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Solution structure of the r(UGGUGGU)4 RNA quadruplex
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 2.0 mM pUGGUGGU, 10 mM phosphate buffer, 50 mM potassium chloride 100% D2O 0.06 M 6.8 1 atm 298 Bruker AVANCE III 700 2 2D 1H-1H NOESY 2.0 mM pUGGUGGU, 10 mM phosphate buffer, 50 mM potassium chloride 100% D2O 0.06 M 6.8 1 bar 333 Bruker AVANCE III 700 3 2D 1H-1H NOESY 2.0 mM pUGGUGGU, 10 mM phosphate buffer, 0.05 mM potassium chloride 90% H2O/10% D2O 0.06 M 6.8 1 atm 278 Bruker AVANCE III 700 4 2D 1H-1H TOCSY 2.0 mM pUGGUGGU, 10 mM phosphate buffer, 0.05 mM potassium chloride 90% H2O/10% D2O 0.06 M 6.8 1 atm 278 Bruker AVANCE III 700 5 2D 1H-13C HSQC 2.0 mM pUGGUGGU, 10 mM phosphate buffer, 50 mM potassium chloride 100% D2O 0.06 M 6.8 1 bar 333 Bruker AVANCE III 700 6 2D 1H-31P COSY 2.0 mM pUGGUGGU, 10 mM phosphate buffer, 50 mM potassium chloride 100% D2O 0.06 M 6.8 1 bar 333 Bruker AVANCE III 700
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE III 700
NMR Refinement Method Details Software molecular dynamics Amber simulated annealing Xplor-NIH
NMR Ensemble Information Conformer Selection Criteria target function Conformers Calculated Total Number 400 Conformers Submitted Total Number 15 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 refinement Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman 2 structure calculation Xplor-NIH Schwieters, Kuszewski, Tjandra and Clore 3 chemical shift assignment Sparky Goddard 4 peak picking Sparky Goddard