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NMR structure of a bimolecular parallel G-quadruplex formed by AAGGG repeats from pathogenic RFC1 gene
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H NOESY 0.9 mM DNA (5'-D(*AP*AP*GP*GP*GP*AP*AP*GP*GP*GP*AP*A)-3'), 1 mM sodium phosphate, 150 mM potassium chloride 99.96% D2O 150 mM 7.0 1 atm 298 Bruker AVANCE 600 2 2D 1H-1H COSY 0.9 mM DNA (5'-D(*AP*AP*GP*GP*GP*AP*AP*GP*GP*GP*AP*A)-3'), 1 mM sodium phosphate, 150 mM potassium chloride 99.96% D2O 150 mM 7.0 1 atm 298 Bruker AVANCE 600 3 2D 1H-1H TOCSY 0.9 mM DNA (5'-D(*AP*AP*GP*GP*GP*AP*AP*GP*GP*GP*AP*A)-3'), 1 mM sodium phosphate, 150 mM potassium chloride 99.96% D2O 150 mM 7.0 1 atm 298 Bruker AVANCE 600 4 2D 1H-13C HMBC 0.9 mM DNA (5'-D(*AP*AP*GP*GP*GP*AP*AP*GP*GP*GP*AP*A)-3'), 1 mM sodium phosphate, 150 mM potassium chloride 99.96% D2O 150 mM 7.0 1 atm 298 Bruker AVANCE 600 5 2D 1H-15N HSQC 0.9 mM DNA (5'-D(*AP*AP*GP*GP*GP*AP*AP*GP*GP*GP*AP*A)-3'), 1 mM sodium phosphate, 150 mM potassium chloride 99.96% D2O 150 mM 7.0 1 atm 298 Bruker AVANCE 600
NMR Spectrometer Information Spectrometer Manufacturer Model Field Strength 1 Bruker AVANCE 600
NMR Refinement Method Details Software simulated annealing Amber
NMR Ensemble Information Conformer Selection Criteria structures with the lowest energy Conformers Calculated Total Number 500 Conformers Submitted Total Number 10 Representative Model 1 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 chemical shift assignment TopSpin Bruker Biospin 2 structure calculation Amber Case, Darden, Cheatham III, Simmerling, Wang, Duke, Luo, ... and Kollman