NDLI: Optimization of Experimental Parameters to Explore Small-Ligand/Aptamer Interactions through Use of $^{1}H NMR$ Spectroscopy and Molecular Modeling

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Optimization of Experimental Parameters to Explore Small-Ligand/Aptamer Interactions through Use of $^{1}H NMR$ Spectroscopy and Molecular Modeling

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Optimization of Experimental Parameters to Explore Small-Ligand/Aptamer Interactions through Use of $^{1}H NMR$ Spectroscopy and Molecular Modeling

Content Provider	World Health Organization (WHO)-Global Index Medicus
Author	Souard, Florence Vanhaverbeke, Cécile Noël, Vincent Fave, Claire Fiore, Emmanuelle Perrier, Sandrine Garcia, Julian Peyrin, Eric
Description	Author Affiliation: Souard F ( DPM, Université Grenoble Alpes, Grenoble, 38000 (France). florence.souard@ujf-grenoble.fr.); Perrier S ( DPM, CNRS, Grenoble, 38000 (France). florence.souard@ujf-grenoble.fr.); Noël V ( DPM, Université Grenoble Alpes, Grenoble, 38000 (France).); Fave C ( DPM, CNRS, Grenoble, 38000 (France).); Fiore E ( ITODYS, UMR 7086 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, 75205 (France).); Peyrin E ( Laboratoire d'Electrochimie Moléculaire, UMR 7591 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Paris, 75205 (France).); Garcia J ( DPM, Université Grenoble Alpes, Grenoble, 38000 (France).); Vanhaverbeke C ( DPM, CNRS, Grenoble, 38000 (France).)
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.
ISSN	09476539
e-ISSN	15213765
Journal	Chemistry - A European Journal
Issue Number	44
Volume Number	21
Language	English
Publisher	Wiley-VCH;ChemPubSoc Europe
Publisher Date	2015-10-26
Publisher Place	Germany
Access Restriction	Open
Subject Keyword	Adenosine Monophosphate Chemistry Aptamers, Nucleotide Tyrosine Analogs & Derivatives Metabolism Binding Sites Ligands Magnetic Resonance Spectroscopy Molecular Dynamics Simulation Nucleic Acid Conformation Research Support, Non-U.S. Gov't
Content Type	Text
Resource Type	Article
Subject	Organic Chemistry Catalysis

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