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Structure of anti-prion RNA aptamer
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 1.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS 95% H2O/5% D2O 10 mM 6.2 1 atm 278 Bruker AVANCE III 950 2 2D JR-HMBC 1.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS 95% H2O/5% D2O 10 mM 6.2 1 atm 288 Bruker AVANCE III 600 3 2D 1H-1H NOESY 1.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS 100% D2O 10 mM 6.2 1 atm 288 Bruker AVANCE III 600 4 2D DQF-COSY 1.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS 100% D2O 10 mM 6.2 1 atm 288 Bruker AVANCE III 600 5 2D 1H-1H TOCSY 1.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS 100% D2O 10 mM 6.2 1 atm 288 Bruker AVANCE III 600 6 2D 1H-13C HSQC 1.0 mM RNA (25-MER), 10 mM potassium phosphate, 10 mM potassium chloride, 10 uM DSS 100% D2O 10 mM 6.2 1 atm 288 Bruker AVANCE III 600
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE III 600 2 Bruker AVANCE III 950
NMR Refinement Method Details Software molecular dynamics Amber
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 100 Conformers Submitted Total Number 10 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 X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 3 chemical shift assignment Sparky Goddard 4 peak picking Sparky Goddard