Exploration of the influence of 5-iodo-2'-deoxyuridine incorporation on the structure of d[CACG(IDU)G].
The first antiviral nucleoside 5-iodo-2'-deoxyuridine (IDU) against herpes simplex virus type 1 and type 2 is a thymidine analogue, i.e. the C5 methyl group is replaced by an I atom. The structure of the self-complementary hexamer d[CACG(IDU)G] was determined by single-crystal X-ray diffraction techniques. The orthorhombic crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 18.16, b = 30.03, c = 41.99 A. Refinement in the resolution range 20-1.3 A converged with a final R1 = 0.167, including 43 water molecules and two cobalt hexammine complexes. The incorporation of a large I atom has only minor consequences for the overall structure as is noticed in the IDU.A base pairs, which are of the common Watson-Crick type. To contribute to the still puzzling mechanism of this historically important agent, details of base stacking, helical parameters, hydration etc. have been studied. A general scheme of cobalt hexammine-binding modes in Z-DNA is provided, revealing similar binding modes for the reported structure.
Schuerman
Geertrui
G
Biomoleculaire Architectuur, Departement Chemie, Katholieke Universiteit Leuven, Celestijnenlaan 200F, B-3001 Leuven (Heverlee), Belgium.
Van Hecke
Kristof
K
Van Meervelt
Luc
L
D003035:Cobalt / Q000737:chemistry; D043542:DNA, Z-Form / Q000737:chemistry*; D006801:Humans; D007065:Idoxuridine / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009705:Nucleosides / Q000737:chemistry*; D013937:Thymidine Kinase / Q000737:chemistry; D014961:X-Ray Diffraction
D043542:DNA, Z-Form; D009705:Nucleosides; C032300:hexaamminecobalt(II); D003035:Cobalt; D013937:Thymidine Kinase; D007065:Idoxuridine