An approach to therapeutic agents through selective targeting of destabilised nucleic acid duplex sequences

• Published in: Dalton transactions : an international journal of inorganic chemistry 2012-06, Vol.41 (21), p.6528-6535
• Main Authors: Li, Fangfei, Weber, Daniel K, Morgan, Joy L, Collins, J. Grant, Keene, F. Richard
• Format: Article
• Language: English
• Subjects: Adenines; Anti-Bacterial Agents - chemistry; Anti-Bacterial Agents - metabolism; Anti-Bacterial Agents - pharmacology; Bacteria; Base Sequence; Binding; Binding Sites; Bulging; Chromosomes, Bacterial - drug effects; Chromosomes, Bacterial - metabolism; Deoxyribonucleic acid; Displacement; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; DNA, Bacterial - metabolism; Models, Molecular; Nucleic Acid Conformation; Oligonucleotides; Oligonucleotides - chemistry; Oligonucleotides - genetics; Oligonucleotides - metabolism; Organometallic Compounds - chemistry; Organometallic Compounds - metabolism; Organometallic Compounds - pharmacology; Ruthenium - chemistry; Segments; Staphylococcus; Staphylococcus aureus - drug effects; Substrate Specificity
• ISSN: 1477-9226; 1477-9234
• DOI: 10.1039/c2dt12146h

The binding of ΔΔ/ΛΛ-[{Ru(phen) 2 } 2 (μ-bb n )] 4+ {where phen = 1,10-phenanthroline, bb n = 1, n -bis[4(4′-methyl-2,2′-bipyridyl)]-alkane (ΔΔ/ΛΛ-Rubb n )} to the non-self complementary oligonucleotide 5′-d(CGCG A TAAGCCGC·5′-GCGGC A TTACGCG) (3-DB) has been examined using a 4′,6-diamidino-2-phenylindole dihydrochloride (DAPI) displacement assay. The 3-DB oligonucleotide contains two single adenine bulge nucleotides that are separated by three base pairs. 1 H NMR spectroscopy data demonstrated that the adenine bases are intra-helical and that the segment containing the two bulge nucleotides and the three A·T base pairs between the bulges forms a destabilised segment within the stable duplex oligonucleotide. The DAPI displacement assay demonstrated that ΔΔ-Rubb 7 -bound 3-DB with higher affinity than the other members of the ΔΔ/ΛΛ-Rubb n series. Molecular models suggested that the seven-carbon chain length in ΔΔ-Rubb 7 was ideal to span the distance between the two bulge sites. The binding of ΔΔ-Rubb 7 to 3-DB was also studied by 1 H NMR spectroscopy and molecular modelling. The selective changes in chemical shifts for the resonances from 3-DB upon addition of ΔΔ-Rubb 7 suggested that the metal complex specifically bound at the destabilised segment between A 5 and A 19 . Observation in NOESY spectra of NOE cross peaks between 3-DB and ΔΔ-Rubb 7 confirmed that one of the ruthenium centres bound at the A 5 bulge site, with the other metal centre positioned at the A 19 bulge. In addition, ΔΔ-Rubb 7 was found to bind chromosomal DNA extracted from a suspension of Staphylococcus aureus that had been incubated with the ruthenium( ii ) complex. As inert dinuclear ruthenium( ii ) complexes are capable of being transported into a bacterial cell and bind chromosomal DNA, it is possible that they could be developed into anti-microbial agents that specifically target destabilised segments of DNA that are recognised by essential DNA-binding proteins. The dinuclear ruthenium complex ΔΔ-Rubb 7 selectively binds a destabilised segment of DNA formed by the insertion of two single adenine bulge residues (shown in purple) into the duplex.