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A G-rich sequence within the c-kit oncogene promoter forms a parallel G-quadruplex having asymmetric G-tetrad dynamics
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 200 micro-M DNA; 10mM potassium phosphate; 93% H2O/7% D2O 93% H2O/7% D2O 10 7.0 ambient 298 2 2D 1H-1H TOCSY 200 micro-M DNA; 10mM potassium phosphate; 93% H2O/7% D2O 93% H2O/7% D2O 10 7.0 ambient 298 3 2D DQF-COSY 200 micro-M DNA; 10mM potassium phosphate; 93% H2O/7% D2O 93% H2O/7% D2O 10 7.0 ambient 298
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 700
NMR Refinement Method Details Software simulated annealing, molecular dynamics Explicit water refinement including potassium ions within the G-tetrads. Sparky
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 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 chemical shift assignment Sparky Goddard 2 processing NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 3 structure solution Amber Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm 4 refinement Amber Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollm