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

Fangfei Li, Daniel K. Weber, Joy L. Morgan, J. Grant Collins*, F. Richard Keene

*Corresponding author for this work

Research output: Contribution to journalJournal articlepeer-review

11 Citations (Scopus)


The binding of ΔΔ/ΛΛ-[{Ru(phen)2}2(μ-bbn)]4+ {where phen = 1,10-phenanthroline, bbn = 1,n-bis[4(4′-methyl-2,2′-bipyridyl)]-alkane (ΔΔ/ΛΛ-Rubbn)} to the non-self complementary oligonucleotide 5′-d(CGCGATAAGCCGC·5′-GCGGCATTACGCG) (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. 1H 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-Rubb7-bound 3-DB with higher affinity than the other members of the ΔΔ/ΛΛ-Rubbn series. Molecular models suggested that the seven-carbon chain length in ΔΔ-Rubb7 was ideal to span the distance between the two bulge sites. The binding of ΔΔ-Rubb7 to 3-DB was also studied by 1H NMR spectroscopy and molecular modelling. The selective changes in chemical shifts for the resonances from 3-DB upon addition of ΔΔ-Rubb7 suggested that the metal complex specifically bound at the destabilised segment between A5 and A19. Observation in NOESY spectra of NOE cross peaks between 3-DB and ΔΔ-Rubb7 confirmed that one of the ruthenium centres bound at the A5 bulge site, with the other metal centre positioned at the A19 bulge. In addition, ΔΔ-Rubb7 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.
Original languageEnglish
Pages (from-to)6528-6535
Number of pages8
JournalDalton Transactions
Issue number21
Publication statusPublished - Feb 2012


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