PMID: 1643044

Authors:

Edwards KJ, Jenkins TC, Neidle S

Title:

Crystal structure of a pentamidine-oligonucleotide complex: implications for DNA-binding properties.

Journal:

Biochemistry. 1992 Aug 11;31(31):7104-9.

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.