481D

CRYSTAL STRUCTURE OF A HEXITOL NUCLEIC ACID (HNA) DUPLEX AT 1.6A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.229 
  • R-Value Observed: 0.183 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of double helical hexitol nucleic acids.

Declercq, R.Van Aerschot, A.Read, R.J.Herdewijn, P.Van Meervelt, L.

(2002) J Am Chem Soc 124: 928-933

  • DOI: 10.1021/ja016570w
  • Primary Citation of Related Structures:  
    481D, 1D7Z

  • PubMed Abstract: 
  • 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 phosph ...

    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.


    Related Citations: 
    • 1',5'-Anhydrohexitol Nucleic Acids, a New Promising Antisense Construct
      Van Aerschot, A., Verheggen, I., Hendrix, C., Herdewijn, P.
      (1995) Angew Chem Int Ed Engl 34: 1338
    • 1',5'-Anhydro-2',3'-Dideoxy-2'-(Guanin-9-Yl)-D-Arabino Hexitol
      Declercq, R., Herdewijn, P., Van Meervelt, L.
      (1995) Acta Crystallogr C 52: 1213
    • Molecular Dynamics Simulation to Investigate Differences in Groove Hydration of HNA/RNA Hybrids as Compared to HNA/DNA Complexes
      De Winter, H., Lescrinier, E., Van Aerschot, A., Herdewijn, P
      (1998) J Am Chem Soc 120: 5381
    • Oligonucleotides with 1',5'-Anhydrohexitol Nucleoside Building Blocks: Crystallisation and Preliminary X-Ray Studies of h(GTGTACAC)
      Declercq, R., Van Aerschot, A., Herdewijn, P., Van Meervelt, L.
      (1999) Acta Crystallogr D Biol Crystallogr 55: 279

    Organizational Affiliation

    Biomolecular Architecture, Department of Chemistry, Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Leuven (Heverlee), Belgium.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-H(*(6HG)P*(6HT)P*(6HG)P*(6HT)P*(6HA)P*(6HC)P*(6HA)P*(6HC))-3'A8N/A
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.60 Å
    • R-Value Free: 0.229 
    • R-Value Observed: 0.183 
    • Space Group: P 32 1 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 33.041α = 90
    b = 33.041β = 90
    c = 38.924γ = 120
    Software Package:
    Software NamePurpose
    BRUTEmodel building
    SHELXL-97refinement
    DENZOdata reduction
    SCALEPACKdata scaling
    BRUTEphasing

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 2002-04-27
      Type: Initial release
    • Version 1.1: 2008-04-26
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance