title: Optimization of Experimental Parameters to Explore Small-Ligand/Aptamer Interactions through Use of (1) H NMR Spectroscopy and Molecular Modeling.
abstract: Aptamers constitute an emerging class of molecules designed and selected to recognize any given target that ranges from small compounds to large biomolecules, and even cells. However, the underlying physicochemical principles that govern the ligand-binding process still have to be clarified. A major issue when dealing with short oligonucleotides is their intrinsic flexibility that renders their active conformation highly sensitive to experimental conditions. To overcome this problem and determine the best experimental parameters, an approach based on the design-of-experiments methodology has been developed. Here, the focus is on DNA aptamers that possess high specificity and affinity for small molecules, L-tyrosinamide, and adenosine monophosphate. Factors such as buffer, pH value, ionic strength, Mg(2+) -ion concentration, and ligand/aptamer ratio have been considered to find the optimal experimental conditions. It was then possible to gain new insight into the conformational features of the two ligands by using ligand-observed NMR spectroscopic techniques and molecular mechanics.
authors.affiliation: DPM, Université Grenoble Alpes, Grenoble, 38000 (France). florence.souard@ujf-grenoble.fr.|DPM, CNRS, Grenoble, 38000 (France). florence.souard@ujf-grenoble.fr.
authors.forename: Florence
authors.initials: F
authors.lastname: Souard
authors.affiliation: DPM, Université Grenoble Alpes, Grenoble, 38000 (France).|DPM, CNRS, Grenoble, 38000 (France).
authors.forename: Sandrine
authors.initials: S
authors.lastname: Perrier
authors.affiliation: ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, 75205 (France).
authors.forename: Vincent
authors.initials: V
authors.lastname: Noël
authors.affiliation: Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, 75205 (France).
authors.forename: Claire
authors.initials: C
authors.lastname: Fave
authors.affiliation: DPM, Université Grenoble Alpes, Grenoble, 38000 (France).|DPM, CNRS, Grenoble, 38000 (France).
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Fiore
authors.affiliation: DPM, Université Grenoble Alpes, Grenoble, 38000 (France).|DPM, CNRS, Grenoble, 38000 (France).
authors.forename: Eric
authors.initials: E
authors.lastname: Peyrin
authors.affiliation: DCM, Université Grenoble Alpes, Grenoble, 38000 (France).|DCM, CNRS, Grenoble, 38000 (France).
authors.forename: Julian
authors.initials: J
authors.lastname: Garcia
authors.affiliation: DPM, Université Grenoble Alpes, Grenoble, 38000 (France). cecile.vanhaverbeke@ujf-grenoble.fr.|DPM, CNRS, Grenoble, 38000 (France). cecile.vanhaverbeke@ujf-grenoble.fr.
authors.forename: Cécile
authors.initials: C
authors.lastname: Vanhaverbeke
mesh_terms: D000249:Adenosine Monophosphate / Q000737:chemistry*; D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000378:metabolism; D001665:Binding Sites; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy; D056004:Molecular Dynamics Simulation; D009690:Nucleic Acid Conformation; D014443:Tyrosine / Q000031:analogs & derivatives* / Q000737:chemistry
chemical_list: D052157:Aptamers, Nucleotide; D008024:Ligands; C036387:tyrosinamide; D000249:Adenosine Monophosphate; D014443:Tyrosine
keywords: NMR spectroscopy; TR-NOESY; aptamers; design of experiments; structure elucidation