481D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.229 

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

  • Primary Citation of Related Structures:  1D7Z
  • Also Cited By: 2BJ6

  • 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: 
    • 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
    • 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.,Sect.C 52: 1213
    • 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.,Sect.D 55: 279


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-H(*(6HG)P*(6HT)P*(6HG)P*(6HT)P*(6HA)P*(6HC)P*(6HA)P*(6HC))-3'A8N/A
Small Molecules
Modified Residues  4 Unique
IDChainsTypeFormula2D DiagramParent
6HA
Query on 6HA
A
DNA LINKINGC11 H16 N5 O6 PDA
6HG
Query on 6HG
A
DNA LINKINGC11 H16 N5 O7 PDG
6HC
Query on 6HC
A
DNA LINKINGC10 H16 N3 O7 PDC
6HT
Query on 6HT
A
DNA LINKINGC11 H17 N2 O8 PDT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • R-Value Free: 0.229 
  • Space Group: P 32 1 2
Unit Cell:
Length (Å)Angle (°)
a = 33.041α = 90.00
b = 33.041β = 90.00
c = 38.924γ = 120.00
Software Package:
Software NamePurpose
SHELXL-97refinement
BRUTEphasing
DENZOdata reduction
SCALEPACKdata scaling
BRUTEmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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