1DNF

EFFECTS OF 5-FLUOROURACIL/GUANINE WOBBLE BASE PAIRS IN Z-DNA. MOLECULAR AND CRYSTAL STRUCTURE OF D(CGCGFG)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Observed: 0.172 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Effects of 5-fluorouracil/guanine wobble base pairs in Z-DNA: molecular and crystal structure of d(CGCGFG).

Coll, M.Saal, D.Frederick, C.A.Aymami, J.Rich, A.Wang, A.H.

(1989) Nucleic Acids Res 17: 911-923

  • DOI: 10.1093/nar/17.3.911
  • Primary Citation of Related Structures:  
    1DNF

  • PubMed Abstract: 
  • The chemotherapeutic agent 5-fluorouracil is a DNA base analogue which is known to incorporate into DNA in vivo. We have solved the structure of the oligonucleotide d(CGCGFG), where F is 5-fluorouracil (5FU). The DNA hexamer crystallizes in the Z-DNA conformation at two pH values with the 5FU forming a wobble base pair with guanine in both crystal forms ...

    The chemotherapeutic agent 5-fluorouracil is a DNA base analogue which is known to incorporate into DNA in vivo. We have solved the structure of the oligonucleotide d(CGCGFG), where F is 5-fluorouracil (5FU). The DNA hexamer crystallizes in the Z-DNA conformation at two pH values with the 5FU forming a wobble base pair with guanine in both crystal forms. No evidence of the enol or ionized form of 5FU is found under either condition. The crystals diffracted X-rays to a resolution of 1.5 A and their structures have been refined to R-factors of 20.0% and 17.2%, respectively, for the pH = 7.0 and pH = 9.0 forms. By comparing this structure to that of d(CGCGCG) and d(CGCGTG), we were able to demonstrate that the backbone conformation of d(CGCGFG) is similar to that of the archetypal Z-DNA. The two F-G wobble base pairs in the duplex are structurally similar to the T-G base pairs both with respect to the DNA helix itself and its interactions with solvent molecules. In both cases water molecules associated with the wobble base pairs bridge between the bases and stabilize the structure. The fluorine in the 5FU base is hydrophobic and is not hydrogen bonded to any solvent molecules.


    Related Citations: 
    • 5-Fluorodeoxyuridine as an Alternative to the Synthesis of Mixed Hybridization Probes for the Detection of Specific Gene Sequences
      Habener, J.F., Vo, C.D., Le, D.B., Gryan, G.P., Ercolani, L., Wang, A.H.-J.
      (1988) Proc Natl Acad Sci U S A 85: 1735
    • 5-Fluoro-2'-Deoxyuridine Incorporation in L1210 DNA
      Kufe, D.W., Major, P.P., Egan, E.M., Loh, E.
      (1981) J Biol Chem 256: 8885

    Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*CP*GP*(UFP)P*G)-3')A, B6N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    C [auth A]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.50 Å
    • R-Value Observed: 0.172 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 17.36α = 90
    b = 31.15β = 90
    c = 45.4γ = 90
    Software Package:
    Software NamePurpose
    NUCLSQrefinement

    Structure Validation

    View Full Validation Report




    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1990-10-15
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance