☰ Navigation Tabs
Solution structure of a G-quadruplex
NMR Experiment Experiment Type Sample Contents Solvent Ionic Strength pH Pressure Temperature (K) Spectrometer 1 2D 1H-1H JR NOESY 0.2-2 mM DNA (28-MER)-1, 0.2-0.5 mM [U-2% 15N] DNA (28-MER)-2, 0.2-0.5 mM [U-100% 2H] DNA (28-MER)-3 90% H2O/10% D2O 90 7 298 2 2D 1H-1H NOESY 0.2-2 mM DNA (28-MER)-4, 0.2-1 mM [U-4% 13C; U-4% 15N] DNA (28-MER)-5 100% D2O 90 7 298 3 2D 1H-1H TOCSY 0.2-2 mM DNA (28-MER)-4, 0.2-1 mM [U-4% 13C; U-4% 15N] DNA (28-MER)-5 100% D2O 90 7 298 4 2D 1H-13C HSQC aliphatic 0.2-2 mM DNA (28-MER)-4, 0.2-1 mM [U-4% 13C; U-4% 15N] DNA (28-MER)-5 100% D2O 90 7 298 5 2D 1H-13C HSQC aromatic 0.2-2 mM DNA (28-MER)-4, 0.2-1 mM [U-4% 13C; U-4% 15N] DNA (28-MER)-5 100% D2O 90 7 298 6 2D 1H-13C JR HMBC 0.2-2 mM DNA (28-MER)-1, 0.2-0.5 mM [U-2% 15N] DNA (28-MER)-2, 0.2-0.5 mM [U-100% 2H] DNA (28-MER)-3 90% H2O/10% D2O 90 7 298 7 15N-FILTERED 0.2-2 mM DNA (28-MER)-1, 0.2-0.5 mM [U-2% 15N] DNA (28-MER)-2, 0.2-0.5 mM [U-100% 2H] DNA (28-MER)-3 90% H2O/10% D2O 90 7 298 8 D-LABELED 0.2-2 mM DNA (28-MER)-1, 0.2-0.5 mM [U-2% 15N] DNA (28-MER)-2, 0.2-0.5 mM [U-100% 2H] DNA (28-MER)-3 90% H2O/10% D2O 90 7 298
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, Distance-restrained molecular dynamics 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 (lowest energy)
Computation: NMR Software # Classification Version Software Name Author 1 refinement Amber Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, ... and Kollman 2 data analysis NMRPipe Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax 3 chemical shift assignment Sparky Goddard 4 data analysis Sparky Goddard 5 peak picking Sparky Goddard 6 collection TopSpin Bruker Biospin 7 geometry optimization X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore 8 refinement X-PLOR NIH Schwieters, Kuszewski, Tjandra and Clore