Abstract: The non-covalent complexes of five bis-β-carbolines alkaloids with five different double-stranded oligodeoxynucleotides were investigated via electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry. These five antitumor compounds all showed DNA binding abilities. The binding affinities in the order of 2>3,4>5,1 were obtained, which mean that the length of the linkage chain between two β-carbolines has a remarkable effect on the formation of the non-covalent complexes. The competition binding experiments results were almost the same as that determined by relative ion abundances. The structure-activity relationships and sequence selectivity were discussed. The non-covalent bindings between the bis-β-carbolines 2, 4 and the nucleotide were then investigated by ESI-MS.

Key words: Bis-β-carbolines, DNA, Nucleotide, Non-covalent interaction, Electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry