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RNA G-quadruplex from the 5'-UTR of human tyrosine kinase 2 (TYK2)
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 0.5 mM RNA (5'-R(*CP*GP*GP*UP*AP*GP*CP*GP*GP*GP*UP*AP*UP*GP*GP*GP*UP*CP*CP*GP*GP*GP*U)-3'), 10 mM potassium phosphate, 10 mM potassium chloride 90% H2O/10% D2O 20 mM 7.0 1 atm 298 Bruker AVANCE NEO 600 2 2D 1H-1H NOESY 1.0 mM RNA (5'-R(*CP*GP*GP*UP*AP*GP*CP*GP*GP*GP*UP*AP*UP*GP*GP*GP*UP*CP*CP*GP*GP*GP*U)-3'), 10 mM potassium phosphate, 10 mM potassium chloride 100% D2O 20 mM 7.0 1 atm 298 Bruker AVANCE NEO 600 3 2D 1H-1H COSY 1.0 mM RNA (5'-R(*CP*GP*GP*UP*AP*GP*CP*GP*GP*GP*UP*AP*UP*GP*GP*GP*UP*CP*CP*GP*GP*GP*U)-3'), 10 mM potassium phosphate, 10 mM potassium chloride 100% D2O 20 mM 7.0 1 atm 298 Bruker AVANCE NEO 600 4 IPAP-edited HSQC 0.8 mM RNA (5'-R(*CP*GP*GP*UP*AP*GP*CP*GP*GP*GP*UP*AP*UP*GP*GP*GP*UP*CP*CP*GP*GP*GP*U)-3'), 10 mM potassium phosphate, 10 mM potassium chloride, 17 mg/mL Pf1 phage 90% H2O/10% D2O 20 mM 7.0 1 atm 298 Bruker AVANCE NEO 600
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE NEO 600
NMR Refinement Method Details Software simulated annealing Amber energy minimization 100 structures obtained from simulated annealing were subjected to energy minimization with applied restraints.
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 collection TopSpin Bruker Biospin 2 chemical shift assignment NMRFAM-SPARKY National Magnetic Resonance Facility at Madison 3 structure calculation Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman