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Crystal Structure of Double Helical Hexitol Nucleic Acids

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    Crystal Structure of Double Helical Hexitol Nucleic Acids
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    Contribution from Biomolecular Architecture, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Leuven (Heverlee), Belgium, Laboratory of Medicinal Chemistry, Rega Institute, Katholieke Universiteit Leuven, Minderbroederstraat 10, B-3000 Leuven, Belgium, and Department of Haematology, University of Cambridge, Cambridge Institute for Medical Research, Hills Road, Cambridge CB2 2XY, U.K.
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    Journal of the American Chemical Society

    Cite this: J. Am. Chem. Soc. 2002, 124, 6, 928–933
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    https://doi.org/10.1021/ja016570w
    Published January 15, 2002
    Copyright © 2002 American Chemical Society
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    A huge variety of chemically modified oligonucleotide derivatives has been synthesized for possible antisense applications. One such derivative, hexitol nucleic acid (HNA), is a DNA analogue containing the standard nucleoside bases, but with a phosphorylated 1‘,5‘-anhydrohexitol backbone. Hexitol nucleic acids are some of the strongest hybridizing antisense compounds presently known, but HNA duplexes are even more stable. We present here the first high-resolution structure of a double helical nucleic acid with all sugars being hexitols. Although designed to have a restricted conformational flexibility, the hexitol oligomer h(GTGTACAC) is able to crystallize in two different double helical conformations. Both structures display a high x-displacement, normal Watson−Crick base pairing, similar base stacking patterns, and a very deep major groove together with a minor groove with increased hydrophobicity. One of the conformations displays a major groove which is wide enough to accommodate a second HNA double helix resulting in the formation of a double helix of HNA double helices. Both structures show most similarities with the A-type helical structure, the anhydrohexitol chair conformation thereby acting as a good mimic for the furanose C3‘-endo conformation observed in RNA. As compared to the quasi-linear structure of homo-DNA, the axial position of the base in HNA allows efficient base stacking and hence double helix formation.

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    †

     Department of Chemistry, Katholieke Universiteit Leuven.

    ‡

     Rega Institute, Katholieke Universiteit Leuven.

    §

     University of Cambridge.

    *

     To whom correspondence should be addressed. Telephone:  +32 16 327609. Fax:  +32 16 327990. E-mail:  Luc.VanMeervelt@ chem.kuleuven.ac.be.

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    Cite this: J. Am. Chem. Soc. 2002, 124, 6, 928–933
    Click to copy citationCitation copied!
    https://doi.org/10.1021/ja016570w
    Published January 15, 2002
    Copyright © 2002 American Chemical Society
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