Electrospray ionization of nucleic acid aptamer/small molecule complexes for screening aptamer selectivity |
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Authors: | Keller Karin M Breeden Megan M Zhang Junmei Ellington Andrew D Brodbelt Jennifer S |
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Institution: | Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin TX 78712, USA. |
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Abstract: | Molecular recognition of small molecule ligands by the nucleic acid aptamers for tobramycin, ATP, and FMN has been examined using electrospray ionization mass spectrometry (ESI-MS). Mass spectrometric data for binding stoichiometry and relative binding affinity correlated well with solution data for tobramycin aptamer complexes, in which aptamer/ligand interactions are mediated by hydrogen bonds. For the ATP and FMN aptamers, where ligand interactions involve both hydrogen bonding and significant pi-stacking, the relative binding affinities determined by MS did not fully correlate with results obtained from solution experiments. Some high-affinity aptamer/ligand complexes appeared to be destabilized in the gas phase by internal Coulombic repulsion. In CAD experiments, complexes with a greater number of intermolecular hydrogen bonds exhibited greater gas-phase stability even in cases when solution binding affinities were equivalent. These results indicate that in at least some cases, mass spectrometric data on aptamer/ligand binding affinities should be used in conjunction with complementary techniques to fully assess aptamer molecular recognition properties. |
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Keywords: | aptamer electrospray ionization molecular recognition nucleic acid |
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