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G-rich VEGF aptamer with LNA modifications
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 0.5 mM DNA(25-MER)-7, 10 mM potassium phosphate-8, 90 mM potassium chloride-9 100% D2O 100 7.0 ambient 298 2 2D DQF-COSY 0.5 mM DNA(25-MER)-7, 10 mM potassium phosphate-8, 90 mM potassium chloride-9 100% D2O 100 7.0 ambient 298 3 2D 1H-1H TOCSY 0.5 mM DNA(25-MER)-7, 10 mM potassium phosphate-8, 90 mM potassium chloride-9 100% D2O 100 7.0 ambient 298 4 2D 1H-1H NOESY 0.5 mM DNA(25-MER)-1, 10 mM potassium phosphate-2, 90 mM potassium chloride-3 90% H2O/10% D2O 100 7.0 ambient 298 5 2D 1H-1H NOESY 0.5 mM DNA(25-MER)-4, 10 mM potassium phosphate-5, 40 mM potassium chloride-6 90% H2O/10% D2O 50 7.0 ambient 298 6 2D 1H-1H NOESY 0.5 mM DNA(25-MER)-1, 10 mM potassium phosphate-2, 90 mM potassium chloride-3 90% H2O/10% D2O 100 7.0 ambient 273
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Varian VNMRS 600 2 Varian VNMRS 800
NMR Refinement Method Details Software simulated annealing Amber
NMR Ensemble Information Conformer Selection Criteria structures with the least restraint violations Conformers Calculated Total Number 100 Conformers Submitted Total Number 10 Representative Model 1 (fewest violations)
Computation: NMR Software # Classification Version Software Name Author 1 structure solution Amber 11 Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman 2 refinement Amber 11 Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman 3 data analysis Amber 11 Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman 4 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 5 chemical shift assignment Sparky Goddard 6 peak picking Sparky Goddard 7 collection VnmrJ Agilent Technologies