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RKEC1 DNA aptamer bound to dopamine
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 2 mM RKEC1 DNA (27-MER), 2.25 mM L-DOPAMINE, 20 mM sodium phosphate, 140 mM sodium chloride, 2 mM magnesium chloride 90% H2O/10% D2O 162 mM 7.4 1 atm 278 Bruker AVANCE NEO 800 2 2D 1H-1H NOESY 2 mM RKEC1 DNA (27-MER), 2.25 mM L-DOPAMINE, 20 mM sodium phosphate, 140 mM sodium chloride, 2 mM magnesium chloride 100% D2O 162 mM 7.4 1 atm 298 Bruker AVANCE NEO 800 3 2D 1H-1H TOCSY 2 mM RKEC1 DNA (27-MER), 2.25 mM L-DOPAMINE, 20 mM sodium phosphate, 140 mM sodium chloride, 2 mM magnesium chloride 100% D2O 162 mM 7.4 1 atm 298 Bruker AVANCE NEO 800 4 2D DQF-COSY 2 mM RKEC1 DNA (27-MER), 2.25 mM L-DOPAMINE, 20 mM sodium phosphate, 140 mM sodium chloride, 2 mM magnesium chloride 100% D2O 162 mM 7.4 1 atm 298 Bruker AVANCE NEO 800
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE NEO 800
NMR Refinement Method Details Software simulated annealing Note that the deposited ambig.tbl, unambig.tbl and dihedrals.tbl were used with ARIA/CNS NMRPipe simulated annealing note that H5' and H5'' were freely swapped during this step CNS molecular dynamics Note that the final refinement with AMBER, and therefore the deposited ensemble, only used the unambig.tbl restraints Amber
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 100 Conformers Submitted Total Number 15 Representative Model 1 (closest to the average)
Computation: NMR Software # Classification Version Software Name Author 1 chemical shift assignment NMRFAM-SPARKY 1.470 Lee, Tonelli and Markley 2 structure calculation CNS 1.2 Brunger, Adams, Clore, Gros, Nilges and Read 3 refinement Amber 24 Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman 4 structure calculation ARIA 2.3 Linge, O'Donoghue and Nilges 5 peak picking NMRFAM-SPARKY 1.470 Lee, Tonelli and Markley 6 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax