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Solution NMR structure of the PTK7-binding DNA aptamer sgc8c
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 0.5 mM DNA, 0.02 mM DSS, 10 mM sodium phosphate, 5 mM Magnesium chloride 99.96%D2O 15 mM 7 1 bar 277 Bruker AVANCE 600 2 2D 1H-1H COSY 0.5 mM DNA, 0.02 mM DSS, 10 mM sodium phosphate, 5 mM Magnesium chloride 99.96%D2O 15 mM 7 1 bar 277 Bruker AVANCE 600 3 2D 1H-1H TOCSY 0.5 mM DNA, 0.02 mM DSS, 10 mM sodium phosphate, 5 mM Magnesium chloride 99.96%D2O 15 mM 7 1 bar 277 Bruker AVANCE 600
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 600
NMR Refinement Method Details Software simulated annealing GROMACS restrained energy minimization 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 (closest to the average)
Computation: NMR Software # Classification Version Software Name Author 1 chemical shift assignment TopSpin Bruker Biospin 2 structure calculation GROMACS Abraham, Alekseenko, Bauer, Bergh, Blau, Briand, Doijade,... and Zhmurov 3 refinement Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman