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Xanthine and 8-oxoguanine in G-quadruplexes: formation of a G G X O tetrad
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 0.7 mM DNA, 20 mM potassium phosphate, 70 mM potassium chloride 90% H2O/10% D2O 90 8.0 ambient 298 2 2D 1H-1H COSY 0.7 mM DNA, 20 mM potassium phosphate, 70 mM potassium chloride 90% H2O/10% D2O 90 8.0 ambient 298 3 2D 1H-1H TOCSY 0.7 mM DNA, 20 mM potassium phosphate, 70 mM potassium chloride 90% H2O/10% D2O 90 8.0 ambient 298 4 2D 1H-13C HSQC aromatic 0.7 mM DNA, 20 mM potassium phosphate, 70 mM potassium chloride 90% H2O/10% D2O 90 8.0 ambient 298 5 2D 1H-13C HSQC aliphatic 0.7 mM DNA, 20 mM potassium phosphate, 70 mM potassium chloride 90% H2O/10% D2O 90 8.0 ambient 298 6 2D 1H-15N HSQC 0.7 mM DNA, 20 mM potassium phosphate, 70 mM potassium chloride 90% H2O/10% D2O 90 8.0 ambient 298
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 600 2 Bruker AVANCE 700
NMR Refinement Method Details Software DGSA-distance geometry simulated annealing, simulated annealing, molecular dynamics X-PLOR NIH
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 X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 2 structure solution X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 3 refinement Amber Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollman 4 chemical shift assignment Sparky Goddard 5 peak picking Sparky Goddard 6 data analysis Sparky Goddard 7 collection TopSpin Bruker Biospin