Interactions of novel phenanthridinium-nucleobase conjugates with complementary and non-complementary nucleotides in aqueous media

A series of novel phenanthridine-nucleobase conjugates were prepared and studied by spectroscopic methods. An analysis of H-1 NMR, UV-Vis and fluorescence spectra in aqueous media revealed intramolecular aromatic stacking interactions between the phenanthridinium unit and the nucleobase, due to the conformation of the molecules. Fluorimetric titrations showed that phenanthridinium-nucleobase conjugates 8, 10 and reference phenanthridine compound 12 form 1:1 non-covalent complexes with nucleotides in water with binding constants ranging from 10 to 100 mol(-1) dm(3). Interestingly, compounds 9 and 11 form intercalative-type 1:1 complexes with the nucleotide aromatic unit inserted between phenanthridinium and covalently attached nucleobase, yielding binding constants of 10(3)-10(4) mol(-1) dm(3). Aromatic pi...pi stacking interactions were found to be dominant in complexes with nucleotides of all compounds studied. Copyright (C) 2002 John Wiley Sons, Ltd.