title: Investigating the malleability of RNA aptamers.
abstract: Aptamers are short, single-stranded nucleic acids with structures that frequently change upon ligand binding and are sensitive to the ionic environment. To achieve facile application of aptamers in controlling cellular activities, a better understanding is needed of aptamer ligand binding parameters, structures, intramolecular mobilities and how these structures adapt to different ionic environments with consequent effects on their ligand binding characteristics. Here we discuss the integration of biochemical analysis with NMR spectroscopy and computational modeling to explore the relation between ligand binding and structural malleability of some well-studied aptamers. Several methods for determining aptamer binding affinity and specificity are discussed, including isothermal titration calorimetry, steady state fluorescence of 2-aminopurine substituted aptamers, and dye displacement assays. Also considered are aspects of molecular dynamics simulations specific to aptamers including adding ions and simulating aptamer structure in the absence of ligand when NMR spectroscopy or X-ray crystallography structures of the unoccupied aptamer are not available. We focus specifically on RNA aptamers that bind small molecule ligands as would be applied in sensors or integrated into riboswitches such as to measure the products of metabolic activity.
authors.affiliation: Ames Laboratory, US DOE, Ames, IA, USA; Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Ames, IA, USA.
authors.forename: Muslum
authors.initials: M
authors.lastname: Ilgu
authors.forename: Tianjiao
authors.initials: T
authors.lastname: Wang
authors.forename: Monica H
authors.initials: MH
authors.lastname: Lamm
authors.forename: Marit
authors.initials: M
authors.lastname: Nilsen-Hamilton
mesh_terms: D015075:2-Aminopurine / Q000737:chemistry; D052157:Aptamers, Nucleotide / Q000737:chemistry*; D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D002021:Buffers; D002151:Calorimetry; D018360:Crystallography, X-Ray; D005456:Fluorescent Dyes / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D059370:RNA Folding; D013050:Spectrometry, Fluorescence; D013816:Thermodynamics
chemical_list: D052157:Aptamers, Nucleotide; D002021:Buffers; D005456:Fluorescent Dyes; D015075:2-Aminopurine
keywords: Affinity measurement; Aptamer; Ionic environment effects; Molecular dynamics simulation