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| - Characterization of Low-Affinity Complexes between RNA and SmallMolecules Using Electrospray Ionization Mass Spectrometry
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| - Electrospray ionization mass spectrometry (ESI-MS) provides a sensitive method for the characterization of low-affinity (∼mM) complexes between nucleic acids and small molecules. Such complexes can begenerated in solution and moved into the gas phase for detection using MS by reducing the energy impartedduring the desolvation process. The affinity and binding stoichiometry of ligands can be determined directlyfrom the observed masses and abundances of the complexes. These benefits are demonstrated for complexesbetween a 27-mer RNA model of the 16S rRNA, 2-deoxystreptamine (2-DOS), and a series of small organicligands. We observe two types of 2-DOS−RNA complexes that undergo collisionally activated dissociation ina quadrupole ion trap mass spectrometer at different energies. Molecular modeling results are consistent withthis observation. When multiple compounds are mixed with the RNA, the mode of binding can be determinedfrom the abundances of the respective ternary complexes and from the activation energies required to effectgas-phase dissociation in the capillary−skimmer interface region of the instrument. ESI-MS should haveconsiderable utility in studies of macromolecule−ligand complexes where the receptor has multiple bindingsites for the ligand.
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