Structure determination of an intercalating ruthenium dipyridophenazine complex which kinks DNA by semiintercalation of a tetraazaphenanthrene ligand

• Published in: Proceedings of the National Academy of Sciences - PNAS 2011-10, Vol.108 (43), p.17610-17614
• Main Authors: Hall, James P, O’Sullivan, Kyra, Naseer, Abeer, Smith, Jayden A, Kelly, John M, Cardin, Christine J
• Format: Article
• Language: English
• Subjects: Aza Compounds - chemistry; Barium; Biological Sciences; Cations; crosslinking; Cruciform DNA; Crystal structure; Crystallography; Deoxyribonucleic acid; DNA; DNA - chemistry; Intercalating Agents - chemistry; Intercalation; Ions; Ligands; Models, Molecular; Molecules; Nucleic Acid Conformation; Nucleic acids; Oligonucleotides; Oligonucleotides - genetics; Organometallic Compounds - chemistry; Phenanthrenes - chemistry; Physical Sciences; Ruthenium; Symmetry
• ISSN: 0027-8424; 1091-6490
• DOI: 10.1073/pnas.1108685108

We describe a crystal structure, at atomic resolution (1.1 Å, 100 K), of a ruthenium polypyridyl complex bound to duplex DNA, in which one ligand acts as a wedge in the minor groove, resulting in the 51° kinking of the double helix. The complex cation Λ-[Ru(1,4,5,8-tetraazaphenanthrene)2(dipyridophenazine)]2+ crystallizes in a 1:1 ratio with the oligonucleotide d(TCGGCGCCGA) in the presence of barium ions. Each complex binds to one duplex by intercalation of the dipyridophenazine ligand and also by semiintercalation of one of the orthogonal tetraazaphenanthrene ligands into a second symmetrically equivalent duplex. The result is noncovalent cross-linking and marked kinking of DNA.