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Structure and dynamics of RNA repeat expansions that cause Huntington's Disease and myotonic dystrophy type 1
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 0.5 mM NA Adenosine, Cytidine,Guanosine, Uridine RNA (5'-R(*GP*AP*CP*CP*AP*GP*CP*AP*G)-3'), 5.0 mM potassium phosphate, 0.25 mM EDTA 100% D2O 0.0112 M 6 1 atm 298 Bruker Avance III HD UltraShield 700 3 2D 1H-1H NOESY 0.5 mM NA Adenosine, Cytidine,Guanosine, Uridine RNA (5'-R(*GP*AP*CP*CP*AP*GP*CP*AP*G)-3'), 5.0 mM potassium phosphate, 0.25 mM EDTA 95% H2O/5% D2O 0.0112 M 6 1 atm 278 Bruker Avance III HD Ascend 850
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker Avance III HD UltraShield 700 2 Bruker Avance III HD Ascend 850
NMR Refinement Method Details Software simulated annealing Amber
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 40 Conformers Submitted Total Number 20 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 collection TopSpin 3.5 Bruker Biospin 2 refinement Amber 16 Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman 3 chemical shift assignment Sparky 3.0 Goddard 4 peak picking Sparky 3.0 Goddard 5 data analysis Amber 16 Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman 6 processing NMRPipe 8.9 Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 7 structure calculation Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman