |January 5, 1983
    PubMed
    Summary
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    Detailed B-DNA dodecamer structures reveal extensive hydration along the phosphate backbone, crucial for stabilizing DNA. This hydration pattern, including a zig-zag spine in the minor groove, was observed across different temperatures and a brominated variant.

    Area of Science:

    • Structural Biology
    • Biochemistry
    • Crystallography

    Background:

    • The double-helical B-DNA structure is fundamental to genetic information storage.
    • Understanding DNA hydration is critical for elucidating its stability and function.
    • Previous studies lacked detailed insights into DNA backbone hydration due to limitations in resolution or temperature.

    Purpose of the Study:

    • To determine the high-resolution crystal structure of a B-DNA dodecamer under various conditions.
    • To investigate the role and extent of water molecule interactions with the DNA backbone and grooves.
    • To characterize the hydration patterns responsible for stabilizing the B-DNA form.

    Main Methods:

    • X-ray crystallography was employed to solve and refine the crystal structure of the C-G-C-G-A-A-T-T-C-G-C-G dodecamer.

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  • Structures were determined at room temperature, low temperature (16 K), and for a 9-bromo variant at 7 °C in a cryoprotectant solution.
  • High-resolution structural data allowed for the identification and characterization of ordered solvent molecules.

    • Main Results:

    • Extensive hydration was observed along the phosphate backbone, particularly in the low-temperature and brominated structures, which was obscured in the native structure.
    • An average of three water molecules per phosphate group were identified, forming extensive networks.
    • A zig-zag spine of hydration in the minor groove, crucial for B-DNA stability, was consistently observed across all three structures.

    Conclusions:

    • The study provides unprecedented detail on DNA hydration, highlighting its significant role in stabilizing the B-DNA conformation.
    • Low temperatures and bromination enhance the visibility of backbone hydration, revealing previously unobserved interactions.
    • The findings underscore the importance of the water spine in the minor groove for maintaining DNA integrity.