The interactions of pyrenylmethyl tributylphosphonium bromide with single strand polynucleotides

The binding of the water soluble derivative of pyrene, pyrenylmethyl tri-n-butylphosphonium bromide (PMTP), to single strand polynucleotides has been characterised by changes in the absorption spectra, fluorescence spectra, the fluorescence lifetime and the time-resolved fluorescence anisotropy of PMTP. For polyguanylic acid at low ionic strength, there are two modes of binding; external ionic binding and intercalation between the bases. The former results in PMTP excimer formation and the latter involves a charge-transfer complex between PMTP and guanine bases. Polyadenylic acid and polyinosinic acid show only external binding and poly[C] exhibits an interaction which is a combination of external binding and partial intercalation. Single strand DNA binds PMTP by intercalation and external binding at low ionic strength. In the presence of 0.2 M sodium chloride, only binding by intercalation between the bases occurs for poly[G]. Single strand DNA bound PMPT by partial intercalation, as well as full intercalation between the bases, but polyadenylic acid, polycytidylic acid and polyinosinic acid showed no significant binding in the presence of 0.2 M sodium chloride. The differences in the binding of PMTP are attributed to variations in the rigidity and form the structures of single strand polynucleotides adopt in solution. A full analysis of the binding isotherms has been made using methods based on Scatchard plots and the McGhee and von Hippel approach, which are critically compared.