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Optimization of Experimental Parameters to Explore Small‐Ligand/Aptamer Interactions through Use of 1 H NMR Spectroscopy and Molecular Modeling
Author(s) -
Souard Florence,
Perrier Sandrine,
Noël Vincent,
Fave Claire,
Fiore Emmanuelle,
Peyrin Eric,
Garcia Julian,
Vanhaverbeke Cécile
Publication year - 2015
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.201501527
Subject(s) - aptamer , biomolecule , ligand (biochemistry) , small molecule , chemistry , oligonucleotide , ionic strength , molecule , nuclear magnetic resonance spectroscopy , flexibility (engineering) , computational chemistry , chemical physics , combinatorial chemistry , dna , stereochemistry , biochemistry , aqueous solution , organic chemistry , biology , genetics , receptor , statistics , mathematics
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.