Binding of dansylamide† derivatives to nucleotides and nucleic acids1

Abstract

Dansylamide† has been modified by the introduction of several side chains into the sulfonamide substituent. Compounds with no, or with only one positive charge at the side chains were found not to be useful for association studies with nucleotides or nucleic acids. Relatively high binding constants with moderate base selectivities have been observed with a ligand obtained from dansyl chloride and N,N′-bis(3-aminopropyl)piperazine, which contains two dansyl units and two permanently charged peralkylammonium centers. Interactions of this ligand with double-stranded nucleic acids show a biphasic binding, the first at base pair concentrations below 10^–7 M being only detectable by a decrease of fluorescence intensity. The second phase is characterized by increased fluorescence and by wavelength changes similar to effects observed in lipophilic solvents and by affinities of up to 5 × 10⁵ M. At higher concentrations bathochromic shifts and extinction changes in UV spectra of the dye suggest an intercalation mechanism, in line with preliminary circular dichroism studies.