Detection of noncovalent interactions of hairpin oligonucleotide with stilbazolium ligands by MALDI TOF mass spectrometry

Matrix-assisted laser desorption ionization time-of-flight (MALDI TOF) mass spectroscopic analysis was carried out to study the noncovalent complexes of aryl stilbazolium ligands with short deoxyoligonucleotide, 5'CGCTTTGCG-3' (sT(3)). The method enables to assess rapidly stoichiometries of complexes. The number of peaks associated with complexes and their relative abundances depended on the structure of aryl moiety of the ligand and reflected DNA-binding mode and affinity of the ligand. The most potent ligands, 9-[2-(N-methylpyridinium-4-yl) vinyl] anthracene and 2- [2-(N-methylpyridinium-4-yl)vinyl] naphthalene formed 1:1, 1:2 and 1:3 complexes with both hairpin and bulged duplex structures of sT(3) oligonucleotide. (C) 2003 Elsevier B.V. All rights reserved.