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NMR structure and free-energy simulations for rational design of myotonic dystrophy RNA inhibitors
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D NOESY 500 uM NA RNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3'), 550 uM NA 1,3-diaminoisoquinoline derivative, 20 mM NA sodium phosphate 100% D2O 20 mM 6.0 1 atm 298 Bruker AVANCE III 800 2 2D TOCSY 500 uM NA RNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3'), 550 uM NA 1,3-diaminoisoquinoline derivative, 20 mM NA sodium phosphate 100% D2O 20 mM 6.0 1 atm 298 Bruker AVANCE III 800 3 2D DQF-COSY 500 uM NA RNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3'), 550 uM NA 1,3-diaminoisoquinoline derivative, 20 mM NA sodium phosphate 100% D2O 20 mM 6.0 1 atm 298 Bruker AVANCE III 800 4 2D NOESY 500 uM NA RNA (5'-R(*GP*AP*CP*AP*GP*CP*UP*GP*CP*UP*GP*UP*C)-3'), 550 uM NA 1,3-diaminoisoquinoline derivative, 20 mM sodium phosphate 95% H2O/5% D2O 20 mM 6.0 1 atm 298 Bruker AVANCE III 800
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE III 800
NMR Refinement Method Details Software simulated annealing Amber
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 100 Conformers Submitted Total Number 20 Representative Model 1 (closest to the average)
Computation: NMR Software # Classification Version Software Name Author 1 refinement Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman 2 structure calculation Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, and Kollman 3 chemical shift assignment Poky Manthey, Tonelli, Clos II, Rahimi, Markley and Lee 4 peak picking Poky Manthey, Tonelli, Clos II, Rahimi, Markley and Lee 5 processing TopSpin Bruker Biospin