Nucleic Acids Research, 2003, Vol. 31, No. 19 5732-5740
© 2003 Oxford University Press
The DNA and RNA specificity of eilatin Ru(II) complexes as compared to eilatin and ethidium bromide
Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0358, USA and 1 School of Chemistry, Tel Aviv University, Ramat Aviv, 69978, Israel
*To whom correspondence should be addressed. Tel: +858 534 6401; Fax: +858 534 5383; Email: ytor{at}ucsd.edu
Present address:
Nathan W. Luedtke, Department of Chemistry and Biochemistry, Yale University, New Haven CT, 06520-8107, USA
Eilatin-containing ruthenium complexes bind to a broad range of different nucleic acids including: calf thymus (CT) DNA, tRNAPhe, polymeric RNAs and DNAs, and viral RNAs including the HIV-1 RRE and TAR. The nucleic acid specificity of 
- and 
-[Ru(bpy)2eilatin]2+ have been compared to that of the ‘free’ eilatin ligand, and to the classic intercalating agent ethidium bromide. Interestingly, all four compounds appear to bind to nucleic acids by intercalation, but the trends in nucleic acid binding specificity are highly diverse. Unlike ethidium bromide, both eilatin and the eilatin-containing coordination complexes bind to certain single-stranded RNAs with high affinity (Kd 
1 µM). Eilatin itself is selective for electron-poor polymeric purines, while the eilatin-coordination complexes exhibit preference for the polypyrimidine r(U). These results show how the binding specificity of an intercalating ligand can change upon its incorporation into an octahedral metal complex.
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