A novel bis-phenanthridine triamine with pH controlled binding to nucleotides and nucleic acids

Abstract

The new bis-phenanthridine triamine (3) is characterised by three pK_a values: 3.65; 6.0 and >7.5. A significant difference in the protonation state of 3 at pH = 5 (four positive charges) and at pH = 7 (less than two positive charges) accounts for the strong dependence of 3–nucleotide binding constants on nucleotide charge under acidic conditions, whereas at neutral pH all 3–nucleotide complexes are of comparable stability. All experimental data point at intercalation as the dominant binding mode of 3 to polynucleotides. However, there is no indication of bis-intercalation of the two phenanthridine subunits in binding to double stranded polynucleotides, the respective complexes being most likely mono-intercalative. Thermal stabilisation of calf thymus DNA (ct-DNA) and poly A–poly U duplexes upon addition of 3 is significantly higher at pH = 5 than at neutral conditions. This is not the case with poly dA–poly dT, indicating that the specific secondary structure of the latter, most likely the shape of the minor groove, plays a key role in complex stability. At pH = 5 3 acts as a fluorimetric probe for poly G (emission quenching) as opposed to other ss-polynucleotides (emission increase), while at neutral conditions this specificity is lost. One order of magnitude higher cytotoxicity of 3 compared to its “monomer” 4 can be accounted for by cooperative action of two phenanthridinium units and the charged triamine linker. The results presented here are of interest to the development of e.g. sequence-selective cytostatic drugs, and in particular for the possibility to control the drug activity properties over binding to DNA and/or RNA by variation of the pH of its surrounding.