The alkaloid berberine presents many biological activities related to its potential to bind DNA structures, such as duplex or G-quadruplex. Recently, it has been proposed that berberine may interact with i-motif structures formed from the folding of cytosine-rich sequences. In the present work, the interaction of this alkaloid with the i-motif formed by the human telomere cytosine-rich sequence, as well as with several positive and negative controls, has been studied. Molecular fluorescence and circular dichroism spectroscopies, as well as nuclear magnetic resonance spectrometry and competitive dialysis, have been used with this purpose. The results shown here reveal that the interaction of berberine with this i-motif is weak, mostly electrostatics in nature and takes place with bases not involved in C·C+ base pairs. Moreover, this ligand is not selective for i-motif structures, as binds equally to both, folded structure, and unfolded strand, without producing any stabilization of the i-motif. As a conclusion, the development of analytical methods based on the interaction of fluorescent ligands, such as berberine, with i-motif structures should consider the thermodynamic aspects related with the interaction, as well as the selectivity of the proposed ligands with different DNA structures, including unfolded strands.

Department of Chemistry Faculty of Science Masaryk University Kamenice 5 62500 Brno Czech Republic

Department of Food Environmental and Nutritional Sciences Section of Chemical and Biomolecular Sciences University of Milan Via Celoria 2 20133 Milan Italy

Dept of Chemical Engineering and Analytical Chemistry University of Barcelona Marti i Franquès 1 E 08028 Barcelona Spain

Institute for Advanced Chemistry of Catalonia CIBER BBN Jordi Girona 18 26 E 08034 Barcelona Spain

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Alkaloid Escholidine and Its Interaction with DNA Structures