title: Crystal structure of a pentamidine-oligonucleotide complex: implications for DNA-binding properties.
abstract: The crystal structure of the complex formed between the dodecanucleotide d(CGCGAATTCGCG)2 and the drug pentamidine, which is active against the Pneumocystis carinii pathogen in AIDS patients, has been determined to a resolution of 2.1 A and an R-factor of 19.4%. Analysis of the structure has shown the drug to be bound in the 5'-AATT minor groove region of the duplex, with the amidinium groups H-bonded to adenine N3 atoms in an interstrand manner. The drug molecule adopts an extended conformation, and the immediate binding site spans four base pairs. Structural details of the drug-DNA interactions are discussed, and comparison is made with the dodecamer complex of the structurally similar berenil ligand.
authors.affiliation: Cancer Research Campaign Biomolecular Structure Unit, Institute of Cancer Research, Sutton, Surrey, U.K.
authors.forename: K J
authors.initials: KJ
authors.lastname: Edwards
authors.forename: T C
authors.initials: TC
authors.lastname: Jenkins
authors.forename: S
authors.initials: S
authors.lastname: Neidle
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000378:metabolism*; D008969:Molecular Sequence Data; D009841:Oligonucleotides / Q000737:chemistry* / Q000378:metabolism; D010419:Pentamidine / Q000737:chemistry* / Q000378:metabolism; D014961:X-Ray Diffraction
chemical_list: D009841:Oligonucleotides; D010419:Pentamidine; D004247:DNA