title: Electrospray ionization of nucleic acid aptamer/small molecule complexes for screening aptamer selectivity.
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.
authors.affiliation: Department of Chemistry and Biochemistry, The University of Texas at Austin, Austin TX 78712, USA.
authors.forename: Karin M
authors.initials: KM
authors.lastname: Keller
authors.forename: Megan M
authors.initials: MM
authors.lastname: Breeden
authors.forename: Junmei
authors.initials: J
authors.lastname: Zhang
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Ellington
authors.forename: Jennifer S
authors.initials: JS
authors.lastname: Brodbelt
mesh_terms: D000255:Adenosine Triphosphate / Q000031:analogs & derivatives / Q000737:chemistry; D052157:Aptamers, Nucleotide / Q000737:chemistry*; D001665:Binding Sites; D005486:Flavin Mononucleotide / Q000737:chemistry; D008024:Ligands; D009690:Nucleic Acid Conformation; D021241:Spectrometry, Mass, Electrospray Ionization / Q000379:methods*; D014031:Tobramycin / Q000031:analogs & derivatives / Q000737:chemistry
chemical_list: D052157:Aptamers, Nucleotide; D008024:Ligands; D005486:Flavin Mononucleotide; D000255:Adenosine Triphosphate; D014031:Tobramycin