Electrospray ionization mass spectrometry (ESI-MS) provides a sensitive method for the characterization of low-affinity (similar to mM) complexes between nucleic acids and small molecules. Such complexes can be generated in solution and moved into the gas phase for detection using MS by reducing the energy imparted during the desolvation process. The affinity and binding stoichiometry of ligands can be determined directly from the observed masses and abundances of the complexes. These benefits are demonstrated for complexes between a 27-mer RNA model of the 16S rRNA, 2-deoxystreptamine (2-DOS), and a series of small organic ligands. We observe two types of 2-DOS-RNA complexes that undergo collisionally activated dissociation in a quadrupole ion trap mass spectrometer at different energies. Molecular modeling results art: consistent with this observation. When multiple compounds are mixed with the RNA, the mode of binding can be determined from the abundances of the respective ternary complexes and from the activation energies required to effect gas-phase dissociation in the capillary-skimmer interface region of the instrument. ESI-MS should have considerable utility in studies of macromolecule-ligand complexes where the receptor has multiple binding sites for the ligand.