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Issue 13, 2013
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The size of the aryl linker between two polyaza-cyclophane moieties controls the binding selectivity to ds-RNA vs. ds-DNA

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Abstract

Aryl-linked (pyridine- vs. phenanthroline-) bis-polyaza pyridinophane scorpiands PYPOD and PHENPOD strongly bind to the double stranded DNA and RNA, whereby very intriguing RNA over DNA selectivity is finely tuned by aryl-linker length and aromatic surface. Moreover, PYPOD and PHENPOD dimer formation at high compound/polynucleotide ratios is highly sensitive to the fine interplay between the steric and binding properties of compound-dimers and the DNA minor groove/RNA major groove. That is demonstrated by significantly different induced CD spectra, which allow spectroscopic differentiation between various DNA/RNA secondary structures. A significantly higher (micromolar) antiproliferative effect of PYPOD and PHENPOD on human cell lines with respect to previously reported pyridine-based tripodal aliphatic polyamines is attributed to masked positive charges and increased hydrophobicity of novel compounds, resulting in more efficient membrane permeation and cellular uptake.

Graphical abstract: The size of the aryl linker between two polyaza-cyclophane moieties controls the binding selectivity to ds-RNA vs. ds-DNA

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Supplementary files

Article information


Submitted
29 Aug 2012
Accepted
21 Jan 2013
First published
21 Jan 2013

Org. Biomol. Chem., 2013,11, 2154-2161
Article type
Paper

The size of the aryl linker between two polyaza-cyclophane moieties controls the binding selectivity to ds-RNA vs. ds-DNA

J. González-García, L. Uzelac, M. Kralj, J. M. Llinares, E. García-España and I. Piantanida, Org. Biomol. Chem., 2013, 11, 2154
DOI: 10.1039/C3OB00032J

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