Binding properties of a phosphonate clip towards nucleic acid building blocks

Water-soluble clips are possible molecules to study the weak, non-covalent interactions, responsible for many biological processes. The complexation behaviour of naphthalene clips, substituted with phosphonate or phosphate groups, has been studied by time-resolved laser-induced fluorescence spectroscopy with ultrafast pulses (fs-TRLFS). As guest molecules we used nucleic bases, nucleosides and nucleotides. The determined association constants for the 1:1 complexes range from log Ka = 3.9 – 4.2 and are around one order of magnitude higher than published in literature. The measured spectra assumes the appearance of excited state species or dimerization of the clip.